Frequently Asked Questions

Chapter 1: Frequently Asked Questions

1.1: Getting Started: How do I install CRYSTALS for Windows under Windows95?

1.2: Getting Started: How do I install older versions of CRYSTALS?

1.3: Getting Started: How do I run CRYSTALS under Windows NT?

1.4: Getting Started: How can I get CRYSTALS to start at the command prompt?

1.5: Getting Started: Organisation of files.

1.6: General: What is CRYSTALS?

1.7: General: Who is responsible for it?

1.8: General: Where is the manual?

1.9: General: Is there an example to work through?

1.10: General: Can I prepare commands to run CRYSTALS in batch mode (like SHELX)?

1.11: General: Is there any command line help?

1.12: General: How can I switch the left and right CRYSTALS windows?

1.13: Solving structures: How do I prepare a job for SIR92 or SHELXS?

1.14: Solving structures: It failed. How do I prepare a different job?

1.15: Solving structures: How do I import the solution back into CRYSTALS?

1.16: CAMERON: How do I see a plot of the structure?

1.17: CAMERON: Can I rotate it and label the atoms?

1.18: CAMERON: How do I delete atoms?

1.19: Fourier: How do I calculate a Fourier map to find missing atoms?

1.20: Refinement: What infomation does CRYSTALS need?

1.21: Refinement: Refinement instructions

1.22: Refinement: Occupancies of an atom or fragment split over two sites?

1.23: Refinement: How do I add restraints?

1.24: Refinement: How do you use Platon's Squeeze from CRYSTALS?

1.25: Refinement: What are parts assemblies and groups?

1.26: Structure: How can I adjust a molecule or fragment to have ideal coordinates?

1.27: Analysis: Find the angle between a plane of atoms and a bond

1.28: Analysis: Calculate intermolecular distances

1.29: Analysis: Find LIKELY H-BONDS with donors or acceptors other the O and N

1.30: Analysis: How do I use ROTAX to test for twin laws?

1.31: Analysis: How do I add hydrogen atoms to water molecules?

1.32: Publication: Editor wants completeness of the data at 25 degrees

1.33: Publication: What's the difference between _theta_max and _theta_full?

1.34: Publication: Diagram shows wrong enantiomer. What to do?

1.35: References: What References should I know about?

1.36: Miscellaneous: Environment variables

The current versions are available from the download page at http://www.xtl.ox.ac.uk/download.html There are various CCP14 mirrors around the world.
You may install crystals in a directory path which contains spaces but some external programs might not work. For the same reason you should try to avoid putting structures in working directories which have a space in their path.

Download and run setup.exe.

Download MarchingCubes, unzip, and run setup.

You should not install CRYSTALS in a directory path which contains spaces.

See http://www.xtl.ox.ac.uk/obsolete.html for installation instructions for older versions.

This is almost identical to using Windows 95, except that a small patch (supplied) has to be installed. Follow the Windows 95 installation instructions.

You need to extend the 'path' environment variable so that it includes the folder where you installed CRYSTALS, e.g.
path=c:\wincrys\;"%path%"
set crysdir=c:\wincrys

Take care with the symbols - get it wrong and you may need to re-boot!

You can also edit AUTOEXEC.BAT to include these lines so that CRYSTALS is automatically available when you open a DOS BOX.

To run CRYSTALS, change to the directory containing the data for the compound and type:
CRYSTALS

1. Organise your computer. Create a master folder to hold other sub-folders, one for each new compound, e.g. c:/cpds/cpd1

2. Copy the crystallographic data in to the sub-folder. This can be a SHELXS hkl file or CAD4/Mach3 data collection and psi curves. Take care: If you open a data file with WORD, you may accidentally save it as a WORD document. Use WORDPAD, notepad, EDIT, or some other text editor

3. Click the CRYSTALS icon, and use the browser to find the folder containing your data. Click OK.

4. The CRYSTALS window is divided into four areas:
The display window, initially filled with the CRYSTALS logo.
The menu bar. The pull down menus represent the principal stages in structure analysis, working from left to right.
The text output window. This displays the results of calculations, or asks the user questions. It has a large scroll-back capability.
The text input line. This is below the output window. The cursor automatically moves to this area when you type. The 'arrow' keys enable you to recover previous input (like the DOSKEY utility).

