Welcome to Adobe GoLive 5 - X-Ray

Welcome to Adobe GoLive 5 - X-Ray

Introduction

General Information

Description

Installation

License Agreement

General Information

Description

X-Seed is a program for small-molecule crystallography. It's two primary functions are:

1. to serve as a graphical user interface to

SHELXL-97

, and

2. to facilitate the production of high-quality molecular graphics images via

POV-Ray

X-Seed also provides a long list of other useful features that are described in detail in this help file.

Reference

L. J. Barbour, X-Seed - A Software Tool for Supramolecular Crystallography,

J. Supramol. Chem. 2001, 1, 189.

Operating systems

Tested under Windows

®

95, 98, Me, NT4, 2000, XP.

Sorry, there is no Linux or Mac version.

Web site http://www.x-seed.net

Author

Len Barbour

Department of Chemistry

University of Stellenbosch

7602 Matieland

South Africa

Tel: +27-21-808-3335

Fax: +27-21-808-3849

[email protected]

(preferred)

[email protected]

1

1

Measure distances as well as bond and torsion angles

• Easily transform atomic coordinates of the asymmetric unit atoms

• Move the asymmetric unit around the unit cell using symmetry information

• Import and export various file formats

• Browser for Cambridge Database DAT files containing multiple structures

High-quality molecular graphics via the POV-Ray interface

Terminology

Throughout this manual, certain terms are used of which the meaning may not be immediately obvious to the reader. Many of these terms are explained or defined below.

ASU

CSD

CCDC dpi pixel

CPU focus fragment

asymmetric unit

Cambridge Structural Database

Cambridge Crystallographic Data Centre dots per inch picture element (a single dot on the screen) central processing unit a window has the "focus" when it is the active window on the computer's desktop

- i.e. will respond to the keyboard a set of atoms where each atom in the set bonds to at least one other atom in the set

The future

As long as the author is able to devote the time required, X-Seed will never be complete. Although already quite functional, new features will continue to be added whilst existing features will be improved in response to practicable suggestions received from users.

Future enhancements, Tips and tricks, Frequently asked questions

Growing lists of these are maintained at X-Seed's home page :

x-seed.net

3

Installation

Installing X-Seed

Run the setup program XSEED_xyz.EXE (xyz = version number) to install X-Seed into any folder of your choice.

Important note:

You MUST have write-access to the folder containing the program files. If

X-Seed is installed on a read-only compact disk or network drive, an error will occur as the program tries to access its temp folder.

3

4

Setting up the ancillary programs

In order to gain the full benefit of X-Seed's ability to communicate with other programs like

SHELXS, SHELXL, RasWin and POV-Ray, these programs must first be gathered from their various sources as described below. Recompiled and slightly modified versions of the third-party programs PARST-97 and LAZY PULVERIX, are included in the X-Seed installation. For X-Seed to be able to invoke the ancillary programs, it also needs to be informed of their respective locations by means of the Preferences | Program Settings menu. These programs are not required to share the same folder with X-Seed.

SHELX programs

SHELXS-86, SHELXS-97 and SHELXL-97 were developed by Professor George M. Sheldrick and must be obtained from him. If you don't already have copies of these programs, details of how to obtain the SHELX-97 software suite can be found at: shelx.uni-ac.gwdg.de/SHELX . If you are already a registered SHELX user, the older version of SHELXS, i.e. SHELXS-86, can be obtained at: www.ucg.ie/cryst/shelxs.htm

.

Note:

it is highly recommended that Build #2 or higher of the SHELX-97 package be used with

X-Seed. The program may well work with Build #1, but has not specifically been tested with this particular version. Do not use SHELXL-93 with X-Seed.

PARST-97

A slightly modified version of PARST-97 is distributed with X-Seed by kind permission of its original author, Professor Mario Nardelli of the University of Parma, Italy.

LAYER, SECTION and CIF2CIF

These programs were developed by X-Seed's author and are included with X-Seed.

POV-Ray

POV-Ray can be obtained as Freeware at www.povray.org

and has its own installation program.

The POV-Ray executable file is called pvengine.exe and is usually located in the bin folder under the POV-Ray installation folder.

LAZY PULVERIX

A modified version of LAZY PULVERIX is distributed with X-Seed by kind permission of

Professor Erwin Parthe of the University of Geneva. The executable files lazy.exe and pulv.exe

MUST be in the same folder (X-Seed's installation procedure takes care of this).

RasWin (RasMol)

The Freeware program RasWin can be found at: www.umass.edu/microbio/rasmol/getras.htm

XRDPLOT

XRDPlot is a part of the X-Seed program suite and is used to display powder patterns calculated by

LAZY PULVERIX. The executable file XRDPlot.EXE MUST reside in the same folder as the

LAZY PULVERIX executable programs lazy.exe and pulv.exe (The X-Seed installation program will usually take care of this).

4

POVLabel

POVLabel is part of the X-Seed program suite and is used to edit and position the atomic labels of

POV-Ray images. POVLabel is not invoked by X-Seed and is merely a utility program for labeling images. If you intend using this program, as you should, a shortcut to it should be placed somewhere on your system to make it easily accessible. The X-Seed installation program puts a link to POVLabel in the X-Seed sub-menu of your Windows Start menu.

Animagic

Using POV-Ray, X-Seed is able to produce files representing the frames of an animation. Many programs are available that can be used to piece the frames together to make a single animated file.

The best program that I have found for this purpose is Animagic. Animagic is a very inexpensive shareware program costing only US$ 29.00, and a working copy can be obtained from www.rtlsoft.com.animagic

.

License Agreement

DEFINITIONS

"Software" the accompanying software and associated materials excluding the programs SECTION, LAYER,

PARST-97 and LAZY PULVERIX

"

Licensee" in this license agreement, you are referred to as "Licensee" or "You" or "The User."

"

Licensor" Leonard J. Barbour or "The Author."

"

Site" a single facility and/or physical user location (i.e., building, facility or department, as appropriate).

Computer equipment on which the Software is used must be located at the Site. This term is extended to include personal computers owned and operated by registered students, faculty and employees of the Site.

"

License" This License Agreement.

USE OF THE SOFTWARE

Licensor grants the Licensee a non-exclusive, non-transferable right to use the Software at the Site subject to the terms and conditions of this Agreement. The Software and all Intellectual Property embodied in the

Software always remains the property of the Licensor. Your use of the Software indicates your acceptance, in full, of the terms and conditions of this agreement.

YOU, THE USER, ARE OBLIGATED TO INFORM ALL USERS AT THE SITE THAT THE SOFTWARE IS

LICENSED.

The demonstration version of the Software is for evaluation only, and its use for any other purposes is strictly prohibited. Evaluation periods are limited to 31 days, and then all copies of the Software must be removed from all computers. All disclaimers described below apply.

PERMITTED USE

You may:

5

5

6

Freely copy the Software at your Site provided that such copies do not infringe upon any other part of this agreement.

Use the Software on any computer at your Site.

Make and use multiple copies of the Documentation.

PROHIBITED USE

You may not:

Reverse-engineer, disassemble, decompile, or make any attempt to discover the source code to or otherwise attempt to derive programming information from all or any portion of the Software.

Translate or create derivative works based on the Software.

Remove, obscure, or alter any copyright notice or other proprietary rights notice related to the

Software, including manuals.

Sub-license, sell, lend, rent, lease or otherwise transfer any portions of the Software to a Site for which a License has not been purchased.

Copy any portion of the Software, except as described above under “Permitted Use.”

Transfer the Software or any direct product to any person or entity in violation of the United States

Export Administration Act.

Use the Software to derive any works that are based substantially in part or in full on the Software or any portion of the Software. Any such derived works will remain the property of the Author.

Supply your activation code to any person for the purpose of using the Software at a Site other than that for which you have purchased a License.

RELEASES / MODIFICATIONS

The User shall not be entitled to receive any new releases, versions, updates, modifications, bug fixes or enhancements ("Updates") of the Software hereunder, and the Licensor shall not be obligated to notify the

User of any such Updates. In the event the User receives any Updates, the terms and conditions of this

Agreement shall govern the use thereof. The supply of new releases of the Software to the Licensee is at the discretion of the Licensor.

TERMINATION OF THIS AGREEMENT

Both this license and your right to use the Software terminate automatically if you violate any part of this agreement or have failed to pay the appropriate purchase price for the Software. In the event of termination, you must immediately destroy all copies of the Software.

SUPPORT

Though the Licensor is not responsible for maintaining or helping you use the Software, he may, at his discretion, offer such support.

LIMITED WARRANTY

The Software is distributed and licensed "AS IS". The Author specifically disclaims all other warranties, express or implied, including but not limited to, implied warranties of merchantability and fitness for a particular purpose, with regard to the Software.

DAMAGES

By using the Software you do so at your own risk. In no event shall the Author be responsible for any damages whatsoever (including but not limited to, damages for loss of business profits, business interruption, loss of business information, or any other pecuniary loss or any other real or consequential damages) arising out of the use or inability to use this product.

LIABILITY

In the event of failure of the Software, for any reason, the Author's sole liability shall be to refund to you the amount paid by you to the Author for the use of the Software.

6

COPYRIGHT

The Software and the Intellectual Property embodied in the Software shall always remain the property of the

Author and is protected by International Copyright Law and International Treaty Provisions.

AGREEMENT

Your use of the Software indicates your agreement with the above terms and conditions. If you do not agree with these terms and conditions then you must destroy all copies of the software in your possession.

CONSUMER RIGHTS

If any clause in the above Software License Agreement is in violation of your rights under your local laws then you must cease using the Software immediately. It is your own responsibility to be aware of your legal rights under your own local laws.

--- END OF LICENSE AGREEMENT ---

User Guide

Program Execution

The Program Window

Model Display

Atom Connectivity

Atom Colors

The Screen Origin

Atom Labels

Selecting Atoms

Hiding Atoms

Showing Thermal Ellipsoid Axes

Using the Keyboard

Using the Mouse

Popup Menu

Double-click an Atom

Using the Toolbar

Space Groups

DOS Windows

Program Execution

It is necessary to assume here that you are somewhat familiar with the Windows operating system.

Normal execution:

X-Seed can be executed in the usual way for Windows programs after which a file can be opened using the main menu.

7

7

8

Drag-and-drop icons

1. An icon representing a structure file (i.e. a SHELX RES or INS file, or a Cambridge

Database DAT) file can be dragged and dropped onto X-Seed's icon. The program will then start up and automatically load the structure file.

2. If X-Seed is already running, a structure file (*.RES, *.INS, *.DAT) can simply be dragged and dropped onto its main window. This is equivalent to loading the structure file using the main menu.

The Program Window

X-Seed's program window can be divided into the following five distinct regions:

1) Main menu

The main menu provides access to a number of options, many of which are also available via the control panel, popup menu and keystroke shortcuts. Details of the function of each of the main menu selections are given under the "

Main Menu ".

2) Control panel

8

The control panel is attached to the left-hand side of the main window and contains several pages.

The most powerful features of the program are accessed via this control panel and navigation through its pages is facilitated by the array of speedbuttons on the main toolbar. Details relating to the utilization of the control panel pages are given under the "

Control Panels ".

3) Main Toolbar

The main toolbar provides speedbuttons for opening an existing structure file or creating a new structure. Both of these options are also available via the main menu. In addition, the toolbar contains speedbuttons for accessing the various pages of the control panel.

4) Model display area

This is where the structural model is displayed as a wire frame object that can be rotated and translated in real-time. Details of how the model is displayed and manipulated are given in the sections below.

5) Status bar

The status bar is the narrow bar at the bottom of the window. This bar provides information regarding the number of atoms present in the model (number of hidden atoms given in parentheses), the name of the atom closest to the mouse cursor, and the length of the bond currently being pointed to. The first subdivision of the status bar will show the progress of operations that may be lengthy (e.g. sorting the atom list, generating a packing diagram, locating hydrogen bonds, etc.)

Model Display

When a structural model containing one or more atoms has been loaded, the structure is displayed in the model window.

Atom Connectivity

The connectivity of the model is determined using the same bonding criteria used by SHELX-97.

Since it is highly desirable that the user sees the connectivity as SHELX "sees" it, there is no provision for changing the bonding radii of the elements. These have been hard-coded into the program. However, X-Seed provides

means to easily add and remove bonds from the connectivity

list and will communicate these changes to SHELX by means of BIND and FREE commands.

9

9

10

Atom Colors

The colors used for the different element types can be customized via the Element Settings dialog

box. These colors are referred to as the CPK colors by X-Seed. Bonds between two atoms of different CPK color are shown split into the respective colors and the position of the color boundary is proportional to the bonding radii of the atoms involved.

The Screen Origin

For the purposes of this manual, the screen is referred to a right-handed Cartesian coordinate system with its origin at the center of the model display area, X increasing to the right, Y increasing upwards and Z perpendicular to the plane of the screen pointing towards the viewer. By default,

X-Seed places the model such that its centroid is on the screen origin. The screen origin can be moved in the XY plane using Shift-Ctrl-Drag (see

Using the Mouse

) and can be repositioned at its

default location using the "Center molecule" option of the Display menu.

Atom Labels

The manner in which X-Seed handles atomic labels may be confusing at first. Each atom is able to

"own" a label. The label can be either its name, or a number representing its peak height (if it's an electron density peak), PART number, Uiso or S.O.F. FVAR number, HFIX number or AFIX number. By default, when a model is loaded, each asymmetric unit atom owns a label, and the label is its name. When symmetry-related atoms are generated, they do not own labels by default.

Turning the display of atom labels on will result in only the labels of atoms that actually own labels to be displayed. The label ownership and format of any atom can be set using the "Labels" page of

the Display Settings control panel .

Selecting Atoms

Many actions taken by X-Seed are performed on ONLY the selected atoms. See

Using the Mouse

and Using the Keyboard

for descriptions of how to (de)select atoms.

10

12

negative rotation about the X-axis

positive rotation about the X-axis

negative rotation about the Y-axis

positive rotation about the Y-axis

negative rotation about the Z-axis

positive rotation about the Z-axis

Other keystrokes

delete selected atoms/bonds

+

(un)select all atoms*

(un)select all bonds*

invoke a popup menu that will allow you to change the element of the selected atoms

* if no atoms/bonds are currently selected, all will be selected. If at least one atom/bond is currently selected, the selection will be cleared.

Resize image (using the mouse is preferable)

zoom in

zoom out

Toggle switches for specific display options

asymmetric unit atoms only

electron density peaks

unit cell

12

atomic labels

stereo view

hydrogen atoms

thermal ellipsoid axes

Using the Mouse

Within the model display window, the mouse is used to perform several different functions. In the text below, "left-drag" means holding down the left mouse button whilst dragging the mouse cursor around the screen. "Ctrl-left-drag" means holding down the "Ctrl" key whilst performing this action, etc...

