Frequently Asked Questions

Chapter 3: General Questions

: 3.1: What is Crystals?; 3.2: Who is responsible for it?; 3.3: Where is the manual?; 3.4: Is there an example to work through?; 3.5: How can I prepare commands with a text editor to run Crystals in batch mode (like SHELX)?; 3.6: Is there any command line help?

3.1: What is Crystals?

The Crystals system consists of Crystals and Cameron and specially recompiled versions of SIR92 and SHELXS.

SIR and SHELXS provide the direct methods. Crystals and Cameron provide everything else including:

absorption corrections

data reduction

powerful atomic and structural parameter editor

hydrogen atom placement

graphical model of the structure

sophisticated refinement with constraints and restraints

various weighting schemes for Fobs

analysis of residuals

fourier maps and contour plots

publication tables and cifs

colour thermal ellipsoid plots

The user interface is either by a command line, or via an interactive dialogue. The dialogue is held in external ASCII scripts so that it can be modified to suit local crystallographic preferences, or used as a teaching aid.

Several conversion utitlities are also provided:

SXtoCRY converts SHELX.INS or .RES files to Crystals format input files.

RC93 prepares data for Crystals from a CAD4 diffractometer.

DIPIN prepares data for Crystals from an Enraf-Nonuis DIP2000 diffractometer.

CSD2CRY converts CSD files to Crystals format input files.

CIF2CRY converts CIFs to Crystals format input files.

The programs are currently available for WINDOWS 95/98/NT/2000

A full implementation of the current program with graphical interface should be available during 2000 for Linux.</P>

3.2: Who is responsible for it?

David Watkin is in charge of most of the code (with the obvious exception of the SHELXS and SIR92

Many people have contributed to the software by adding new functionality or donating useful standalone programs.

Bob Gould in Edinburgh has donated the program SXTOCRY, which will generate a file in CRYSTALS format from SHELX.INS files. This may not work completely for very complex SHELX.INS files, but it is a quick way to get started in CRYSTALS.

Neil Henson (UCSB) has updated the SGI version of CRYSTALS/CAMERON, and we believe it is working well. One user in Oxford has installed it on his SGI and is pleased with it.

3.3: Where is the manual?

The CRYSTALS documentation is currently being revised and updated.

Up-to-date manuals are included in the downloadable distribution kit at http://www.xtl.ox.ac.uk/download.html/

The new documents are as Postscript files ( .ps) and adobe acrobat files (.pdf).

The Postscript is formatted for the lesser of European A4 paper and US Letter (8 1/2 x 11).

CAMERON.PS, CAMERON.PDF, http://www.xtl.ox.ac.uk/cameron-1.html 02/05/96 The graphics manual (50 pages)

PRIMER.PS, PRIMER.PDF, http://www.xtl.ox.ac.uk/primer-1.html 08/10/96 An overview of the program - pre-release

CRYSTALS.PS, CRYSTALS.PDF, http://www.xtl.ox.ac.uk/crystals-1.html 14/01/97 The CRYSTALS reference manual - pre-release (125 pages)

GUIDE.PS, GUIDE.PDF, http://www.xtl.ox.ac.uk/guide-1.html 14/01/97 A summary of the features available - not quite finished.

3.4: Is there an example to work through?

Yes. The distribution contains two data sets:

Nket: A small organic molecule. There are instructions for processing the data, and solving and refining the structure in the file NKET.DOC.

Hex: A smaller organic molecule. Used as the data for the Crystals 'test deck'. Run Crystals in this directory and type \USE HEXAMPLE.DAT to exercise most of the Crystals commands. The file hexample.dat is commented, so that you can follow what it does.

3.5: How can I prepare commands with a text editor to run Crystals in batch mode (like SHELX)?

Type the commands into a file with your favourite text editor. Then start crystals and type \USE filename

Including the command _{I\SET _{IEXPORT _{ION will cause Crystals to write out a file called EXPORT.DAT at the end of a run, which contains atomic co-ordinates and refinement setup instructions, which may be edited for the next run.

3.6: Is there any command line help?

As a basic memory aid, you can type ? at any point and you will be given a list of relevant options. (i.e. if you have already typed a \Instruction, you will see a list of directives.)