5. CRYSTALS creates many files:
A binary database for each structure, always named CRFILEV2.DSC. NEVER try to edit this file. This file enables CRYSTALS jobs to be restarted from where they were left off. All other files may be opened with a text editor e.g. notepad, wordpad, or edit.
Text files BETACRYS.Lnn and BETACRYS.Mnn. The number nn is automatically incremented with each run of the program. These files can generally be deleted without looking at them unless the analysis begins to go wrong. They provide post-mortem information.
PUBLISH.* files. These are final listings for preparing papers.

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.

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.

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.

All manuals are available as adobe acrobat files (.pdf) from http://www.xtl.ox.ac.uk/download/manuals.zip

HTML: http://www.xtl.ox.ac.uk/cameron.html 02/05/96 The graphics manual (50 pages)

HTML: http://www.xtl.ox.ac.uk/primer.html 08/10/96 An overview of the program - pre-release

HTML: http://www.xtl.ox.ac.uk/crystalsmanual.html 14/01/97 The CRYSTALS reference manual - pre-release (125 pages)

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

Yes. The distribution contains two old 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.
Other examples: From the "Help" menu, choose "Demo". There are many 'workshop' structures. The documentation for these may be in the "Crystals Worked Examples" manual distributed with CRYSTALS.

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

Including the command \SET EXPORT ON 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.

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.)

Edit \WINCRYS\GUIMENU.SRT

Find the section beginning:

^^WI         ITEM GRID _GR_TEXT_AND_INPUT NROWS=1 NCOLS=1 {

(lines 11-25) and swap it with the section beginning:

^^WI         ITEM GRID _GR_MODEL NROWS=1 NCOLS=1 {

(lines 26-51). Check the indentation remains intact. You may want to back up your old guimenu.srt when first experimenting.

Input the necessary data:

List 1 - Cell
List 2 - Symmetry
List 6 - Reflections
List 29 - Asymmetric unit contents

Type: \FOREIGN SIR92 or \FOREIGN SHELX

Exit CRYSTALS (\END) and run the direct methods program (Sir92 or Shelxs).

Type: \FOREIGN SIR92 DIFFICULT or \FOREIGN SHELX DIFFICULT

Exit CRYSTALS (\END) and run the direct methods program (Sir92 or Shelxs).

Type \SCRIPT INEMAP and follow the instructions given. (You will be asked which program you used to solve the structure.)

Type:\SCRIPT PLOT To exit CAMERON, type END or click File/Exit in the menus.

Some basic commands:

VIEW - update the graphics (v. important)
XROT n - rotate about x by n degrees
YROT n - rotate about y by n degrees
ZROT n - rotate about z by n degrees
CURSOR - rotate using cursor keys
LABEL ALL - label all the atoms
NOLABEL ALL - remove labels
EXCL H - hide all H atoms
INCL H - show all hidden H atoms
MENU ON - turn on the menu bar

Type EXCL followed by the atom name (or just click on the atom. You can restore a deleted atom by typing INCL followed by the atom name, or INCL ALL to bring everything back.

You must have already entered the following required information:

List 1 - Cell
List 2 - Symmetry
List 3 - Scattering factors
List 5 - Parameters (model)
List 6 - Observations (reflections)
List 14 - Fourier limits
List 29 - Asymmetric unit contents

From the Fourier pull-down menu, choose the type of Fourier map that you wish to calculate. You will be presented with a dialog box which allows you to control the subsequent peak search routine.

Use an F-obs map for completing structures with atoms other than hydrogen missing. You will also be given the option to use the Fourier map to refine the positions of existing atoms in the structure.

Use a difference map for completing structures that are almost complete, e.g. to find hydrogen atoms. Using the Add hydrogen option from the Structure menu will place hydrogen geometrically on carbon skeletons and allow you to compare these positions with a difference Fourier map.