Rotating, translating and zooming

Left-Drag

- rotate the model about the X- and Y-axes

Shift-Left-Drag

- rotate the model about the Z-axis

Ctrl-Left-Drag

- zoom in and out

Shift-Ctrl-Drag

- translate molecule in XY plane (actually, this action translates the screen origin)

Right-Drag

- zoom in and out

Selecting atoms/bonds*

Left-Click

- (un)select the atom/bond closest to the cursor

Ctrl-Left-Click -

(un)select all atoms/bonds of the entire fragment

Shift-Left-Click

- (un)select all atoms/bonds of the same type

Alt-Left-Click

- (un)select all atoms of the same PART number

Shift-Ctrl-Click

- combination of Ctrl-Click and Shift-Click

Ctrl-Alt-Click

- (un)select all instances of this atom/bond (i.e. ASU and symmetry-generated)

* The cursor must be within 0.6Å of the atom or bond (in the plane of the screen) for the selection to take place. The distance of the cursor to the bond is measured to the canter of the bond. Either an atom or a bond can be selected, depending on which is closer when the mouse button is clicked.

13

13

14

Selected atoms are displayed as filled circles and selected bonds are shown as thick lines. If the atom or bond clicked on is already selected, it will become "un-selected". If selection requires a group of atoms/bonds to be (un)selected (e.g. Ctrl-left-click), the selection/unselection of the entire group will depend on the current selection status of the clicked-on atom/bond.

Popup Menu

If you right-click when the mouse cursor is over the model display area, a popup menu will appear.

This menu has several options that are also available either on the control panel or via the main menu, or both. Being able to invoke the popup menu means that options can become available to you with minimal movement of the mouse cursor. Extensive mouse movement can become annoying if required often. In addition, the desired control panel may not always be visible, and the popup menu allows you to access options for which you might otherwise have to change the currently-displayed control panel page. The options available on the popup menu will usually depend on the selection status of the model (e.g. if no atoms are selected, the "Delete Atom(s) menu item will not be present).

Double-click an Atom

This activates the following dialog:

14

17

Select "Properties", and this dialog will appear:

Ensure that the "Close on exit" property is set, and then click "OK". Close the DOS window and, from now on, the DOS window for this particular process will always close automatically - i.e. you will not be required to do this again for that process.

Information for advanced Windows users

The DOS window settings are stored in a PIF file. By default, PIF files do not exist for the DOS programs. Once you change the properties for these DOS processes, a PIF file will be generated in their folders.

Main Menu

17

18

The main menu of the program is dynamic - i.e. only options that are applicable according to the current status of the model will be presented or enabled. Thus, although the actions of all the possible menu options are described here, they may not always be accessible.

Many of the options available on the main menu are also available via shortcut keystrokes (Using the keyboard), the main toolbar (Using the toolbar), the model display area popup menu (Using the mouse) and the control panel (Control panel overview ).

File

Edit

Display

Select

Delete

Preferences

Interface

Information

File

New Structure

Use this option to create a new SHELX structure by activating the Crystal Data dialog.

Open File

Read a SHELX INS or RES file, a Cambridge Database FDAT (.DAT) file, a Cartesian coordinate file (.XYZ) or a PDB file. When the "Open" dialog box appears, select the file type using the "Files of type" dropdown list box.

File formats can be notoriously non-conventional, depending on how the files were produced. See

Input File Formats

in the Appendix for details on file formats acceptable to X-Seed.

Close Structure

Closes the current structure and recuperates the memory used by it.

Export Structure

Allows you to export the current structure in either SHELX, PDB, FDAT or XYZ format. See

Output File Formats

in the Appendix for details.

The SHELX formatted file will be saved as a rather minimalist INS file, which contains only essential structural data. No special SHELX instructions regarding solution or refinement procedures will be added to this file. Only the asymmetric unit is saved.

When exporting to a PDB formatted file, all the currently shown atoms are exported. This includes symmetry-generated atoms. The PDB file is also rather minimalist, but contains enough information for PDB-oriented programs such as RasWin.

Exporting to an XYZ file causes the Cartesian coordinates of all currently shown atoms to be written to a file. Each line in the XYZ file contains an atom's atomic symbol and its X, Y and Z

18

Cartesian coordinates.

Exporting to an DAT file writes all of the current coordinates to a CSD FDAT formatted file.

Note

: more file formats will gradually be added to this list. See Future Plans for further details.

Reopen

A list of the last 10 accessed files is kept in the registry, and you can open one of them using this option.

Exit

Closes the current structure and exits X-Seed.

Edit

Options shown below with

blue headings

are also available on the View/Edit Atoms

control panel and via the

popup menu .

Note

: Some of these options are only enabled if one or more atoms are selected.

Crystal Data

Activates the

Crystal Data dialog box which allows you to alter various parameters relating to the

unit cell and its contents.

Change Element

Allows you to change the element of the selected atom(s). A list of elements constructed from the current molecular formula is presented.

Add Hydrogens

Activates the

Generate H-Atoms (HFIX) control panel.

Make Isotropic

Alters the properties of the selected atoms such that SHELX-L will refine them isotropically in the next run. When this option is applied to anisotropic atoms, the starting value of U iso

is calculated from the current U ij

values.

Make Anisotropic

Alters the properties of the selected atoms such that SHELX-L will refine them anisotropically in the next run (facilitates the generation of ANIS cards in the next INStruction file).

Change Q's to C's

If carbon atoms are present in the molecular formula, this option will reassign all the currently displayed peaks as carbon atoms. This option is especially useful after the solution of an organic structure where most of the peaks may represent carbon atoms.

19

19

20

Generate Centroid

If two or more atoms are selected, this option generates a non-weighted centroid using the atomic positions of the selected atoms. If necessary, the centroid can be assigned an element type and can subsequently be refined as an atom (if chemically relevant, of course).

Locate All H-Bonds

Locates all possible hydrogen bonded contacts according to the criteria set in the Program Settings dialog box. If necessary, symmetry generation of atoms will occur. This option is also available of

the Add/Remove Bonds control panel.

Sort Atom List

Sorts the asymmetric unit atoms using criteria based on their names. Realistically, this is only of consequence with regard to the generation of the next SHELX INStruction file (and when the

model is exported). This option is also available on the Atom Names control panel.

Constrain

Activates the

Constrain

(SHELX-L) control panel.

Transform Coordinates

Activates the

Transformations

control panel.

Duplicate Atom

This menu option is active if one and only if one atom is selected. The following dialog pops up: and the settings of the currently selected atom are already filled in. You can change these settings as you wish, and pressing the "Add" button will cause another atom to be added to the asymmetric unit.

Add New Atom

20

Allows you to add a new atom to the asymmetric unit using this dialog:

21

Hide Selected Atoms

Hides the selected atoms. See Model display for details.

Unhide All Atoms

Unhides all hidden atoms.

Grow Special

Activate the " Grow Special " control panel.

Display

Many of the following options are available as shortcut keystrokes ( Using the Keyboard

), on the

Display Settings control panel and via the popup menu (see Using the Mouse ).

Stereo

Toggle stereo display. Advanced stereo settings can be adjusted on the Display Settings control panel.

Unit Cell

Toggle unit cell display. Advanced unit cell display settings can be adjusted on the Display Settings control panel.

Hydrogen Atoms

Toggle display of hydrogen atoms.

Peaks

Toggle display of electron density peaks.

Atom Labels

21

22

Toggle display of atomic labels.

Hydrogen Bonds

Toggle display of hydrogen bonds.

ASU Only

Toggle between displaying only the asymmetric unit atoms or all atoms, including those that are symmetry generated.

Thermal ellipsoid axes

Toggle display of axes of the 50% probability ellipsoids of anisotropic ASU atoms.

Center Molecule

If the model has been translated on screen using Shift-Ctrl-drag (see Using the mouse), selection of this option will once again place the overall centroid on the screen origin.

Reset Rotation Matrix

The rotation matrix referred to here is the one that controls the orientation of the molecule in the model display area. This orientation matrix responds to the rotations that you perform using the

mouse

or keyboard . Resetting this rotation matrix gives you the default view once again - i.e. the

view you get when you first load the molecule (down c* with a pointing to the right).

Animate

Activates the

Animate control panel.

Latest SHELX-S Results

Activates the

SHELX-S LST File Summary

dialog.

Latest SHELX-L Results

Activates the

SHELX-L LST File Summary

dialog.

Report

Activates the

Structure Report dialog.

Molecular Volume

The van der Waals volume of just the selected atoms is calculated according to the radii given in

Element Settings .

Select

The options presented here are mostly self-evident and I will not insult your intelligence by elaborating on them.

22

23

Clear Selection

Unselects all selected atoms. Pressing the spacebar has the same effect. This option does not clear bond selection. Use Ctrl-Spacebar to do this.

Select All...

This should be self-explanatory.

Deselect All...

This should be self-explanatory.

Toggle All...

This should be self-explanatory. The selection status of atoms that fall into the category chosen will be toggled.

Allow Bond Selection

Turns bond selection on and off. At times it is not desirable to select bonds and it can become rather annoying when, in attempting to select atoms, you also end up selecting bonds owing to inaccuracy in your hasty pointing and clicking. When such a time arises, you can disable the bond selection feature. You cannot turn off atom selection because this is the most commonly used selection feature by far.

Delete

Atoms present in the model can be deleted. When deleting a series of atoms, symmetry-generated atoms are deleted without warning. However, if you attempt to delete atoms belonging to the asymmetric unit, you will be warned and prompted to either continue with, or cancel this operation.

Symmetry-generated atoms are dependent on their asymmetric unit "parents" for their positional and other information. If you delete an asymmetric unit atom of which there are symmetry-generated instances, the latter will also be removed from the model as they will no longer have "parents". Once deleted, asymmetric unit atoms can be recovered, but their symmetry-related instances will have to be re-generated.

Undelete Atoms

Activates the “Undelete Atoms” dialog to allow recovery of deleted ASU atoms.

Selected Atoms

Deletes all selected atoms.

Selected Bonds

Deletes all selected bonds

All Peaks

23

24

Deletes all electron-density peaks.

All Residual Peaks

Deletes all "residual" peaks. Residual peaks are peaks that are too close to established atoms to be indicative of atoms missing from the model. Is it especially common for such peaks to appear close to "heavy" atoms after refinement. Using the Program Settings dialog, you can set the program's distance criteria for deciding what "too close" means. After a SHELX-L refinement run, this menu option allows you to quickly "clean" a structure that contains numerous peaks that are obviously not candidates for missing atoms. Be aware that residual peaks may be indicative of disorder in some cases.

All Hydrogen Atoms

Deletes all hydrogen atoms.

All Symmetry-generated Atoms

Deletes all atoms not belonging to the asymmetric unit (excluding peaks and centroids).

Clear BIND List

Removes all bonds that were manually added to the connectivity list.

Clear FREE List

Restores all bonds that were manually removed from the connectivity list.

Clear Hydrogen Bonds

Removes all hydrogen bonds from the connectivity list.

Inter-SYMOP Bonds (selected atoms)

Deletes all bonds between selected atoms where both atoms of each bonded atom pair do not have the same symmetry relationship to their asymmetric unit parent atoms.

Preferences

Display Settings

Activates the

Display Settings control panel.

Program Settings

Activates the

Program Settings

dialog.

Element Settings

Activates the

Element Settings

dialog.

Control Panel

24

Shows or hides the control panel.

Interface

The interface menu is the gateway to the programs with which X-Seed cooperates. Some of the programs (i.e. LAYER and RasWin) are invoked immediately whilst others first require further fine-tuning of their instructions via an appropriate dialog box or control panel. The interfacing programs are all described in further detail in subsequent section of this help file.

SHELXS

Activates the

SHELX-S dialog for structure solution.

SHELXL

Activates the

SHELX-L dialog for structure refinement.

Layer

Runs the program

LAYER using the current structure's HKL file as input to that program.

Section

Runs the program

SECTION

using only the currently displayed atoms as input to that program.

POV-Ray

Activates the

POV-Ray

control panel.

Lazy Pulverix

Activates the

Lazy Pulverix dialog.

RasWin

X-Seed writes a PDB file containing all the currently displayed atoms to its TEMP folder and invokes RasWin using this file as input.

PARST

Activates the

PARST-97

dialog.

Information

X-Seed Help

Activates this help file.

About X-Seed

25

25

26

Displays X-Seed's splash screen.

About LAZY-PULVERIX

Displays the credits for LAZY-PULVERIX.

About PARST-97

Displays the credits for PARST-97.

E-Mail Author

The author is highly receptive to any questions, suggestions and bug-reports relating to X-Seed.

Should you wish to contribute any information falling into this category, you can use this option to invoke your default E-Mail program with the author's e-mail address already filled in.

X-Seed Home Page

Invoke your default web browser to load X-Seed's home page. The home page will be maintained as indefinitely as possible and will contain information that may well be useful to you. Such information will include sections relating to frequently-asked questions, updates and bug fixes, tips and tricks and any other relevant material.

SHELX-97 Manual

Invoke your default web browser to load the SHELX-97 manual in HTML format.

Control Panels

Much of the capability of X-Seed is accessed via the control panels. In most cases, these panels are activated using the speedbuttons on the toolbar.

The following control panels are available:

View/Edit Atoms

Display Settings

Atom Names

Grow

Grow Special

Add/Remove Bonds

Generate H-Atoms (HFIX)

Measure

Transformations

Animate

Constrain

CSD Browser

POV-Ray

View/Edit Atoms

26

This is the default control panel and is activated when a new structure is loaded (unless the structure is embedded in a CSD DAT file). The upper half of the panel is intended for informative purposes only. The parameters relating to the atom currently pointed at are shown here. The lower half of the panel allows you to perform various operations on selected atoms and, in some cases, bonds. Each of the lower-half controls is explained in turn below.

For further elaboration of some of the concepts referred to below, see the subtopic Model display. In order to apply certain operations to atoms, the atoms must first be selected. When you click on one of the control panel speedbuttons, the relevant operation is immediately applied to the selected atoms and the atom selection will also be cleared.

27

Delete the selected atoms. You will be warned before asymmetric unit atoms are removed.

Removal of an asymmetric atom will result in its symmetry-generated instances being deleted too. If bonds and atoms are selected, only the atoms will be deleted. If only bonds, and no atoms, are selected, the bonds will be deleted. When a bond is deleted, it is placed in the FREE list unless it is contained in either the BIND or H-Bond list in which case it will simple be removed this list.

Hide the selected atoms. Note that there is a difference between specifically hiding an atom and suppressing the display of certain atom types. When you specifically hide an atom, it remains hidden until you "unhide" all atoms. You can suppress the display of atom types like electron density peaks, asymmetric unit atoms and hydrogen atoms but this is not the same as hiding them. The "hide atoms" feature is useful when you want to exclude these atoms from being exported or rendered with POV-Ray, but don't want to delete them for that purpose.

Unhide all hidden atoms. This only applies to atoms that were specifically hidden, and not to atom types for which display is currently suppressed.

Change element type. You can select the new element type to assign to the selected atoms or peaks from a popup menu list, which is dynamically, constructed using the information

27

28 contained in the current molecular formula.

Make the selected atoms anisotropic. This option does not apply to the atoms immediately.

It only flags the selected atoms for anisotropic refinement during the next SHELXL-97 run.

No action is taken for selected atoms that are already anisotropic, or for hydrogen atoms or peaks.

Make the selected atoms isotropic. If the selected atoms are anisotropic, this selection will flag them for isotropic refinement during the next SHELXL-97 run. X-Seed will also immediately regard these atoms as being isotropic and will calculate their equivalent Uiso values from their current anisotropic thermal parameters.