List 1 - Cell
List 2 - Symmetry
List 3 - Scattering factors
List 4 - Weighting scheme (default - unit weights)
List 5 - Parameters (model)
List 6 - Observations (reflections) AND/OR List 16 - Observations (restraints)
List 12 - Refinement instructions
List 23 - Refinement options
List 28 - Reflection acceptance criteria (default - all)
List 29 - Asymmetric unit contents

List 12 can be entered in the following manner:

 \LIST 12
 FULL I(1,X'S,U'S) C(7,X'S) O(1,Y) O(1,U[ISO]) UNTIL C(6)
 GROUP C(1) UNTIL C(6)
 END

This example refines the position and Uij's of I(1), the position of C(7), the y-coordinate of O(1) and the isotropic thermal parameters of atoms O(1) until C(6) based on the order they appear in list 5. It also refines the positions of atoms C(1) to C(6) as a rigid-body.

Alternatively, choose Guided Automatic from the Refinement menu to run a script which automatically writes List 12 and refines the structure based on its assessment of the current state of progress.

Use constraints. Constraints are set up using List 12, so you must be prepared to eschew the GUIDE and write your own constraint instructions. Here is how:

Step one:
Before you do anything, ensure that the occupancies of the two sites add up to one. A constraint only affects the shifts applied to parameters: if the sum of the parameters is not sensible to begin with, it never will be.
There are several ways to do this. In these examples the occupancy of each fragment is set to 0.5:

  1. Use the graphical interface - right click an atom, choose Edit from
     the popup menu and change the occupancy in the dialog box. Click Apply.
     Repeat for each atom. 
  2. Use the \EDIT command (changing the atom names, of course):
          \EDIT
          CHANGE C(1,OCC) C(10,OCC) UNTIL C(15) 0.5
          CHANGE C(101,OCC) C(110,OCC) UNTIL C(115) 0.5
          END
     Please remember that UNTIL sequences are dependent on the order
     of atoms in LIST 5, don't use them if you're not sure.
  3. 'Punch out', edit, and read back in the parameters (LIST 5). There
     are menu and toolbar options to do this, or just type:
          \SCRIPT SYSED5

Step two:
Setup the constraints. If you like using the GUIDE, then it will already have produced a basic LIST 12 (constraints) for you.
To edit List 12, there are menu and toolbar options, or just type:

          \SCRIPT EDLIST12

Presumably, the first two lines of the LIST 12 instruction will be something like this:

        
          \LIST 12
          BLOCK SCALE X'S U'S

There may also be lots of RIDE constraints if you have chosen to ride the hydrogen atoms.
Add the following lines after those and before the 'END' statement (changing the atom names, of course):

          \   This is a comment.
          \   The EQUIVALENCE constraint, split over two lines here
          \   maps all the model parameters following it onto one
          \   least squares parameter. ie. for all the occupancies
          \   given here only one value will be refined.
          EQUIVALENCE C(1,OCC) C(10,OCC) UNTIL C(15)
          CONTINUE C(101,OCC) C(110,OCC) UNTIL C(115)
          \   This is a comment.
          \   The weight instruction means that the derivatives and
          \   shifts of the listed parameters will be multiplied by
          \   the given weight. This has the effect of ensuring that
          \   the sum of the occupancies of the two sites remains
          \   constant.
          WEIGHT -1 C(101,OCC) C(110,OCC) UNTIL C(115)

Save and close the file, CRYSTALS will automatically read it back in.

Step three:
Carry out the refinement. Don't use the GUIDE, it will overwrite all your hard work typing in those constraints. Instead use one of the following methods to initiate some cycles of least squares:

    1. Just type:
      \SFLS
      REFINE
      REFINE
      REFINE
      END
 or 2. Type \SCRIPT XREFINE to get a dialog with a few options.
    3. Choose "Refinement"->"Refine" from the menus, or the 
       equivalent toolbar button ("R").

Verify that the occupancy values after refinement make sense. Check that they add up to one, and confirm that only the occupancies that you intended to refine have in fact been refined.

Restraints are set up using list 16.

For easy generation of simple restraints select two, three or more atoms in the model window. Right click on one of the group and choose an option from the pop-up restraints sub-menu. Any restraints generated in this way will be appended to the existing restraint instructions in list 16.

An example List 16 could be:

 \LIST 16
 DIST  1.39 , .01 =      C(1) to C(2)
 DIST  0.0  , .01 = MEAN C(3) to C(4), C(4) to C(5)
 VIBR  0.0  , .01 =      C(6) to C(7)
 U(IJ) 0.0  , .02 =      C(8) to C(9)
 PLANAR                  C(1) until C(6)
 SUM                     K(1,OCC), K(2,OCC), K(3,OCC)
 LIMIT                   U[11] U[22] U[33]
 END

The first instruction restrains the bond C(1) to C(2) to be 1.39 angstroms with an e.s.d. of .01 angstroms.
 
The second instruction is a similarity restraint which restrains the difference between two bonds (C3-C4 and C4-C5) to be zero with an e.s.d of .01 angstroms.
 
The third restrains the difference between the mean square displacement of each atom along the direction of a bond to be zero, with an e.s.d of .01. Isotropically refined atoms will also be dealt with correctly.
 
The U(IJ) restraint between C(8) and C(9) restrains the difference between the corresponding Uij components to be zero with an e.s.d of .02.
 
The planar restraint restrains atoms C(1) to C(6) (based on the list 5 order) to be planar. The e.s.d defaults to 0.01.
 
The sum restraint holds the sum of the specified parameters (in this case the occupancy of three postassium atoms) to be constant during the refinement. The default e.s.d is 0.0001. This is useful where disordered atoms occupy more than two sites, since in these cases the total occupancy cannot be held constant using constraints.
 
The limit restraint attempts to limit the shift of the specified parameters to zero (in this case all the Uii anisotropic parameters). This is useful for controlling refinements of poor starting models. The default e.s.d is 0.01. Lowering it to 0.001 will effectively fix the parameter, and raising it to 10 will have almost no effect unless the shift due to the X-ray observations is huge.

I gave it a try but doesn't seem to make much difference. I am not sure that I am using it in the right way.
(1) You must make sure there is a void in the structure. (ie. delete the solvent that you want squeeze to take care of) - this is the a common misunderstanding about running squeeze.
(2) Run Squeeze from the Refinement menu. Three things might happen:
(a) CRYSTALS asks where platon.exe is. Tell CRYSTALS and carry on. If you don't have a copy of PLATON, them download one.
(b) Something flickers quickly onto the screen and then disappears, and CRYSTALS asks whether you want to use the results from Squeeze. Don't. It didn't work. You could try downloading a new version of Platon, and testing that Platon can be started in interactive mode by choosing 'Platon' from the Tools menu.
(c) Platon starts and grinds through some calculations for a while. If it ends in error, the don't apply the results when CRYSTALS asks. If something went wrong, then maybe your trying to squeeze to large or small a void or something.
(3) Look at the summary in the Platon dialog window. Close the Platon dialog window.
(4) CRYSTALS will ask 'Do you want to apply the results?'. Click Yes.
Instead of doing the usual 'Squeeze thing' of altering your FObs values (generally considered to be a BAD THING), CRYSTALS and PLATON together do something much nicer: the A and B components of the structure factor which are due to scattering from the 'void' are stored in your list of reflections; the F-obs value is unchanged. When calculating structure factors, the program adds together the scattering from the atomic electron density as usual, and then adds in the pre-computed A and B parts aswell. Not only does this avoid meddling with the FObs values, but it also (a) keeps the phase information from the scattering from the 'void', and (b) allows you to iteratively reapply squeeze if you think you've improved the model at all and (c) ditch the squeeze correction if you don't like it.

 \REGULARISE REPLACE
 GROUP 8
 TARGET C(101) C(102) C(103) C(104) C(105) C(106) C(107) C(108)
 SYSTEM 10.433 11.857 16.054 86.44 76.81 75.44
 ATOM  .7930 .5259 .5059
 ATOM  .8696 .4140 .4641
 ATOM  .9491 .3689 .3994
 ATOM 1.0055 .2640 .3753
 ATOM  .9669 .1771 .4394
 ATOM  .8941 .2227 .5072
 ATOM  .8292 .3231 .5311
 ATOM  .7351 .3958 .6018
 END

Note that for pdb-type coordinates, you should give "SYSTEM 1 1 1 90 90 90".