Generate the centroid of the currently selected atoms. The non-weighted average position of the selected atoms is calculated and a special atom of type "Centroid" is created at this position. The centroid "atom" can be treated as any other atom but will not be written to any files as long as it is assigned as a centroid. A centroid "atom" will not bond naturally to any atom, but you can manually add bonds to it if you like (e.g. for producing images). The centroid atom becomes part of the asymmetric unit, so changing its element type is a way to add atoms to the ASU.

This option will assign the selected atoms as asymmetric unit atoms. If multiple instances of the same atom are selected, the final instance of that atom in the program's internal list will become the asymmetric unit atom. This operation is useful for manually assigning which instances of the atoms should be regarded as the asymmetric unit. Remember, only the asymmetric unit atoms are written to SHELX INS files for refinement of the structure.

Here you can change the site occupancy factor, Uiso parameter as well as the AFIX and PART number of the selected atoms. When you press the "Apply" button, the checked parameters are applied to all the currently selected atoms.

This feature lets you identify atoms with U iso

values that are either too high or too low. Making any change to the controls here will cause only the atoms meeting the selected criteria to become selected.

Display Settings

Use this control panel to change various display settings. Most of the settings on this panel are self-evident and will thus only be described in brief below. In order to accommodate the many display settings that can be altered, this control panel contains four pages:

28

The first page contains miscellaneous display setting options.

You can suppress the display of electron density peaks, hydrogen atoms and bonds, symmetry-generated atoms and thermal ellipsoid axes. When the display of electron density peaks is not suppressed, you can set the maximum number of peaks to be displayed. Peaks are contained in the program's internal atom list in descending order of intensity. Thus, if you only choose to have 10 peaks displayed, these will be the 10 strongest peaks in the list. Use the "Del. Rest" button to delete only the peaks that are further down the list than the maximum number of peaks chosen for display. Usually, the current model is displayed with its non-weighted center of mass on the screen origin

(i.e. at the center of the model display area). When the display of certain types of atoms is suppressed, the centroid is not recalculated for just the displayed atoms. If this were to occur, the model would appear to "jump" around the screen when you, for example, turn off the display of hydrogen atoms. This would quickly become annoying if all you want to do is turn various atoms on and off for clarification of the structure. If you want the molecule to be re-centered, you will have to specifically "hide" the atoms not desired in the current view. See

Model Display for further details relating to how the model is

displayed.

The "Perspective" value represents the angle in degrees between the left and right hand edges of the model display area and the viewpoint. This perspective value is also used by POV-Ray when the image is ray-traced.

The "Image Scale" setting can be used to adjust the size of the model precisely - using the ctrl-mouse-drag or right-drag method is not precise. Use this setting if you would like to compare two structures, displayed at the same scale, using two instances of X-Seed on your desktop. The

"X/Y Rotation Sensitivity" slide bar can be used to adjust the sensitivity of rotation about the screen

X and Y axes to the movement of the mouse whilst left-dragging.

By default, X-Seed displays bonds using thin lines. Check "Thick Bonds" if you have difficulty seeing the wireframe model properly. Dotted lines can't be shown as thick lines too, so hydrogen bonds will remain thin.

Use the "Immobilize Model" setting to "freeze" the model in its current orientation so that it cannot be rotated. If the model has been translated away from the screen origin using Shift-Ctrl-left-drag

(see Using the mouse), it can be re-centered using the "Center Molecule" button. This button is only enabled if the molecule is not currently centered on the screen origin.

29

29

30

Using the second page, you can turn the display of atom labels on and off. Just turning labels on does not necessarily mean that all atoms will be labeled - it merely means that atoms that actually own labels will have their labels displayed. By default, asymmetric unit atoms and electron density peaks own labels. The labels of the former are their names while the labels of the latter are their peak heights as determined by SHELX. Also by default, symmetry-generated atoms do not own labels. Any atom can be provided with a label. An atom's label can consist of its name, peak height (in the case of peaks), PART number, the number of the free variable to which it's Uiso or site occupancy factor is tied or the HFIX or AFIX number currently assigned to the atom. The four buttons on this page allow you to (un)label all the atoms or just the selected ones according to the status of the radio buttons. If

"Name" and "Pk. Ht" are both checked, peak names will be their heights as described above. If "Pk. Ht." is not checked, the peaks will be assigned the names assigned to them by SHELX.

Use this page to turn the display of the unit cell on and off. You can customize the color of the unit cell edges by clicking on the color panel and selecting a color from the standard Windows color dialog.

Additional features include the display of all 12 cell edges, or just the three principal edges as well as the cell axis labels.

Two stereo modes are available. If you choose to display the model in stereo representation, it can be shown in red/blue or side-by-side stereo mode. When using the red/blue mode, you will need special stereo glasses with a red filter over the left eye and a blue or green filter over the right eye. Both the view angle and separation can be customized.

The view angle represents the rotation angle in degrees of the left-eye model relative to the right-eye model. A mid-range value of about 6 degrees is usually considered to be optimum. The stereo separation is based on an arbitrary scale and can be selected according to personal preference.

30

This panel lets you view the model perpendicular to either a plane or a vector defined by the Miller indices.. Enter the desired Miller indices and press "Go1". Alternatively, if you'd like to use a shortcut means of viewing perpendicular to a unit cell face, or along a unit cell axis, the appropriate shortcut keys are provided.

31

Atom Names

X-Seed considers the name of an atom to consist of three parts - i.e.

the atomic symbol, a number and a suffix. For example, if an atom's name is Na3B, the element is sodium, the number is 3 and the suffix is "B". The only part of the name that is essential is the atomic symbol. The number and suffix, while optional, are generally required to distinguish atoms from one another. Indeed, SHELX requires that all of the names of the atoms of the asymmetric unit be unique. Therefore it is logical to include numbers in the atom names.

In addition to numbers, it may also be logical to add an alphabetic suffix to the name in cases where the model contains separate molecular entities. SHELX only allows atoms names of up to four characters in length. Since X-Seed is largely based on cooperating with SHELX, this constraint is adhered to very strictly. Although

SHELX does not require the atomic symbol to be in the atom's name,

X-Seed insists on it since this is just good practice. Nevertheless,

X-Seed will correctly recognize atoms read from a structure file that do not conform to this naming convention, but, if renamed, these atoms will be forced to conform. When you assign an atom name using X-Seed, the first character

(or two if the symbol consists of two characters) of the name will consist of the atomic symbol of the assigned element. This leaves either two or three characters for the number and suffix. X-Seed will also insist that the suffix be an uppercase character. When peaks are assigned as atoms by changing the element type, these newly created atoms will assume names based on their atomic symbol and the original peak number. At some stage during refinement, you will probably want to rename all the atoms to conform to some naming convention of your preference. Generally, such naming conventions involve sequentially numbered atoms with or without a suffix. When you activate this control panel, atom selection is switched off and "re-naming" mode is turned on. The mouse cursor changes to indicate that when you click on an atom, its name will change according to the settings on the control panel. You can set the starting number and current suffix in the "Next

#" and "Suffix" fields respectively. When you click on an atom its new name will consist of the element symbol plus the current number and suffix. The "Next #" field will increment by 1 automatically. Since the atom name is tied only to the parent ASU atom, it doesn't matter whether you click on ASU or symmetry-generated atoms. It will be the name of the parent atom that changes. It is advisable to have atom labels displayed when performing this operation so that you

31

32 can immediately see the changes taking effect. Whilst in re-naming mode, you can quickly reset the

"Next #" field to "1" by pressing "R" on the keyboard. If the current suffix is in the range "A" ...

"Y", pressing "T" will increment the character to the next letter of the alphabet. This can also be achieved using the up/down spin button control to the right of the "Suffix" field.

Note

: An atom's name may be no longer than 4 characters in length! If you click on, for example, a sodium atom when the current number is 56 and the suffix is B, the new name of the atom will be

Na56 and not Na56B.

When you click on the "Sort" button, X-Seed will sort the asymmetric unit atom list. The effects of this operation are only of consequence to SHELX INStruction file creation. When sorting the atom list, the priority is assigned according to the three criteria in the list as shown. Changinh the order in this list is probably non-intuitive at first. You can't manipulate the items of the list directly. Instead, use the up/down spinedit button to move the central item up or down in the list.

Example:

If the priority is: Suffix > Number > Atomic Weight, the atom list will be sorted according to the atom suffix. If two atoms have the same suffix, the next priority is the atom's number. When two atoms have the same number and suffix, the higher priority is the atomic weight. If atomic positions are riding on parent atoms (e.g. hydrogen atoms in calculated positions, AFIX 6 atoms, etc.), this is usually indicated by a non-zero AFIX parameter. X-Seed tries very hard to keep these atoms together, using only the name of the parent atom as the sort criterion for the entire AFIX'ed series.

Owing to the many parameters that need to be considered, sorting might be a lengthy process for large structures. During sorting, X-Seed suspends all other operations and displays the progress of the sorting procedure on the program's status bar.

Grow

32

X-Seed provides a number of powerful routines for extending the structure using space group symmetry. When the "Grow" control panel is activated, atom selection is turned off and the mouse cursor changes to indicate that grow mode has been entered. In this mode, clicking on an atom (i.e. the target atom) will cause X-Seed to extend the structure according to the current settings on the control panel. When in

"Covalent" connection mode, one can click on any atom in order to extend the fragment from the target atom. X-Seed will then use space group symmetry information to spawn all symmetry-generated instances of asymmetric unit atoms that can be attached to the target atom. If "Sphere of Inclusion" mode is active, X-Seed will generate all atoms within the specified radius (in Å) of the target atom. Using

"Locate H-Bonds" mode, you can click on a target atom to locate any atoms that are defined in the Program Settings dialog as hydrogen-bond donors or acceptors (of course the target atom must also be in the donor/acceptor list). If H-Bond participants are 1-3 connected within a fragment, a hydrogen bond will not be generated (.e.g. the oxygens of a nitrate anion). Generally, 1-4 connected hydrogen bonds should not be generated either. However, in some cases (e.g. resorcinol) 1-4 donors and acceptors may be hydrogen bonded, and for such cases, you can allow 1-4 H-bonds by checking the appropriate box on the control panel. Currently, X-Seed ignores any hydrogen atoms attached to the donor and acceptor atoms. The criteria for evaluating possible hydrogen bonded contacts are specified in the Program Settings dialog.

Important Note:

See the "Connectivity" subtopic in the Model display section for details of how

X-Seed evaluates whether or not two atoms should be bonded.

The panel labeled "Attach" is used to specify what should be attached. If "Atom" is checked, only individual atoms that meet the growth criteria are generated. If "ASU Fragment" is checked, an entire instance of the relevant part of the asymmetric unit will be generated if at least one of its atoms meet the criteria.

The "Pack Range" panel is used to quickly generate a packed model. The limits specified in this panel refer to unit cell coordinates. When you press the "Pack" button, X-Seed generates all atoms

(or, if in "ASU Fragment" attach mode, fragments that have at least one atom) within the specified limits. It is up to you to make sure that the ASU fragment is within these limits. This is easily achieved using the Transformations control panel.

The "Limit" button is used to remove any symmetry-generated atoms that lie outside the specified range. This function is performed automatically when you press the "Pack" button. The "Pack" feature takes the current "Attach" mode setting into account, but the "Limit" function does not.

33

Grow Special

33

34

This control panel can only be accessed from the main menu under

Edit

.

This allows you to extend selected atoms of the model using a transformation matrix M. A transformation of an atom's coordinates entails multiplication of the coordinate vector by a 3x3 matrix, followed by translation of the resultant vector.

The transformation matrix M to be applied is represented by the 3x4 matrix shown on the control panel. The first three columns represent the 3x3 matrix mentioned above and the 4th column represents the translation vector. The matrix can be edited manually (much caution needed here) or generated from a valid symmetry operator of the current structure's space group. If you choose a symmetry operator from the dropdown list, the matrix will be updated immediately to reflect the chosen symmetry transformation.

Pressing the buttons marked "M" or "M

-1

" will apply the current transformation matrix or its inverse to only the selected atoms. Shortcut buttons are also provided to perform simple unit cell translations.

Add/Remove Bonds

Refer to the "Connectivity" subtopic in Model display for details of how X-Seed handles the connectivity settings of the model and how it transmits this information to SHELXL-97. When this control panel is activated, normal atom selection is turned off. In this mode, atoms are selected in pairs in order to manually create or remove bonds between them. Automatic bond generation is accessed via the buttons on the control panel. When two non-bonded atoms are selected, a normal or hydrogen bond between them will be added to the connectivity list

(depending on which option is checked in the "Manually" panel). If the atoms are bonded according to the connectivity list, the bond will be removed. Bond generation and removal between any two atoms also applies to all symmetry-equivalent instances of the atoms. Use the automatic mode to locate hydrogen bonds. Pressing the "Locate all

Unique H-Bonds" button will initiate a search for all possible hydrogen bonds to all the donor/acceptor atoms in the current model according to the criteria specified in the Program Settings dialog. If necessary, symmetry-generated atoms will be added to the model.

However, pressing the "Locate All H-Bonds" button will initiate a search for all hydrogen bonds within the current model. No symmetry-generated atoms will be created in this case. A checkbox is included to allow 1-4 hydrogen bonds, if desired. Normal bonds are bonds created by X-Seed strictly according the bonding radii assigned to the different elements. All other bonds that are added are contained in either the BIND or the H-Bond list. When normal bonds are removed manually they are retained in the FREE list, and thus not drawn. This control panel contains three buttons that allow you to clear these lists. These functions are also available via the Delete submenu of the main menu. It is also possible to delete bonds between

34

specific atom types that fall outside a specified range. Use of this feature should be intuitive, but it should be noted that this operation applies only to currently selected bonds.

35

35

36

Generate H-Atoms (HFIX)

This control panel allows you to instruct SHELXL-97 to add hydrogen atoms (in calculated positions) to the model.

Select the atoms to which hydrogen atoms of a particular type (see

HFIX and AFIX in the SHELXL-97 instruction manual) have to be added and press the appropriate button. It is important to note that when you use this feature, X-Seed will not actually add the hydrogen atoms to the current model - it will only instruct SHELXL-97 to do so during the next refinement run (i.e. it will add the appropriate HFIX cards to the next INStruction file). After the refinement run, the model will be updated to include the hydrogen atoms added by SHELX.

All of the SHELX models for adding hydrogen atoms are supported.

The actual HFIX parameters for each type of model can be customized using the "Hydrogen Atoms" tabbed page on the Program Settings dialog. Use the "Other" button to associate a customized HFIX instruction to atoms. If you wish to cancel any HFIX associations that you may have applied erroneously to any atoms, apply the "Other" setting to these atoms with the "mn" and "U" values set to zero.

It is the user's responsibility to ensure that the HFIX associations make sense, as X-Seed will not check the validity of these associations. The worst problem that can occur is that the next

SHELXL-97 run will terminate prematurely with an informative error message, after which you can correct any mistakes using the "Other" button. Any HFIX associations applied to atoms will override previous such associations. Naturally, HFIX associations are no longer retained if the next

SHELXL-97 run is successful and the model is updated.

The default settings for the different HFIX models, as set in the Program Settings dialog, can be altered according to your own preferences. When you exit X-Seed, your preferred settings will be written to the Windows Registry and thus retained for future use.

Measure

Measure bond lengths and bond and torsion angles. Select the desired option and click on atoms to make the measurements.

36

37

When measuring distances, if the distance between the two selected atoms is not the shortest contact between instances of the atoms, the closest such contact will be given, along with the symmetry operator by which the second selected atom needs to be transformed to produce the shortest contact.

Transformations

Note

: If the main toolbar speed button for this control panel is disabled, it probably means that you have symmetry-generated atoms present in the model. You will have to delete all symmetry-generated atoms before being allowed to use this feature.

37

38

Use this control panel to transform the positional coordinates of selected asymmetric unit atoms. This feature is not available if the model contains any symmetry-generated atoms since they could "get in the way" of transformed asymmetric unit atoms. A transformation of an atom's coordinates entails multiplication of the coordinate vector by a 3x3 matrix, followed by translation of the resultant vector.

The transformation matrix M to be applied is represented by the 3x4 matrix shown on the control panel. The first three columns represent the 3x3 matrix mentioned above and the 4th column represents the translation vector. The matrix can be edited manually (much caution needed here) or generated from a valid symmetry operator of the current structure's space group. If you choose a symmetry operator from the dropdown list, the matrix will be updated immediately to reflect the chosen symmetry transformation.

Shortcut buttons are also available to reset the matrix to the identity matrix, or to generate a matrix that will invert the structure. Using the buttons with the blue inscriptions, you can apply either the transformation M, or its inverse M

-1

, to the selected atoms. The model will be updated immediately. You can also set whether you would like the selection to be cleared after a transformation has been performed.

In addition to symmetry transformations, you can also perform simple unit cell translations on the selected atoms using the set of three up/down buttons. Inversion of the structure is possible even if the space group is non-centrosymmetric since the need for doing this may well arise from time to time. X-Seed will follow your instructions faithfully and assume that you know what you are doing. You can use this feature of X-Seed to positions any asymmetric unit atoms exactly where you want them - this may be useful when your asymmetric unit consists of fragments that are far apart, or if the atoms or fragments are far from the origin.

If individual atoms are selected, you can translate them along the unit cell axes by small increments using the "Move atoms" panel.

It is also possible to define a vector (i.e. a bond) along/about which selected atoms can be translated/rotated. To define such a vector, select the first atom and press next to "Atom(1)".

Do the same for the a second atom to define Atom(2). Having thus defined a vector, the spinbuttons

can be used to rotate or translate the selected atoms by the values indicated.

Note: a vector terminus can only be defined if one and only one atom is selected. If you exit this control panel and then return to it, the previously defined vector is cleared.

Animate

38

This is a relatively useless feature that is only available because it was easy to implement. In fact, there is no shortcut tool button for this control and you have to activate it from the Display menu. I suppose you could use this feature to set your model spinning whilst you sit back and contemplate your structure. The controls should be fairly self-evident

39

Constrain

This control panel is still under development and will be extended at a later date to perform more functions. It is activated via the Edit |

Constrain menu. Currently, this control allows you to add DFIX restraints to the model for the purposes of refinement with

SHELXL-97. Select bonds and then press the "Add" button. DFIX cards with the currently set "d" and "s" parameters will be added to the

"Extra Cards" list in the SHELX-L dialog. Bond selection is automatically cleared when you press the "Add" button. At present you can only use this feature for atom pairs that are in the connectivity list. Of course, you can still manually add any DFIX cards you like to the "Extra Cards" list.

Note

: for now, the "Add" button will only be activated if no symmetry-generated atoms are present

- to avoid the possibility of DFIXing non-existant bonds. When support is added for EQIV cards with respect to this option, this will no longer be the case.

CSD Browser

X-Seed only reads CSD files in the FDAT format. FDAT files can be written by QUEST or by

ConQuest.

When using QUEST, you need to make sure that "Save FDAT" is selected before doing the search.

If, instead, you use ConQuest, do the following once the search has been completed:

In ConQuest, select "File" - "Export Entries as...", and then under "Select file type:" choose

"FDAT: Legacy CSD crystallographic format:" and save the file as name.DAT. If you would like to access bibliographic information using X-Seed, you must also export a "TAB: Tab separated list" as "name.TSV".

39

40

A CSD DAT file usually contains several structures. When such a file

has been read (see File under the Main Menu topic), this control panel

is activated. You can browse through the structures using the buttons with the red arrows, or by selecting a particular entry from the dropdown list box which contains the CSD REFCODE codes of all the structures. If a particular entry does not contain any atoms, a message to this effect will be displayed in the model display area. The unit cell parameters, cell volume and space group of the current entry are displayed on the panel. Each time a structure entry is loaded, X-Seed determines which atoms belong to the asymmetric unit and which are symmetry-generated, and then displays all the atoms contained in the current entry. X-Seed will also attempt to determine atom site occupancies and the molecular formula of the entry (taking Z = 1). The current entry can be exported in any of the supported formats using the

File | Export Structure menu option. Structure entries usually contain annotations, which include the R-factor and other relevant information such as notes on disorder etc. You can view these annotations by checking the "View Annotations" checkbox.

If X-Seed locates a name.JNL or name.TSV file corresponding to the current name.DAT file, and in the same folder, the bibliographic information of the entry is also displayed in the "Annotations" box (an example is shown below).

Once loaded, the structure can be manipulated in much the same manner as a SHELX structure (i.e.

you can change the connectivity, delete atoms, extend the structure, make POV-Ray images, compute XRD powder patterns using Lazy Pulverix, etc.). Note that any modifications made to the structure will not be retained when a new REFCODE entry is loaded.

POV-Ray

X-Seed's POV-Ray related features are quite extensive. In the present section, I will only explain briefly how to set the controls and what they mean. The POV-Ray control panel consists of four pages, each with many different, and sometimes non-intuitive controls.

You can start rendering by pressing the "Render" button, or the title bar of this control panel. If the

"Quick" render option is checked, the image will be rendered one quarter of the set size, and with

40

all the time-consuming high-quality settings (i.e. antialiasing, shadows, metallic) turned off. The

"Quick" option is useful for rapid checking of placement of the model with respect to the image borders without having to adjust the high quality settings desired for the final image.

Image Page

Keep antialiasing

turned off until you are ready to produce the final image. Antialiasing will improve the quality of the image enormously, but the price to pay for this is time. By default, antialiasing is turned off. POV-Ray does not use the background color setting of the model display window. Click on the "Background Color" color indicator box to choose any background color you like.

Additional image effects include:

"No Shadows" to suppress the generation of "realistic" shadows in the image,

"Grayscale" to produce a monochrome image,

"Matte" to produce non-shiny objects,

"Metallic" to give the image a metallic look,

By default the rendered image is not saved to disk. Most often, you will probably end up changing and re-rendering the image several times before you are satisfied with the view. When you are ready to produce the final image, check the box marked "Save POV File". The next time you render the image, you will be prompted for a file name and the image will be saved.

The image file format is PNG (for Portable Network Graphics). In terms of disk space, this is a very economical format without sacrificing quality. Image formats such as TGA (Targa) or BMP

(Windows Bitmap) are no longer an option in X-Seed. The PNG format is generally a superior choice because these files are significantly smaller in size with no loss in image quality.

If you are an advanced POV-Ray user, you will know what to do with an INI file. In short, the INI file can be used together with the POV file to rerender an image without X-Seed (e.g. if you would like to change the image size).

If you wish to create an image that can be labeled, ensure that "Generate POVLabel File" is checked. This will instruct X-Seed to also write a file called name.LBL to accompany name.PNG

written by POV-Ray. The utility program POVLabel.exe (part of the X-Seed program suite) can then be used to read name.LBL and allows you customize the positions and text properties of the atomic labels. See the section on using

POVLabel

for further details.

By default, the ray-traced image will have the same dimensions as the current model display area .

However, the image can be made any size (in pixels) you like by using the "Custom" option.

The scale setting allows you to create an image that is scaled up according to the current size settings.

Note

: X-Seed uses only the horizontal size of the model display area to determine the scale of the

41

41

42

POV-Ray image.

If you check the "Show POV Colors" checkbox, atoms will be displayed in the colors chosen for

POV-Ray image creation (useful to keep track of how POV-Ray will display the model if atoms have been assigned custom colors for this purpose).

42

Atoms Page

IMPORTANT

: if you wish to change how an atom is portrayed by

POV-Ray, you must (1) customize the atom settings on the control panel, (2) make sure the atom is selected and (3) click on the "Apply" button.

When you press the "Apply" button, all of the checked settings will apply to the selected atom(s). Check "Clear Selection" to clear the atom selection each time the "Apply" button is pressed. If you wish to leave a certain setting of the atom unchanged, make sure that none of the settings in this category are checked. Any atom can be assigned any color. The CPK color of the atom is taken to be the color used for that element by X-Seed. These colors can be changed using the Element

Settings dialog. Alternatively, you can apply a custom color to selected atoms. Click on the custom color indicator box to select the color to be applied. It is also possible to use predefined textures for atoms. These textures can be selected from the "Texture" dropdown list. The textures in this list are extracted from the file "textures.inc" that is supplied with

X-Seed. If you wish, you can add or remove textures from this file. By default, atoms are shown as spheres of radius 0.2 times that of their van der Waals radii (0.15 for hydrogen atoms). The van der Waals radii used for the different elements can also be changed in the Element

Settings dialog. In addition, you can set a fixed radius. Three shortcut

buttons are available to quickly set the radii for stick, ball-and-stick and spacefilled representations. These buttons only change the settings

- you still have to apply these settings to the selected atoms. An example of each type of representation is given below.

Checking "Transparent v.d.W. Sphere?" will generate a semi-transparent sphere around the atom. The level of transparency is set on the "Misc" page of this control panel (see below).

43

43

44

When only one atom is selected, this button will appear. The button allows you to change the atom settings on the control panel to correspond to those of the selected atom.

Stick representation. If an atom has been assigned a radius of zero, it will be shown with the same radius as the thickest bond to it. Thus terminal bonds are shown with rounded rather than flat ends.

Ball-and-stick representation. Individual atom and bond radii can be set to any value.

Space filled representation.

Anisotropic atoms can also be shown as thermal ellipsoids. In order to do this, check the "Ellipsoids" setting in the "Display as" panel. The

"Radius" panel will be replaced by controls that allow you to set various options relating to how ellipsoids are shown. The probability factor (default = 50%) can be selected from a dropdown list. There are several effects that can be applied to ellipsoids. These are best illustrated by the examples shown below, but you are encouraged to experiment with different settings yourself. By default, an ellipsoid's interior color is the same as its CPK color.

An ellipsoid with no special effects.

44

46

Octant cutout + tori.

As above with axes and hatching.

Special note

: A sliced ellipsoid with no border cannot be hatched.

Bonds Page

IMPORTANT

: in general, if you wish to change how a bond is portrayed by POV-Ray, you must (1) customize the bond settings on the control panel, (2) make sure the bond is selected and (3) click on the "Apply" button. However, for convenience, buttons are also available to apply the current settings to all normal or all hydrogen bonds, regardless of which are selected.

Check "Clear Selection" to clear the bond selection each time the

"Apply" button is pressed. Any bond can be assigned any combination of radius, color and fragmentation settings. If a bond is assigned to have CPK colors, the color of the bond will depend on the colors of the two atoms involved. If the two atoms do not have the same color, by default, the bond will be split into two colors with the position of the color division being a proportional to the bonding radii of the atoms.

However, you can use the "50:50" option to force the color split to occur midway between the two atom positions. If a bond is given a fixed color or texture, it can also be fragmented. Up to 30 equally-spaced fragments are allowed. By default, the bond fragments are sliced cylinders. However, the fragments can also be represented as spheres. Note: only fixed-color/texture bonds can be fragmented.

When only one bond is selected, this button will appear. The button allows you to change the bond settings on the control panel to correspond to those of the selected bond.

46

Misc. Page

Show Centroids as Spheres:

If you have defined centroids in the structure, these will only be shown if this box is checked. Thus, by default, bonds that have been added between atoms and centroids will be shown, but not the centroids themselves. However, if you would like to have the centroids displayed, you can use this option to turn them on.

Atom Transparency:

Set the transparency level of any atoms that have been selected to also have semi-transparent van der Waals surfaces (see

Atoms page above). Rendering transparent atoms is slow.

There are several pages for various other settings:

Wall:

Place a wall behind the model. The wall can have a vertical gradient from one color to another. It is best to experiment with the settings to get a feel for how they work.

Floor:

Place a checkered floor below the model.

Unit Cell:

By default, the unit cell color will be the same as that used in the display. However, it is possible to use a special texture for the unit cell edges. The radii of the edges can also be set.

Animate:

Create a series of frames for animations. An animation consists of a full 360° rotation. Select the axis about which the animation will take place, and the number of images per rotation. When you press the "Render" button, POV-Ray will begin to render all the images of the animation. An animator program such as Animagic can be used to piece the frames together and thus to construct a single animation file that can be placed on a web page.

Slice:

It is possible to cut a section through selected atoms (e.g. to show the cross section of a cavity or channel, etc.). Just select the atoms that you'd like "sliced" and press the "Slice selected atoms" button. Check "Slice Structure" if you want to create a cross section. You can select whether or not the unit cell axes will also be cross-sectioned. By default, the structure will be sliced in the plane of the screen, and through the centroid of the structure. You can change the height of the slice in Z relative to this plane. The surface of the sectioned portion can be assigned a color or texture. Finally, it is also possible to rotate the sliced strcuture in X, Y and Z - otherwise the slice will always be perpendicular to the direction of the view. In the edit box next to "Roate Image", enter three numbers. These three numbers represent the angles in degrees about which to rotate the sliced model in X, Y and Z respectively AFTER slicing.

Lights:

The three numbers in the "Position" field define the position of a light source. Two types of light sources can be defined - relative and absolute.

Relative light sources are light sources that are positioned on a sphere centered at the visible structural model's centroid (i.e. the image origin), and the radius of the sphere is the distance of the

"camera" from this origin. The "Position" of a relative light source is defined by rotations about the

X, Y and Z axes. The light source starts at the "camera" and rotates about X, then Y and then Z by the three numbers in the "Position" field respectively.

Absolute light sources also utilize the three numbers in the "position" field. These three numbers now define the position of the light source in the Cartesian space of the model (in angstrom units).

A certain amount of guesswork is required here. You don't really have a way to determine actual positions in Cartesian space and may have to use the trial-and-error approach to get the lighting effect that you want. Usually, the default light sources will be quite adequate.

47

47

48

Up to four light sources are available. To turn them on or off, just check or uncheck them. Each light source can have its own intensity, position (absolute or relative), place to point at, and can either cast a shadow or not.

Dialog Boxes

Much of the functionality of X-Seed is accessed via numerous dialog boxes. The most important of these are described in turn below.

The following dialog boxes are available:

Element Settings

Crystal Data

SHELX-S LST File Summary

SHELX-L LST File Summary

Structure Report

Program Settings

Undelete Atoms

SHELX-S

SHELX-L

Lazy Pulverix

PARST

Element Settings

48

49

The Element Settings dialog is used to customize the display colors and van der Waals radii of the different elements. The first 95 elements, as well as deuterium, tritium, peaks and centroids are available for modification.