  \GEOMETRY
  ATOMS C(3) C(4) C(5) C(6) C(7) C(8)
  PLANE
  ATOMS C(1) O(2)
  LINE
  DIHEDRAL 1 AND 2
  END

This calculates the best plane of atoms C(3) through to C(8), and the line through the bond C(1) O(2). The dihedral command prints the angle between the vector normal to the best plane and the vector defined by the bond.
i.e. if the bond is at right angles to the ring, the angle will be zero, and if the bond is in the same plane as the ring, the angle will be 90.

Changing PLANE to LINE, or LINE to PLANE will allow you to find the angle between two planes or the angle between two lines!

   \dist
   select range=limits
   limit 2.0 4.0 2.0 4.0
   include N(6) O(8)
   end

This will give all the bond lengths and angles involving the specified atoms (so only bond lengths in this case!) that fall in the range 2.0 to 4.0 Angstroms. The first range 2.0->4.0 is for bonds, the second is for bond that form angles.
If you want su's too, then add this line before 'end':

    e.s.d yes

You can specify atom types instead of specific atoms, e.g. to look for only O-O contacts just use

    include O

The manual details other options for selecting atoms such as exclude, pivot etc.

 
  \dist
  out mon=all
  select range=limits
  limit 1.5 2.2 0.7 2.2
  pivot H
  bonded O N
  end

The 'pivot' atoms can only be at the centre of an angle or one end of a bond, and the 'bonded' can only be at the edges of an angle or the other end of the bond.
For other acceptors, add element to the BONDED directive (e.g. CL) in the above command and extend the bonding limits to something reasonable for a H--CL distance e.g. from 2.2 to about 3.7(?). It will then find all H--CL bonds and O-H--CL, or N-H--CL angles.
Becuase the distance command doesn't let you specify different limits for each side of an angle no distinction can be made between donors and acceptors, (i.e. you cannot get separate listings of O--H-N and N--H-O angles)

 \PARAM
 END

will show you what the twin elements scales have refined to.
To undo it all, choose Analyse-> Rotax Analysis/Twins-> Remove Twin Laws.

The following will work to find short O--O or O--N contacts in the range 2 - 3 Angstroms around a water atom O(6). Adjust the numbers on the LIMITS line to look at different ranges. Type this into the CRYSTALS command line (the small edit box below the text output), press return after each line.

    \DIST 
    OUTPUT MON=DIST 
    SELECT RANGE=LIMITS 
    LIMITS 2.0 3.0  0.0 0.0 
    PIVOT O(6)
    BONDED O N
    END

The PIVOT line specifies the single water atom (O(6)) at one end of the bond, while the BONDED line specifies that the other end of the bond must be a nitrogen or oxygen atom.
Once you have found a likely H-bond, say to O(21), you can place the H by typing in the following set of commands:

    \HYDROGEN
    DISTANCE 0.9
    HBOND O(6) O(21)
    END

i.e. O(6) is the donor and O(21) is the acceptor.

Is there a way to get that from CRYSTALS? The current data in the CIF is something like this:

 
 _diffrn_reflns_theta_min              4.123
 _diffrn_reflns_theta_max             28.884 
 _diffrn_measured_fraction_theta_max   0.934 
  
 _diffrn_reflns_theta_full            21.098
 _diffrn_measured_fraction_theta_full  0.996

Those pesky editors. Here's what to do:
1) Choose "X-ray data"->"Edit goodies".
2) Locate the box labelled "Theta full (set -ve to fix at absolute value)", and change the value to -25.00
3) Click OK.
4) Make a new CIF.

_diffrn_reflns_theta_max             28.884 
_diffrn_measured_fraction_theta_max   0.934 
 
_diffrn_reflns_theta_full            21.098
_diffrn_measured_fraction_theta_full  0.996

Theta_max is the very highest theta angle found in all of your data. The _diffrn_measured_fraction_theta_max is the completeness (number measured/number reflections expected) at this angle.

Theta_full allows you to specify a value of theta at which you are prepared to call your data set 'complete'. Because 100% completeness is very tricky to acheive, there is no hard and fast rule for deciding where to set theta_full. By default, CRYSTALS will choose a value for you, trading off decreasing theta with increasing completeness (though it is worth noting that in many cases, a few missing reflections at low theta - e.g. due to beam stop - will mean that completeness actually increases with increasing theta). An analysis of completeness is given amongst the "Tabbed initial analysis" graphs from the "Analyse" menu in CRYSTALS.