Click on an element in the periodic table to load its current settings into the lower panel:

Here the van der Waals radius and color of the atom can be set. Its bonding radius is shown, but cannot be altered. A shortcut method of changing the color associated with a particular element is to double-click on its entry in the periodic table. This activates the color selection dialog directly.

Other controls on this dialog are described below.

X-Seed can generate a set of default parameters for the elements. Use this button to generate these default values for all the elements.

Re-generates the default values for the currently selected element only.

Save the current element settings to disk.

Retrieve a previously saved set of element setting

49

50

You can save any number of sets of element preferences to disk for later use. When you exit

X-Seed, the program automatically saves the current element settings to a file called "last.elt". The next time X-Seed is executed it loads and uses this set of element parameters.

The Element Settings dialog is also the only facility that X-Seed has for changing the background color of the model display area

Crystal Data

This dialog is activated when a new structure is created using the File | New Structure menu option

or when the user wishes to alter any crystal data parameters (Edit | Crystal Data). When activated via the "New Structure" menu choice, the "Import From SHELX File" button will be visible. You may either enter the crystal data manually, or import them from an already existing SHELX INS or

RES file using this button. When you import such a file, only the relevant crystal data parameters are extracted - any atoms present in the file will be ignored. If you wish to import the atoms too, use the File | Open File menu instead. The fields in this dialog should be largely self-evident. Only fields shown in black text are editable. Changing the current space group is as simple as typing in the space group symbol - see Space Groups for details of space group notation. In accordance with

SHELX, the origin of a centrosymmetric space group MUST lie on a center of symmetry. As long as they meet this requirement, all settings of the 230 space groups are supported. The molecular

50

formula represents the molecular entity that you regard as being the formula unit - not necessarily the entire contents of the unit cell (unless Z = 1). When you change the formula or Z, the

"Calculated Density" field will be updated. If the calculated density is less than 0.8 or greater than

3.0, the density field will be shown in red to indicate a possible error in either Z or the molecular formula. The "HKL name" is the logical name of the structure - i.e. the name of the HKL file name

(excluding the .HKL extension) and also the name that will be assigned by X-Seed to the SHELX

INStruction file. If you change this name, you should make sure that an HKL file with the new name does indeed exist in the working folder. All editable fields in this dialog, with the exception of the title, crystal dimensions and data collection temperature, are essential before structure solution by SHELXS can proceed.

Press "OK" to accept the current parameters, or "Cancel" to discard any changes that have been made. If an HKL file corresponding to the structure's logical name cannot be located, a warning to this effect will be given. You will also be warned if the crystal data are not sufficient to allow proper creation of a SHELX INStruction file.

If this dialog is activated via the Edit | Crystal Data menu choice, and the structure already contains atoms, you will not be able to alter the unit cell parameters since this would change the positions of the atoms relative to one another.

51

SHELX-S LST File Summary

This dialog is activated via two different routes. The first is by selecting "Latest SHELX-S Results" from the "

Display " menu. The second is immediately after a SHELX-S solution run. X-Seed

searches for a name.LST file (name is the logical name of the structure) in the structure's folder and attempts to determine if the file was created by SHELXS-86 or SHELXS-97. Depending on the origin of the LST file, the dialog summarizes the pertinent parameters that it is able to extract from this file. If the dialog has been activated via the main menu, it will contain a button labeled "OK" to return back to the main program. However, if the dialog is activated at the completion of a

SHELX-S run, you can use it to evaluate whether or not you would like to accept the result. If you press the "Accept" button, the current model is updated as control is returned to X-Seed's main window. If you choose to "Reject" the run, the model will not be updated and the SHELX run will be ignored. The LST and RES files of a rejected run will be deleted and their previous instances restored.

The pertinent parameters extracted from the LST files are summarized in informative data fields or as bar charts. The meaning of these parameters should be quite self-evident and will not be explained here in any further detail.

The dialog also contains buttons that allow you to view the actual RESults and LST text files.

Pressing these buttons will activate the Windows Notepad program which will automatically load the relevant file.

SHELX-L LST File Summary

51

52

This dialog is activated via two different routes. The first is by choosing "Latest SHELX-L Results" from the "

Display

" menu. The second is immediately after a SHELX-L refinement run. X-Seed searches for a name.LST file (name is the logical name of the structure) in the structure's folder and summarizes the pertinent parameters that it is able to extract from this file. If the dialog has been activated via the main menu, it will contain a button labeled "OK" to return back to the main program. However, if the dialog is activated at the completion of a SHELX-L run, you can use it to evaluate whether or not you would like to accept the result. If you press the "Accept" button, the current model is updated as control is returned to X-Seed's main window. If you choose to "Reject" the run, the model will not be updated and the SHELX run will be ignored. The LST and RES files of a rejected run will be deleted and their previous instances restored.

The pertinent parameters extracted from the LST files are summarized in informative data fields or as bar charts. The meaning of these parameters should be quite self-evident and will not be explained here in any further detail.

The dialog also contains buttons that allow you to view the actual RESults and LST text files.

Pressing these buttons will activate the Windows Notepad program which will automatically load the relevant file.

Structure Report

Choose "Display | Report" from the main menu. The "Structure Report" dialog currently shows only a few details about the structure and will be extended in a later version of X-Seed to include more information. In order to identify possible discrepancies, the assigned molecular formula of the unit cell contents can be compared with the molecular formula of the current model. The assigned molecular formula is calculated by multiplying the formula unit given in the

Crystal Data dialog by Z while the model's formula is calculated by summing the element types over all the asymmetric unit atoms of the current model using their site occupancy factors and space group multiplicities.

Use this button to adjust the assigned formula to match that of the model. Only use this facility if you are certain that the model is complete.

52

It is also useful to know if any anisotropically refined atoms have non-positive definite thermal parameters.

Program Settings

The "Program Settings" dialog is activated via the Preferences | Program Settings menu selection.

Currently, this dialog contains four pages.

File Paths

53

X-Seed is able to execute several DOS and Windows programs automatically. Use this dialog to tell X-Seed where their program executable files are located. You can either type the FULL path names of the programs (e.g. C:\Software\X-Ray \SHELX-97\Shelxs.exe) or browse your hard drive to locate the files (preferred method).

Note: the POV-Ray executable file is usually called "pvengine.exe" and is located in the "bin" subfolder of the POV-Ray installation folder.

Adding Hydrogens

53

54

This is where you can customize the form of the SHELXL-97 HFIX instruction cards for hydrogen atom generation (when you use the Generate H-Atoms (HFIX) control panel). The default values should be adequate for most purposes, but if you know what you're doing you can alter the settings.

Consult the SHELXL-97 instruction manual for the meaning of the HFIX parameters - see HFIX and AFIX. The description field allows you to specify the text in the hint box that pops up when the mouse cursor is over the relevant button in the Generate H-Atoms (HFIX) control panel.

Miscellaneous Settings

This panel allows you to fine-tune X-Seed's definition of what constitutes a "residual peak".

Residual peaks are peaks of electron density that are clearly not indicative of atoms that have to be added to the model. These peaks appear at relatively short distances from established atoms of the model, especially "heavy" atoms. You can delete such peaks manually, or save time by selecting

"All Residual Peaks" from the "Delete" menu. Only peaks that meet the criteria set out in this panel will be removed.

54

55

When X-Seed generates H- bonds automatically at your request, it uses the criteria laid out in this panel. Only elements that are listed in the "Valid Donor / Acceptor" field are considered during automatic hydrogen bond generation (although you can manually add H-bonds between any two atoms - see Add/Remove Bonds). You can add or remove any elements to/from this list. The element symbols in this field must be separated by spaces. You can also set the distance criteria for hydrogen bond generation as outlined in the panel. The "Use H-Bonds ... " checkbox can be checked if you wish hydrogen-bonded connectivity to be considered when X-Seed decided what constitutes a fragment.

Furthermore, using this page, one can choose to suppress the splash screen on startup (this is not suppressed by default).

Un-check "Confirm Before Closing Structure" if you would like X-Seed to wait for final confirmation before a structure is removed from its memory (e.g. when switching from one structure to another).

You can choose whether or not peaks are considered as parts of fragments. This affect selection of fragments, but not growing - i.e. peaks can't be generated by the application of symmetry transformations.

It is recommended that you use small fonts as a general Windows setting. X-Seed can warn you if you don't have this set - but you can choose not to be warned.

While XPREP dies a rather nice job of checking systematic absences to determine centering and space groups, there is no check to see if an axis may inadvertantly have been doubled, trebled, etc.

You can let X-Seed do this check for you whenever a new structure is loaded. A check will then be made of the HKL file to identify possible multiplicity of a unit cell axis. You can also set the

I/sigma(I) limit for this check.

Associations

Press these buttons in turn to instruct Windows to associate files with INS and RES extensions with

X-Seed. Once this is done, you should be able to click on an icon representing a SHELX file to load it using X-Seed. You should have Administrator privileges in order to do this. In the same way,

HKL files can also be associated with LAYER.

When you exit X-Seed, your preferred settings will be retained in the Windows registry

55

56

Undelete Atoms

When asymmetric unit atoms are deleted, they can still be restored - until the results of the next SHELX run have been accepted. Use this dialog (activated via the "Delete | Undelete Atoms" menu) to restore any asymmetric unit atoms that have been deleted.

To undelete an atom, make sure that the checkbox next to its name is checked when you click on the

"OK" button. Time-saving buttons are available to select, unselect and toggle selection of the atoms in the list. Symmetry-generated atoms, when deleted, are not retained for "undeletion" since it is possible to re-generate these atoms from the space-group and asymmetric unit atom list information

SHELX-S

This dialog provides the interface to structure by means of either SHELXS-86 or SHELXS-97 and is activated via the "Interface | SHELXS" menu selection.

On the first page of the dialog the "type" of SHELXS run is selected from "Direct Methods"

"Patterson" and "Partial Structure Expansion". The rest of the dialog provides a means of setting the parameters for the various SHELXS instruction cards - see the topics describing the SHELXS-86 and SHELXS-97 instructions for details. Some of these cards are specific to the type of SHELXS run and the pages that are shown on the dialog depend on the run type selected. By default,

SHELXS-97 will be used, but you can instruct X-Seed to use SHELXS-86 instead. There are slight differences in the cards used by the two separate programs, and X-Seed is sensitive to these differences.

The "LST File Verbosity" setting represents the parameter on the MORE instruction card while the time limit, if required, represents the TIME card parameter. If "Notify on Completion" is checked, your computer will use the Windows' "Exclamation" sound to inform you when the SHELXS run has completed.

The "Process Priority" setting influences how much of the CPU can be hogged by SHELXS. A priority of "Normal" will be adequate for most purposes. Increasing the process priority will not necessarily make SHELXS run faster unless other CPU intensive processes are running at the same

56

time. If you want SHELXS to run in the background and not cause other processes to slow down much, use the "Low" priority setting. If you are willing to allow SHELXS to use the CPU almost exclusively, use the "Real Time" setting, but don't expect to be able to get much response from your computer until SHELXS completes.

When you press the "Solve!" button, X-Seed will write the SHELXS INStruction file to disk, invoke SHELXS and minimize itself until SHELXS completes. While SHELXS is running, you will see its progress in the DOS window as usual. The SHELX run can be cut short by pressing Esc or aborted by pressing Control-C (when its DOS window has the focus). In either of these cases,

X-Seed will ascertain what has occurred from the text in the resulting LST file and will reactivate the SHELXS dialog. If the run completes normally, the LST File Summary dialog will be activated, from which you can choose to either accept or reject the results.

If you wish to preview the INS file to be created according to the current settings, but not activate

SHELX, the "Preview Instructions" button is available for this purpose.

57

SHELX-L

This dialog provides the interface to structure refinement by means of SHELXL-97 and is activated via the "Interface | SHELXL" menu selection.

Refer to the SHELXL-97 topic in this manual for details of the SHELXS-97 instruction summary.

SHELXL accepts a large number of instructions, and most of these can be set using this dialog. The separate pages on the dialog will each be discussed in turn below. Cards shown with checkboxes in this dialog will only be included in the INStruction file if the boxes are checked.

General

The L.S. and CGLS instruction cards both accept four parameters which can be set on the "Least

Squares Refinement" panel. These two cards are mutually exclusive and thus you have a choice between them. Using the "Settings" panel, you can influence the verbosity of the resulting LST file

(MORE card) and set a time limit for the run, if needed (TIME card). By checking the "Notify on

Completion" you can instruct X-Seed to play the standard Windows "Exclamation" sound when

SHELXL-97 completes. An ACTA card can be included in the INStruction file for a final run and a value of 2-Theta provided if needed.

The "Process Priority" setting influences how much of the CPU can be hogged by SHELXL. A priority of "Normal" will be adequate for most purposes. Increasing the process priority will not necessarily make SHELXL run faster unless other CPU intensive processes are running at the same time. If you want SHELXL to run in the background and not cause other processes to slow down much, use the "Low" priority setting. If you are willing to allow SHELXL to use the CPU almost exclusively, use the "Real Time" setting, but don't expect to be able to get much response from your computer until SHELXL completes.

Variables

This page gives you access to the parameters that SHELXL will refine in addition to atomic coordinates, site occupancies and thermal parameters. The FVAR parameters are entered in the

"Free Variables" field. Only one number may be entered per line and the position of the number in the list is its "FVAR" number. The EXTI and SWAT cards are mutually exclusive and one or neither of these cards can be selected for inclusion in the INStruction file. A WGHT card will only be included if the WGHT checkbox is checked.

57

58

Comments

Any comments that you would like to add to the INStruction file can be entered on this page. Each line in the edit box will be added to the INS file and preceeded by a REM instruction. Comments are retained when a SHELX INS or RES file is imported and will also appear here.

Extra Cards

Any instruction cards that are not directly facilitated by X-Seed can be entered here. See the section on How X-Seed interacts with SHELX for a list of these cards. When X-Seed imports a SHELX

INS or RES file, many of these unsupported, but recognized, cards will be imported too and will appear on this page of this dialog.

Reflections

Use this dialog to fine-tune how SHELX handles the reflection data. When the dialog is activated,

X-Seed searches through the last LST file for the 50 worst fitting reflections. These are added to the dialog for possible omission from the next refinement run. The reflections are listed in decreasing order of badness of fit and if checked, are omitted from the next run (by generation of OMIT - type

2 - cards). When the refinement run is complete, these OMIT cards are transferred to the bottom of the "Extra Cards" edit field.

Fourier Peaks

Use this dialog to set the parameters on the FMAP, GRID and PLAN cards. Leave the checkboxes unchecked to omit these cards from the INStruction file. Omission of these cards will cause

SHELXL-97 to just use default values for these parameters.

When the "Refine!" button is pressed, X-Seed writes the SHELXL INStruction file to disk, invokes

SHELXL and minimizes itself until SHELXL completes. While SHELXL is running, you will see its progress in the DOS window as usual. The SHELX run can be cut short by pressing Esc or aborted by pressing Control-C (when its DOS window has the focus). In either of these cases,

X-Seed will ascertain what has occurred from the text in the resulting LST file and will reactivate the SHELXL dialog. If the run completes normally, the LST File Summary dialog will be activated, from which you can choose to either accept or reject the results. If SHELXL-97 aborts with an error, this error message will be displayed and you will be returned to the main Windows to make the necessary changes to the model or to the SHELX instructions. The model as it was before refinement was attempted will still be intact and you can try again.

If you wish to preview the INS file to be created according to the current settings, but not activate

SHELX, the "Preview Instructions" button is available for this purpose.

Lazy Pulverix

58

59

For a description of the Lazy Pulverix program suite, see the relevant topic in this help file. In order to function properly, the DOS programs lazy.exe and pulv.exe MUST be in the same folder (the install program puts them in a folder named "lazyp" in the X-Seed installation folder). If you wish to see the resulting powder pattern displayed after it has been calculated, the Windows program xrdplot.exe must also be in the Lazy Pulverix folder. All of the settings available to Lazy Pulverix can be set using this dialog. When you press the "Calculate" button, X-Seed will prepare and save a

LAZY input file (in the structure's folder) and then execute the programs LAZY and PULVER in turn. When PULVER completes, X-Seed will execute the program XRDPlot and automatically load the calculated powder pattern trace. XRDPlot can be used to view and print the powder trace. If

XRDPlot does not display a powder pattern, it means that the Lazy Pulverix run was unsuccessful.

See the DOS Windows subtopic for important information about the DOS windows in which the ancillary programs are run.

Important

: Do not hide the DOS windows if they are not set to close automatically. If you do this, the DOS windows will be hidden, but will wait for you to close them. It will not be obvious to you how to do this, and X-Seed will appear to "hang" as it waits for LAZY PULVERIX to terminate

PARST

59

60

For a description of the PARST-97 program, see the relevant topic in this help file. Use this dialog to set up the instruction file for PARST-97. In order for X-Seed to be able to run PARST-97 automatically, you need to use the modified version of PARST called xPARST97.exe. After the

PARST run, the results are displayed using the Windows program Notepad. The PARST interface is still under development and thus far standard deviations are not included in the calculations.

When the PARST interface is completed, X-Seed will have the ability to extract the e.s.d's from the

SHELX LST file in order to include them in the PARST input file. For further details, see Running

PARST-97 from X-Seed.

See the DOS Windows subtopic for important information about the DOS windows in which the ancillary programs are run.

Important

: Do not hide the DOS window if it is not set to close automatically. If you do this, the

DOS window will be hidden, but will wait for you to close it. It will not be obvious to you how to do this, and X-Seed will appear to "hang" as it waits for PARST to terminate.

Program Interfaces

X-Seed provides interfaces to a number of other programs:

SHELX Support

PARST-97

LAZY PULVERIX

Layer

60

Section

POV-Ray

POVLabel

CIF2CIF

SHELX Support

X-Seed is fully compatible with most of the SHELXL instructions, but not all of them. Because

SHELX is instruction-based, and accepts all of its instructions from text files, it is a very powerful and versatile program. Instruction files can become quite complex when coded by an expert and it would be difficult to design a graphical interface that could be fully compatible with all of its features. Most small-molecule X-ray structures can be completed quite satisfactorily without resorting to some of the more advanced and obscure features of SHELX.

When X-Seed executes SHELX-S, it minimizes itself and waits for the run to complete. When the run is complete, X-Seed checks the LST file to make sure that the run was not aborted by the user or that it didn't crash. If the run was successful, the results are displayed graphically in a dialog. The user can inspect the results and then choose whether or not to accept the outcome. If the results are accepted, X-Seed renames the name.LST file to name.XS so that it doesn't get replaced by a subsequent LST file with the same name. The name.RES file is then read and the model displayed for editing.

Running SHELX-L follows much the same procedure. In this case, the name.LST file is renamed to

name.XL.

SHELX Command support

X-Seed supports the SHELXS-86, SHELXS-97 and SHELXL-97 commands to varying degrees from full to no support. In the description given below, commands used by both SHELX-S and

SHELX-L are shown in black, cards used specifically by SHELX-S are shown in blue and those used only by SHELXS-86 are in green .

Fully supported:

Parameters on the following cards are correctly extracted from SHELX name.INS or name.RES files and can also be accessed via X-Seed dialog boxes and/or are processed internally when the atom and connectivity lists are constructed:

TITL

REM

WGHT

CELL

EXTI

AFIX

ZERR

SWAT

PART

LATT

SIZE

SYMM

TEMP

HKLF

FVAR

Conditionally supported:

The SFAC card can take two forms. The first form specifies only the element symbols on a single card while the second specifies the element symbol and scattering factors etc. of an individual element. The second form of the SFAC is not supported when a

SHELX file is read by X-Seed (i.e. the parameters are ignored). However, the second

61

61

62 form is specifically used for each element when a SHELXS-86 run is to be initiated since SHELXS-86 does not contain the relevant parameters for all the elements.

X-Seed contains all of the relevant parameters for all elements internally and is able to generate these cards when writing a SHELXS-86 INS file.

The UNIT card must contain only integer values.

Partially supported:

Parameters for the following cards are accessible via X-Seed dialog boxes, or are correctly generated by X-Seed as necessary, but are not extracted from SHELX

name.INS or name.RES when these files are opened:

ACTA ANIS BIND CGLS FMAP EGEN

END

INIT

OMIT

SUBS

EQIV

L.S.

PATT

TEXP

ESEL

LIST

PHAN

TIME

FREE

MERG

PHAS

TREF

GRID

MORE

PLAN

VECT

HFIX

MOVE

SHEL

Not specifically supported:

The following cards are not specifically supported, but can be easily implemented using the "Additional Cards" field in the SHELX-L dialog:

BASF BUMP BOND CHIV CONF CONN

DAMP

EADP

LAUE

DANG

EXYZ

MPLA

DEFS

FLAT

NCSY

DELU

HOPE

DFIX

HTAB

DISP

ISOR

SPEC

FRAG

STIR

FEND

SUMP

SAME

RTAB

TWIN

SADI

WPDB

SIMU

BLOC*

When a SHELX name.INS or name.RES file is loaded, X-Seed automatically places these cards in the "Additional Cards" field. Note that many of these cards refer to atoms by name and you should therefore be aware that if you change atom names, the cards below may become invalid and cause SHELX to terminate with an error. Note that the parameters on the BASF card will be updated after a SHELX-L run since these values are refined.

*

Use the BLOC n1 n2 atomnames form for this command and put it in the "Additional

Cards" field. Use the second form (i.e. embedded in the atom list) is not permitted or supported.

Ignored completely:

The following cards are completely ignored when a SHELX file is read:

MOLE PSEE SPIN

62

Not supported:

No support is provided for the

RESI

command since X-Seed is intended for use by small-molecule crystallographers.

PARST-97

A system of computer routines for calculating molecular parameters from results of crystal structure analyses.

by:

M. Nardelli

Dipartimento di Chimica Generale ed Inorganica, Chimica Analitica,

Chimica Fisica della Universita` degli Studi di Parma,

Centro di Studio per la Strutturistica Diffrattometrica del C.N.R.,

Viale delle Scienze, I-43100

Parama

Italy

February 1998

Published in:

Computer & Chemistry 1983, 7, 95 and

J. Appl. Cryst. 1995, 28, 659.

PARST

calculates:

• Niggli's reduced cell

• orthogonal coordinates

• principal axes of thermal ellipsoids

• bond lengths (uncorrected and corrected for thermal motion),

• angles

• torsion angles

• least-squares planes

• least-squares lines

• angles formed by planes and lines

• puckering and displacement asymmetry parameters of rings

• spherical polar coordinates for stereographic projections

• intramolecular and intermolecular contacts

• possible hydrogen bonds

• coordinates of hydrogens in typical groups for a given set of atoms.

• The s.u.'s for all these magnitudes are calculated.

Input Data

When running PARST-97 from within X-Seed the entire input file of the former is created by the latter. However, for reference purposes, the format of the PARST input file is outlined below. The following text was extracted from the comments at the beginning of the PARST-97 source code:

63

63

64

1.Title card: TITLE (80A1)

2.Space group card: symbol of the space group (80A1)

It is important that the character in column 1 is the symbol of the Bravais lattice.

N.B.- Rombohedral lattices must be indicated as P when a rombohedral cell is chosen, as

R when the cell is hexagonal (obverse cell: -h+k+l = 3n )

3.Control card (free format):

N,D3,DM,NH1,NTN,LSP,LSL,NPR,NST,KL,KY,KC,KO,KB,KA,KT,KD,KE,KOR,NI

N=Total number of atoms (max. 500)

N=Total number of atoms (max. 500)

D3=Minimum distance for non-bonding intramol. contacts (dummy)

DM=Maximum distance for non-bonding contacts

NH1=Number of groups of hydrogen atoms whose coordinates must be calculated (max.

number of H-atoms: 500-N)

NTN=Number of distances or angles formed by non-bonded atoms

LSP=Number of planes (max. 50)

LSL=Number of lines (max. 50)

NPR=Number of rings (max. 50)

NST=Number of stereographic sets

KL=Code for the format of the atomic parameters

KY=0 no crystal data (cards 4 and 5 must not be given)

=1 crystal data are printed

KC=0 no coordinates, =1 coordinates are printed

KO=0 no orthog. coord., =1 orthog. coord. are printed

KB=0 no bond distances, =1 bond distances are printed

KB=-1 only bond distances not involving hydrogens are printed

KA=0 no angles, =1 angles are printed

KA=-1 only bond angles not involving hydrogens are printed

KT=0 no torsions, =1 torsion angles are calculated

KT=-1 only torsion angles not involving hydrogens are printed

KD=0 no interatomic contacts, =1 interatomic contacts are calc.

KD=-1 only intra-contacts not involving hydrogens are printed

KE=0 no intermolecular contacts, =1 intermolecular contacts less than DM and possible hydrogen bonds are calculated

KE=-1 only inter-contacts not involving hydrogens are printed

KOR=0 no thermal parameters in the input

KOR=1, beta: exp[-(beta11*h**2+...+2*beta12*h*k+...)]

KOR=2, U: exp[-2*pi**2(U11*h**2*(a*)**2+...+2*U12*h*k*(a*)*(b*)+...)]

KOR=3, B: exp[-0.25*(B11*h**2*(a*)**2+...+2*B12*h*k*(a*)*(b*)+...)]

KOR=4, b: exp[-(b11*h**2+...+b12*h*k+...)]

KOR=5, U*:exp[-2*pi**2(U11*h**2*(a*)**2+...+2*U12*h*k*(a*)*(b*)* cos(gamma*) +...)]

KOR=6, B*: exp[-0.25*(B11*h**2*(a*)**2+...+2*B12*h*k*(a*)*(b*)* cos(gamma*)+...)]

KOR=7, anisotropic thermal parameters given in the input, but not processed and printed

N.B.-If there are isotropic atoms together with anisotropic ones, the thermal parameter for them is given as U11 (or B11, etc.) and zeros must be given for U22, U33, U12, U13, U23

NI=Number of pairs of subset of atoms whose coordinates are to be compared.

If NI is negative only research of missing symmetries is carried out.

4.Data card (free format): NNS,Z,AL

NNS=Number of atomic species in the chemical formula

64

Z=Number of molecules in the unit cell

AL=Wavelength (Cu or Mo K-alpha)

5.Formula card (free format): symbols of the atoms, within apices, followed by their numbers

6.Parameter card (free format): a,b,c,sigma(a),sigma(b),sigma(c), alpha,beta,gamma,sigma(alpha),sigma(beta),sigma(gamma)

7.Coordinate format card: Format of the coordinate cards (80A1); this card is not given if

KL=4

8.Coordinate cards (thermal parameters are given only if KOR is not equal to zero)

If KL=1:

ATOM(6A1),X,Y,Z,S(X),S(Y),S(Z),B11,B22,B33,B23,B13,B12,S(B11),S(B22),

S(B33),S(B23),S(B13),S(B12)

If KL=2: ATOM(6A1),X,Y,Z,B11,B22,B33,B23,B13,B12,S(X),S(Y),

S(Z),S(B11),S(B22),S(B33),S(B23),S(B13),S(B12)

If KL=3: ATOM(6A1),X,S(X),Y,S(Y),Z,S(Z),B11,S(B11),B22,S(B22),

B33,S(B33),B23,S(B23),B13,S(B13),B12,S(B12)

If KL=4: FORMAT UNIMOL (7X,6A1,2X,3F8.5,12X,3(5A1,3X))

KOR must be 0

N.B.- When KY=0, i.e. the formula card is not given, the second character of the atomic labels cannot be alphabetic when the chemical simbol requires only one character (e.g.: H,

B, C, N, O, F, O, S,... ).

When KY=1, i.e. the formula card is given, there is no restriction for the second character of the labels of these atoms.

9.Cards for hydrogens in calculated positions: KDG,D,SB

(these cards mustn't be given if NH1=0)

If KDG=1,(methyl):SB=ATOM1,ATOM2,ATOM3 (I1,1X,F6.4,3(6A1))

ATOM1 is bonded to hydrogens and to ATOM2; ATOM2 is bonded to ATOM1 and to

ATOM3

If KDG=2,(methylene): as for methyl, ATOM2 and ATOM3 are bonded to ATOM1

If KDG=3,(tert-C):SB=ATOM1,ATOM2,ATOM3,ATOM4 (I1,1X,F6.4,4(6A1)

ATOM1 is bonded to hydrogen,ATOM2,ATOM3,ATOM4

If KDG=4 (benzene): as for methylene

If KDG=5 (alkyne): SB=ATOM1,ATOM2 (I1,1X,F6.4,2(6A1))

ATOM1 is bonded to hydrogen and to ATOM2

If KDG=6 (ethylenic system): as for tert-C; ATOM1 is bonded to two hydrogens and to

ATOM2 which is planarly bonded to ATOM1 ATOM3 and ATOM4

N.B.- If KOR is not equal to zero, an isotropic thermal parameter is assigned equal to the arithmetic mean of the anisotropic parameters of the atom the hydrogen is attached to D =

ATOM1-H distance (F6.4)

SB= Labels of the non-hydrogen atoms

10.Cards for distances or angles formed by non-bonded atoms.

IF two atoms are given:

ATOM1,ATOM2 (FORMAT (2(6A1)) the distance between them is given.

If three atoms are given: ATOM1,ATOM2,ATOM3 (FORMAT (3(6A1)) the angle at ATOM2 is calculated.

While, if four atoms are given:

ATOM1,ATOM2,ATOM3,ATOM4 (FORMAT (4(6A1))

65

65

66 a torsion angle is calculated.

11.Cards for LQ-planes: NT,NFP,names of the atoms

FORMAT (2I2,4X,12(6A1)/(12(6A1)))

NT=Total number of atoms (max 40)

NFP=Number of the atoms not defining the plane

12.Cards for LQ-lines: NT,NFP,names of the atoms

FORMAT (2I2,4X,12(6A1)/(12(6A1)))

NT=Total number of atoms (max 40)

NFP=Number of the atoms not defining the line

13.Cards for puckered rings: NP,Names of the atoms in the right sequence

FORMAT (I2,6X,12(6A1)/(12(6A1)))

NP=Number of the atoms of the ring (max 40)

14.Cards for stereographic projections: KO,NP,NQ,names of the atoms in the right sequence

FORMAT(I1,2I2,3X,12(6A1)/(12(6A1)))

KO=1,origin at 1st atom,Z axis along ATOM1-ATOM2

KO=2,origin at 1st atom,Z axis perpendicular to the mean plane through the first NQ atoms, excepting ATOM1

KO=3,origin at the center of the first NQ atoms, Z axis perpendicular to the plane through them

NP=Total number of atoms (max 40)

NQ=Number of the atoms defining the projection plane inclusive of first atom

15.Data for intermolecular contacts (it must be given even if KE=0):

IC,NE,NT (Free FORMAT)

IC=1 if the space group is acentric

=-1 if the space group is centric

NE=Number of the equivalent positions (the general, X Y Z, and the centrosymmetric ones must be omitted)

NT=Maximum translation required (suggested 1 when the set of atoms in the general position is the nearest to the origin, 2 in the other cases)

16.Equivalent position cards: one equivalent position per card

(38A1). Examples: 1/2-X,1/2+Y,1/2+Z

Y-X,-X,1/3+Z

17.Card with the total number of atoms whose coordinates are compared (free FORMAT).