If you just want a diagram, you can edit the cif by multiplying all the atomic coordinates by -1, but this isn't a good idea when producing material for publication.
It's generally better to do it in CRYSTALS:
For most space groups you can just use the 'invert structure' option from the 'structure' menu. Alternatively you can do the same thing from the command line by issuing:

\edit
transform -1 0 0 0 -1 0 0 0 -1 all
end

These will probably give you a model in which the asymmetric unit lies well outside the standard unit cell. Look at a packing diagram in Cameron to find a better choice of molecule, save the changes then do another cycle of refinement. A new cif will have the correct symmetry operators if there are any bonds leading from one asymmetric unit to another, which is the main reason for not just modifying the original cif.
WARNING: there are certain space groups for which this procedure is insufficient. One type is where the space group contains a screw axis with a rotation component <180 degrees and all the symmetry operators have the same hand. In this case it is necessary to change the space group symbol. There are 11 pairs of this type: if your structure is one of these it should be interchanged with the other member of the pair:

P 41      <-> P 43
P 41 2 2  <-> P 43 2 2
P 41 21 2 <-> P 43 21 2
P 31      <-> P 32
P 31 2 1  <-> P 32 2 1
P 31 1 2  <-> P 32 1 2
P 62      <-> P 64
P 61      <-> P 65
P 62 2 2  <-> P 64 2 2
P 61 2 2  <-> P 65 2 2
P 41 3 2  <-> P 43 3 2

Change the space group from the 'edit spacegroup' option of the 'X-ray data' menu, then invert the structure and choose the best asymmetric unit as above.
There are also 7 space groups in which the origin also has to be changed - the offending ones are:
F d d 2, I 41, I 41 2 2, I 41 m d, I 41 c d, I -4 2 d and F 41 3 2. If you have a structure in one of these, get help!

Please note the references for CRYSTALS and CAMERON, and cite them with each structure you publish, along with references to any other software programs that you have used. In the current difficult financial atmosphere in the UK, employers have begun to count the numbers of citations for work, as well as publications, so we will need clear support from the user community if the work is to continue.

CRYSTALS
   Betteridge, P. W.,  Carruthers, J. R.,  Cooper, R. I.,
   Prout, K., Watkin, D. J. (2003). J. Appl. Cryst. 36, 1487.

CAMERON References

CAMERON
     Watkin, D.J. Prout, C.K., Pearce, L.J. (1996). CAMERON, Chemical
     Crystallography Laboratory, University of Oxford, Oxford, UK.

RC93 References

RC93
     Watkin, D.J., Prout, C.K., Lilley, P.M.deQ. (1994), RC93, Chemical
     Crystallography Laboratory, University of Oxford, Oxford, UK.

Sir92 References

SIR92
     Altomare, A., Cascarano, G., Giacovazzo G., Guagliardi A.,
     Burla M.C., Polidori, G. & Camalli, M. (1994)
     SIR92 - a program for automatic solution of crystal structures by
     direct methods. J. Appl. Cryst. (27), 435

Chebychev weighting References

CHEBYCHEV WEIGHTING
     Carruthers, J.R. and Watkin, D.J. (1979), (Chebychev Weighting)
     Acta Cryst, A35, 698-699

SHELXS References

SHELXS86
     Sheldrick, G.M. (1986).  SHELXS86. Program for the solution of
     crystal structures.  Univ. of Gottingen, Federal Republic of Germany.

DIFABS References

DIFABS
     Walker, N., and Stuart, D. DIFABS. Acta Cryst, A39, 158-166

CRYSTALS will substitute for any environment variables when opening files or spawning processes. The variable is identified by appearing before a colon (e.g. CRYSDIR:script/test.scp will be expanded to something like /usr/local/crystals/script/test.scp where CRYSDIR=/usr/local/crystals/).

Any environment variable that refers to paths or files may be a comma separated list of alternative locations.

When opening files for reading, CRYSTALS will look in each location in turn and open the first file that exists. When opening files for writing, they will always open in the first location in the list.