18.Cards with the labels of the atoms whose coordinates are compared (12(6A1)). First the atoms of the first subset, then the atoms of the second subset exactly in the same sequence.

Of course card 17 and cards 18 are not given if NI=0.

Running PARST-97 From X-Seed

From X-Seed's main menu, select "Interface | PARST-97" to activate the PARST-97 dialog. The

PARST executable file to be used is xPARST.exe which is supplied with X-Seed. This file is a slightly modified version of the original program. The modification allows X-Seed to execute the program automatically. The PARST interface is still under construction. Since X-Seed currently reads SHELX INS and RES files as well as CSD files, the E.S.D.'s of the atomic coordinates and thermal parameters are unknown and can therefore not be written to the PARST input file. A future

66

version of X-Seed will be able to read a structure from a SHELX LST file together with positional

E'S'D's and will thus be fully capable of exploiting all of PARST's features (with the possible exception of the feature that allows the comparison of two substructures).

LAZY-PULVERIX

A program to calculate theoretical X-Ray and Neutron diffraction powder patterns.

by:

Klaus Yvon, Wolfgang Jeitschko and Erwin Parthe

Laboratoire de Cristallographie aux Rayons-X

Universite de Geneve

24 Quai Ernest Ansermet

CH 1211 Geneva 4

Switzerland

December 1 1977

Published in

J. Appl. Cryst. 1977, 10, 73

LAZY PULVERIX

consists of two programs:

LAZY

decodes the input data and prepares the data file for PULVERIX

PULVERIX

reads the input file and calculates the powder pattern

Running Lazy Pulverix from X-Seed

Select "Interface | Lazy Pulverix" from X-Seed's main menu. This will activate the Lazy Pulverix dialog which provides access to the various settings that can be used. Both the programs Lazy and

Pulv MUST be in the same folder. If you wish to view the resultant powder pattern using the program XRDPlot, this program too must be in the Lazy Pulverix folder. The Program Settings dialog only requires you to specify the path to Lazy.exe and it is assumed that the other two programs share the same folder.

If the executable path is set correctly (see Program Settings), Lazy and Pulv will be executed in turn when you press the "Calculate" button. Once the powder pattern has been calculated, the program XRDPlot will be executed and the trace loaded automatically. XRDPlot, also written by

Len Barbour, is a simple program (for now) and merely provides a means of reading, displaying and printing a powder pattern which is contained as a series of lines in the file name.LIN. XRDPlot reads the powder lines and simulates a trace that consists of the summed Gaussian representations of the calculated peaks.

The Lazy Pulverix program suite is particularly sensitive to correct formatting of its input file.

Coding such a file manually is prone to errors and can be very frustrating to do correctly by trial and error.

X-Seed reduces the task of calculating the powder pattern of the currently loaded structure (SHELX file, CSD structure, etc) to merely changing some settings on a dialog box and pressing a button.

Currently, the only limitation is that Lazy Pulverix is dimensioned such that the input file cannot contain more than 500 atoms of the same type (i.e. in the asymmetric unit).

67

67

68

Layer

A computer program for the graphic display of intensity data as simulated precession photographs.

LAYER

was conceived, developed and continues to be maintained by:

Len Barbour

Department of Chemistry

University of Stellenbosch

7602 Matieland

South Africa

Tel: +27-21-808-3335

Fax: +27-21-808-3849 [email protected]

(preferred)

[email protected]

Published in:

J. Appl. Cryst. 1999, 32, 351.

Operation

LAYER is a 32-bit Microsoft Windows-based program that reads intensity data in SHELX type 4 format and displays any level of the reciprocal lattice net. The program is primarily intended for instructive purposes, but may also prove useful as a visual complement to statistically based numeric analysis of diffraction data for space group determination.

Program outline

The executable file can be placed in any system folder while a shortcut to the program can be created on the system desktop. If an icon representing a SHELX type 4 name.HKL file is dragged onto the program's icon (or that of its shortcut) a new instance of the program is activated and the reflection data are loaded into memory. Alternatively, if LAYER is already running, an HKL file can be loaded by clicking the "Open File" speed button. When loading a name.HKL file, LAYER also searches the current folder for a SHELX name.RES or name.INS file in order to determine the corresponding unit cell parameters and radiation wavelength (only the CELL card is read). If the program fails to locate an INS or RES file, these parameters can be entered manually. The only restriction applied to the HKL input file is that the data must be consistent with the FORTRAN format convention 3I4,2F8.2. The user can easily select the reciprocal cell axis down which to view the r.l. planes and navigation through successive levels is achieved by left- and right-clicking with the mouse cursor positioned in the data display area. Moving the mouse cursor about the data display area causes the parameters h, k, l, 2-theta, intensity and I/Imax pertaining to the closest reflection spot to be displayed. Display options that can be turned on or off include the reciprocal axis and horizontal and vertical indexing lines. Since intensity data sets rarely constitute a full sphere, it is also possible to substitute Friedels for missing reflection, thus reducing the occurrence of gaps in the display. The scale of the display can be altered by means of a slide bar control.

Similarly, the user can control the relative spot intensities as well as the shade of the "film" background.

In grayscale mode, all reflection spots are shown as small circles 9 pixels in diameter while the darkness of each spot represents the reflection intensity. Since darkness values can range from 0 to

256 (from white to black), reflection intensities can range from the darkness of the film background to 256. Grayscale mode can only be used if the computer is capable of displaying more than 256 colors at a minimum screen resolution of 1024 x 768 pixels (this depends on the capability of the monitor as well as the memory capacity of the video adapter). If the computer is not capable of displaying more than 256 colors, grayscale mode can be turned off and the reflections are then

68

shown as black circles with their radii varying logarithmically according to relative intensity.

Although the non-grayscale mode produces an unrealistic image, it is still possible to view symmetry relationships between the reflections, which, after all, is the main objective of the program.

Running Layer from X-Seed

Select "Interface | LAYER" from X-Seed's main menu. If the path to its executable file is set correctly (see

Program Settings ), LAYER will execute and the current structure's HKL file will be

loaded and displayed automatically.

Section

A computer program for the graphic display of cross-sections through a unit cell.

SECTION

was conceived, developed and continues to be maintained by:

Len Barbour

Department of Chemistry

University of Stellenbosch

7602 Matieland

South Africa

Tel: +27-21-808-3335

Fax: +27-21-808-3849 [email protected]

(preferred)

[email protected]

Published in:

J. Appl. Cryst. 1999, 32, 353.

Operation

SECTION is a 32-bit Microsoft Windows-based program that displays cross-sectional slices through a packed crystal structure. Unit cell dimensions as well as the unique atomic positions and symmetry operations are read from SHELX instruction files.

Program outline

The executable file can be placed in any system folder while a shortcut to the program can be created on the system desktop. If an icon representing a SHELX type name.INS or name.RES file is dragged onto the program's icon (or that of its shortcut) a new instance of the program is activated and the reflection data are loaded into memory. Alternatively, if SECTION is already running, a

name.INS or name.RES file can be loaded by clicking the "Open File" speed button. Unit cell parameters, symmetry information and fractional atomic co-ordinates of the asymmetric unit are read from the file. In order to map the voids occupied by the guest molecules in the host lattice, the guest atoms should first be deleted from the input files. No additional modification of the input file is necessary; electron density peaks are ignored and all symmetry-equivalent atoms of the provided asymmetric unit are generated. The program display consists of two areas, i.e. display setting controls and data display, respectively. The latter shows a van der Waals cross-section through the unit cell (and an adjacent unit cell in each direction) according to the current display settings. Areas occupied by atoms are shaded while unoccupied regions are represented as white space. Alteration of any of the settings causes the data display area to be updated immediately.

Only cross-sections parallel to the unit cell faces can be defined and can be viewed in projection

69

69

70 along a unit cell axis (by default) or along the normal vector of the slice plane. A plane is specified by the height in Å above the corresponding unit cell face. Left and right clicking whilst the mouse cursor is positioned in the display area causes the slice height to decrement and increment respectively (the increment can be set to any value). Additional display settings include a scaling factor and three different shading options. Clicking on the &"temp0053.html">Program Settings),

X-Seed will write a file (in SHELX format) containing only the currently displayed atoms to its

"temp" folder. SECTION will be envoked and this file will be loaded automatically.

Note

: When X-Seed terminates, it clears the temp folder of all files. If you write any SECTION images after invoking SECTION from within X-Seed, the INS file and any saved images will be deleted. Thus, if you wish to keep these files, move them to another location before exiting X-Seed.

POV-Ray

POV-Ray is a Freeware ray-tracing program and can be downloaded from this web site:

http://www.povray.org

POV-Ray uses a sophisticated scene description language and is extremely well-suited to rendering

"realistic" looking ray-traced images containing balls and cylinders - the basic building blocks of molecular graphics.

X-Seed is able to create valid POV-Ray scene description files to produce high-quality molecular graphics images with a wide variety of settings that can be applied to the atoms and bonds. In addition to writing the scene files, X-Seed will invoke POV-Ray automatically in order to render the images.

It is not necessary for you to know anything about POV-Ray's scene description language to make stunning images using X-Seed's POV-Ray interface.

Installation and Settings

POV-Ray must be obtained and installed independently of X-Seed. At the time of writing this, the latest version of POV-Ray was 3.5 and this version is recommended over older versions. When you install POV-Ray, select "Options", "Script I/O Restrictions" and check "No Restrictions". When you exit POV-Ray, this setting will be remembered; i.e. you only need to do this once. If the beep at the end of each rendering annoys you, select "Render" from the main menu and under "On

Completion", make sure that "Do Nothing" is checked. It is also better to set the following: "Options", "Render Window" and then turn "Keep Above Main" off.

In the Program Settings

dialog of X-Seed, make sure that the POV-Ray executable path is set. The

POV-Ray executable file is usually called "pvengine.exe" and should be located in the "bin" folder under the POV-Ray installation folder.

Running POV-Ray from X-Seed

The library file "textures.inc" that is supplied with X-Seed must be placed in the X-Seed installation folder (X-Seed's installation procedure does this automatically). This folder contains a set of predefined textures that can be used for atoms and bonds.

By default, all atoms and bonds have a plastic-like texture and finish.

70

72 turned off. A "Quick Render" option has been built into the program for this purpose.

Animations

Remember, when you create an animation, POV-Ray has to render as many files as there are frames. Unless you have a lot of time on your hands, keep these frames small (e.g. 100x100 pixels).

The more frames you have in the animation, the smoother the rotation - 36 frames per 360 degree rotation seem to produce a relatively smooth animation.

POVLabel

POVLabel

still needs a lot of work. However, it is perfectly functional in its present form. A more detailed description of its features is deferred until the program is more complete.

POVLabel

POVLabel reads a name.LBL file written by X-Seed and a corresponding name.PNG file written by

POV-Ray. The image is displayed on screen. Double-click on an atom to make its label visible.

Double-click on a label to hide it. When you click on a label, it becomes the "current" label described below. When you click on the image, an not on any label in particular, ALL labels become current. The font settings tool window can be used to change the settings of the current label(s). Use the left mouse button to drag the labels around until you are happy with their placement. Using the menu, you can save the label properties so that you can exit the program, but continue with the current settings at a later stage. When you select the save option, the name.LBL file is overwritten. When you export the labeled image, the labels are merged into the background i.e. they become part of the image. You are advised not to overwrite the original name.PNG file unless you're absolutely sure you will never need it again.

If the image is larger than the screen's display area, you can use the left mouse button (click on the image backgrond, keeping the mouse button down) to drag it around.

POVLabel is still under development and will be extended in the future.

CIF2CIF

Copyright 2002

Len Barbour

Department of Chemistry

University of Stellenbosch

7602 Matieland

South Africa

Tel: +27-21-808-3335

Fax: +27-21-808-3849 [email protected]

(preferred)

[email protected]

License:

The program is part of the X-Seed software system. CIF2CIF will only run on your system if X-Seed is enabled, or if your X-Seed trial period has not expired. The X-Seed license agreement and disclaimers apply to CIF2CIF.

72

Installation

CIF2CIF.exe must be placed in the X-Seed installation folder. It uses the X-Seed library file "space groups.lib".

What does it do?

CIF2CIF was designed to work with CIF files created by SHELXL-97 Build

"Arial,Helvetica,Geneva,Swiss,SunSans-Regular" size="2">When you read a name.CIF file, the program first clears all the fields. Then it reads a file named "DEFAULT.CIF" from its installation folder (if this file exists).

The entries set in the default file are filled in. Then name.CIF is read and all of its non-blank fields are entered.

Any fields set by the default file will be overwritten if these fields have entries in name.CIF too. CIF2CIF will attempt to determine the space group using the library file "space groups.lib" that comes with X-Seed. Then, if you wish, you can overlay any entries from a profile file in order to complete your CIF. A profile file is only needed if you have several different ways of completing structures (e.g. if you have two or more different type of diffractometer).

You can create a default file by clearing all fields, and then entering text into the fields that you'd like to have defaulted. Then save the default file. You can create a profile file in the same way.

You can use the last tabbed page labeled "RTF Report" to generate text that can be inserted into the reference or footnote section of a paper. Just press the "Create RTF Report" button, check that everything looks correct, and then press "Copy to Clipboard". Then you can paste the report text into, for example, a

Word 2000 document.

You can load a CIF file by pressing the "Open CIF File" button, or by dragging a CIF file icon onto the program window.

1. Test Structure

This tutorial consists of a worked example of the determination of the structure of tryptamine HCl.

If you follow the procedure in this chapter exactly, you will complete the solution and refinement of a "well-behaved" structure and will be exposed to some of the most commonly used features of

X-Seed

.

Schematically, tryptamine HCl has the following structure:

73

X-Seed'

s installation procedure places the data files required for the tutorial structure in the "test" folder under the X-Seed installation folder. This folder should contain the files trypt.ins and

trypt.hkl. The HKL file was collected on a Brucker SMART CCD system and the INS file was created by the program XPREP (part of the SHELX-TL program package). Of course the HKL file is essential, but if you know the cell parameters and space group, you don't need the INS file.

73

74

However, having an INS file that contains at least the cell parameters makes life a little easier.

trypt.ins contains the following text:

TITL Tryptamine.HCl in Pbca

CELL 0.7107 8.4691 10.0580 23.9490 90.000 90.000 90.000

ZERR 8.0000 0.0020 0.0024 0.0059 0.000 0.000 0.000

LATT 1

SYMM 0.5-X, -Y, 0.5+Z

SYMM 0.5+X, 0.5-Y, -Z

SYMM -X, 0.5+Y, 0.5-Z

SFAC C H N CL

UNIT 88 96 16 8

TEMP -100

SIZE 0.40 0.35 0.10

TREF

HKLF 4

It is assumed here that you have already set the paths to SHELXS and SHELXL using the Program

Settings Dialog.

Structure Solution

1) Start X-Seed.

2) Select File | New from the Main Menu, or press the button on the toolbar to activate the

Crystal Data dialog.

3) Press the button labeled "Import From SHELX File" and navigate your system to find and select

trypt.ins. X-Seed will import the relevant data from the file and will complete the data fields in the dialog accordingly. Note that the molecular formula is incorrect for tryptamine HCl - the numbers for carbon and hydrogen on the SHELX UNIT card are intentionally incorrect for the purposes of this tutorial.

4) Close the Crystal Data dialog by pressing "OK" and then select Interface | SHELXS from the

Main Menu. On the SHELXS dialog, press "Solve!" to invoke SHELXS as a routine, default solution run using Direct Methods.

5) If the SHELXS DOS window does not close automatically when SHELXS completes, consult the section "DOS windows" in Chapter 2 of this manual, and then close the window.

6) A dialog will appear that summarizes the pertinent parameters extracted from the file trypt.lst.

This dialog merely presents these parameters visually, but tells you nothing that you can't find in the LST file.

7) Since this is a "well-behaved" structure and has most likely been solved successfully, press the

"Accept" button.

8) The peaks and atoms contained in the file trypt.res will be displayed in the Model Display

Window and you can use the mouse to rotate and resize the model.

9) Activate the Display Settings control panel by pressing the button on the toolbar. On the

74

"Misc." page, you can see that 22 peaks are currently being displayed. Some of the more intense peaks represent atoms while some of the weaker ones need to be discarded (the higher the peak number, the less intense it is). You can suppress the display of the weaker peaks by decreasing the number next to "Peaks". When you have reduced this number to 12, you should see the outline of what appears to be a sensible model for the structure.

10) To save some time, select Edit | Change Q's to C's from the Main Menu to convert all the currently displayed peaks to carbon atoms. Now select the two nitrogen atoms by clicking on them

– when selected, atoms are shown as small filled circles. Press the F2 key and then select

"Nitrogen" from the popup menu to update the model. The structure is now solved and the atoms need to be labeled systematically.

Labeling Atoms

1) Press "L" to turn on atomic labels. The atoms are labeled according to the peak numbers from which they were derived.

2) Press the button to activate the Atom Names control panel.

3) Starting at N1, click on the atoms of the model in a logical sequence to label them systematically as shown below. You should see the labels change as you click on the atoms.

75

4) Press "L" again to turn labels off.

Structure Refinement

1) Select Interface | SHELXL from the Main Menu and press "Refine!" to invoke a routine refinement using SHELXL.

2) If the SHELXL DOS window does not close automatically, refer to section (5) in "Structure

Solution" above. This procedure must be completed separately for each DOS program, but once it has been done, does not need to be done again.

3) Once again the file trypt.lst is summarized in an appropriate dialog. After inspecting the parameters, press "Accept" to accept the refinement.

(Note: if you reject the run, the model will not be updated, the res and lst files pertaining to the latest SHELXL run will be deleted, and the previous res and lst files will be restored).

4) In the Model Display Window, you should see that the difference electron density peaks correspond to the positions of the missing hydrogen atoms. Peaks have the same bonding radius as carbon atoms, and will thus appear to be bonded to too many atoms in this case. Since we are going

75

76 to place hydrogen atoms in calculated positions, we can ignore the peaks.

5) Press "Q" to suppress display of the peaks.

6) If you would like to view the parameters associated with any atom, press the button to activate the "View/Edit" control panel. Just point at any atom to view its parameters on the control panel. Note that when you point at a bond, its length is given on the status bar at the bottom of the window.

Adding Hydrogen Atoms

1)

IMPORTANT

: X-Seed doesn't actually generate hydrogen atoms. It instructs SHELXL to do this in the next refinement using HFIX cards.

2) Press the button to activate the Generate H-Atoms (HFIX) control panel.

3) Select C5, N6, C8, C9, C10 and C11 and press to mark these atoms for HFIX 43 hydrogen atom generation.

4) Select C2 and C3 and press to mark these atoms for HFIX 23 hydrogen atom generation.

5) You may wish to verify that N1 is protonated (of course it is, but this is instructive) before using a geometric model to place its hydrogen atoms, so run another routine SHELXL refinement at this stage.

6) Use the Display Settings control panel to display only the strongest three peaks. Two of these are satellites of the chloride anion (as may be expected for a relatively heavy atom), so increase the number of peaks. When you display the strongest 6 peaks, you will see that three of these are attached to N1 at positions consistent with the hydrogen atoms of a protonated amine, and in a staggered arrangement with respect to the substituents on C2.

7) Turn off the display of the peaks ("Q") and go back to the Generate H-Atoms (HFIX) control panel. Select N1 and then press to instruct SHELXL to generate three hydrogen atoms using the staggered model.

Continue Refinement

76

1) Refine the model again. When the refinement completes, it will be seen that the residual electron density peaks do not indicate that the model may be incomplete, so you can delete all the peaks select Delete | All Peaks from the main menu.

2) Now it's time to refine non-hydrogen atoms anisotropically.

3) Press to activate the View/Edit control panel. Press the space bar to select all atoms.

Additional controls will appear on the control panel (in response to atom selection).

4) Press to instruct SHELXL to treat the selected atoms anisotropically in the next refinement

(hydrogen atoms, although selected, will not be treated anisotropically).

5) Run another routine refinement. R1 should have dropped to about 0.0367 by now. Delete the peaks again.

6) Press "E" to display the 50% probability thermal axes. Turn off display of hydrogen atoms (Press

"H") to see the thermal ellipsoid axes more clearly. Note that the atoms appear to be relatively well-behaved, thermally. When you are satisfied that the thermal motion is reasonable, you can restore the hydrogen atoms by once again pressing "H" and turn off the thermal ellipsoid axes

("E").

7) You will have noticed that the model is complete, but SHELXL still reports that

"** Cell contents from UNIT instruction and atom list do not agree **". This means that the model does not agree with the SFAC/UNIT cards. Select Display | Report from the Main Menu to activate the Structure Report dialog. The assigned unit cell contents are C

88

H

96

N

16

Cl

8

. However, the model, together with Z, indicates that it should be C

80

H

104

N

16

Cl

8

. If you press the button

77 the assigned formula will be updated according to the model and Z.

Note

: only use this feature if the model is complete.

8) Now it's time to run the final refinement. Select Interface | SHELXL. On the SHELXL dialog's

"General" page, ensure that "ACTA" is checked (there is no need to impose a 2-theta limit for this structure, so you can leave this field blank). On the "Variables" page, check "WGHT" to use the weighting scheme suggested by SHELXL. Go to the "Reflections" page. The 50 worst reflections

(extracted from the latest lst file) are listed in descending order of ∆ F

2

/e.s.d. If you wish to suppress any of these reflections (e.g. if it appears that they may have been obscured by the beam-stop - i.e.

Fc >> Fo), check them and they will be inserted as OMIT h k l cards in the next refinement run. In this case,

F

2

/e.s.d. does not appear to be unacceptable for any of the reflections, so OMIT h k l cards are unnecessary.

9) Run SHELXL once more. After the final refinement, the value of R1 has dropped to 0.0355, the

GoF is 1.018, the highest peak in the difference electron density map is 0.25 e

-

3

- and the structure is complete. Inspect the "Analysis of Variance" page of the SHELXL summary to make sure that the weighting scheme is sensible - which, in this case, it should be.

The final structure should look something like this:

77

78

Running Layer

1) Select Interface | Layer from the Main Menu to invoke layer.

2) Layer automatically loads the reflections from the file trypt.hkl and the cell parameters from

trypt.ins.

Running LAZY PULVERIX

1) Select Interface | LAZY PULVERIX from the Main Menu to calculate the powder pattern for the structure.

2) Adjust the settings on the LAZY PULVERIX dialog as required, and press the "Calculate" button to run first LAZY, then PULVERIX and then XRDPLOT. You may have to follow the procedure outlined above and in Chapter 2 to set the DOS windows to close automatically when the

DOS processes complete.

3) Barring any glitches, XRDPLOT should appear showing you the powder pattern for tryptamine

HCl.

Final note

X-Seed

has many features that were not used in this example. You will need to experiment with the program, and read this instruction manual to familiarize yourself with these features. Although I strongly encourage questions from users, I have been asked many questions that have been

78

addressed in the instruction manual and on X-Seed's web page under "Tips and Tricks" and

"Frequently Asked Questions". Please consult these resources before asking questions about

X-Seed

.

Input File Formats

1. SHELX (INS, RES)

X-Seed should read almost any legal SHELX .ins or .res file. However, it would be impossible to guarantee that there are no bugs.

2. CCDC (DAT)

CSD files in the FDAT file format should all be readable.

3. Cartesian coordinates (XYZ)

This must be an ASCII file. The first line contains n, the number of atoms to be read. The second line is ignored, but must not conatin any atoms. The next n lines contain the atoms. The first contiguous string on an atom line gives its atomic symbol. The next three strings give the cartesian coordinates. Any further parameters on an atom line are ignored.

Example:

C

C

C

C

C

C

C

N

C

C

C

13 trypt 0.00

Cl

N

1.15162

0.12703

-0.17379

-0.24197

1.07455

-0.80059

-1.75785

0.27143

-0.94761

0.05724

-1.02655

1.39054

0.87595

3.98862

-3.15799

1.30696

-0.18052

1.87041

-3.22296

-2.00494

1.06496

0.21969

-0.65797

-0.69921

1.35333

0.11961

-2.36887

-1.74476

-1.12879

0.57566

0.96699

-0.57485

-0.57413

0.15200

-1.54383

1.85430

-0.51977

2.22455

2.68150

Brookhaven Database File (PDB)

79

79

80

X-Seed will not read just any PDB file because PDB files can be rather complicated. X-Seed only reads the lines that begin with the keyword ATOM. It is assumes that Cartesian coordinates are given. A cubic unit cell length 10 Angstroms is created.

Each line beginning with ATOM (or HETATM) is interpreted as follows:

• the first 4 characters starting at column 13 are taken as the atom name - the element symbol is extracted from this name.

• the first 8 characters starting at columns 31, 39 and 47 are taken to be the X, Y and Z coordinates.

• if present, the first 6 characters starting at column 55 are taken as the site occupancy

Example:

Output File Formats

X-Seed can export the following file types:

SHELX INS

CSD DAT

Cartesian XYZ

Brookhaven Database PDB

When Exporting a SHELX INS file, you are asked whether you would like to export it as a P1 structure. If you say yes to this, all the atoms, including the symmetry-grown ones, will be written to a file assigned the space group P1. If you say no, just the asymmetric unit is written, and the

80

space group is retained.

A single structure can be exported to a CSD type FDAT file.

X-Seed outputs XYZ and PDB files using the format specifications given in "

Input File Formats ".

All of the currently displayed atoms (including those generated by symmetry) are written to the output file. The connectivity is also written to the PDB file (i.e. CONNECT lines are generated).

Antialiasing and Raytracing

81

From: http://www.webopedia.com/TERM/A/antialiasing.html

"In computer graphics, antialiasing is a software technique for diminishing jaggies - stairstep-like lines that should be smooth. Jaggies occur because the output device, the monitor or printer, doesn't have a high enough resolution to represent a smooth line. Antialiasing reduces the prominence of jaggies by surrounding the stairsteps with intermediate shades of gray (for gray-scaling devices) or color (for color devices). Although this reduces the jagged appearance of the lines, it also makes them fuzzier."

Below is a more detailed description of how the process is handled:

Original by Chris Cooksey

Converted by Paul Bourke

January 1994

http://astronomy.swin.edu.au/~pbourke/rendering/aliasing/

Sampling Problems And Antialiasing

Ray tracing is a point sampling process; the rays used to assess light intensities are infinitely thin.

However, each pixel of a rendered image has a finite width. Ray tracing in its basic form overcomes this incompatibility by tracing a single primary ray through the centre of each pixel and using the colour of that ray as the colour of the entire pixel.

Since the resultant colour of each pixel is based upon one infinitely small sample taken within the centre of each pixel and because pixels occur at regular intervals frequency based aliasing problems often arise. Aliasing refers to the inclusion of characteristics or artifacts in an image that could have come from more than one scene description.

Example

The scene descriptions below both (a) and (b) lead to the same rendered image in (c). The scene in

(a) and (b) consist of vertical bands of different widths, the dotted lines represent the pixel boundaries.

Staircasing

81

82

This is the most prevalent form of aliasing and occurs in regions of abrupt change in intensity.

Examples of such regions are object or shadow boundaries or the boundaries of sharp highlights.

The next figure illustrates the staircasing effect. (a) shows an example object as it should appear and (b) shows the rendered result. The dashed lines in are the pixel boundaries.. Most of the pixels spanning the object's boundaries end up being shaded incorrectly as either wholly within the object or not at all within the object. Note also that there are an infinite number of polygons which would generate the image in (b)

Interference

Another important aliasing problem occurs across whole regions of an image in which constituent objects alternate at a high frequency. The samples taken by a ray tracer can sometimes generate images containing what are called Moiré interference patterns. The following shows an example rendered image that contains Moiré interference patterns.

Antialiasing

Antialiasing is the name given to the process that attempts to eliminate or reduce the impact of aliasing artifacts in rendered images. Antialiasing algorithms can be classified as either analytic or discrete.

Analytic algorithms perform a thorough analysis of the elements of a scene and filter out any high frequencies prior to sampling. Although very effective, these algorithms tend to be complicated and time consuming, requiring expensive analysis of the geometrical properties of the objects involved.

Discrete methods such as ray tracing treat a scene as a set of unrelated intensity values. To avoid the complications of incorporating an analytic filter, methods have been devised to improve the nature of the actual sampling performed to help reduce aliasing effects.

Supersampling

The simplest discrete method available is known as supersampling. It involves casting more than one regularly spaced sample per pixel and using the average of the results for the pixel intensity.

For example, a pixel could be subdivided into the grid illustrated in below. To render the pixel, primary rays are cast through each of the indicated sample points. The intensity value of the pixel is the average of all the samples.

Adaptive Sampling

Adaptive sampling is similar in nature to supersampling. Each pixel to be traced has a primary ray cast through each of its corners. If the intensity of any of the four rays varies significantly from the other three, then the pixel is split into four rectangular portions. Each of the new quadrants has primary rays cast through their corners. Any quadrant for which the new rays display any significant difference are further subdivided and the process is repeated for that quadrant. The subdivision process can be repeated to an arbitrary level. Note that quadrants at a new level have rays in common with the previous level and with each other thus reducing the amount of actual tracing that needs to be performed.

Adaptive sampling works very well on boundary edges. However, certain scenes will still cause

82

problems since they can cause the sampler's subdivision phase to stop prem

83

83

84

84

Was this manual useful for you? yes no
Thank you for your participation!

* Your assessment is very important for improving the work of artificial intelligence, which forms the content of this project

Download PDF

advertisement