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Frequently Asked QuestionsChapter 1: Frequently Asked Questions
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.
[Top] [Index] Manuals generated on Wednesday 8 November 2006 1.1: Getting Started: How do I install CRYSTALS for Windows under Windows95?Download and run setup.exe. Download MarchingCubes, unzip, and run setup. [Top] [Index] Manuals generated on Wednesday 8 November 2006 1.2: Getting Started: How do I install older versions of CRYSTALS?See http://www.xtl.ox.ac.uk/obsolete.html for installation
instructions for older versions. [Top] [Index] Manuals generated on Wednesday 8 November 2006 1.3: Getting Started: How do I run CRYSTALS under Windows NT?This is almost identical to using Windows 95, except that a small patch (supplied) has to be installed. Follow the Windows 95 installation instructions. [Top] [Index] Manuals generated on Wednesday 8 November 2006 1.4: Getting Started: How can I get CRYSTALS to start at the command prompt?You need to extend the 'path' environment variable so that it
includes the folder where you installed CRYSTALS, e.g.
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: [Top] [Index] Manuals generated on Wednesday 8 November 2006 1.5: Getting Started: Organisation of files.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:
5. CRYSTALS creates many files:
[Top] [Index] Manuals generated on Wednesday 8 November 2006 1.6: General: 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: 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: 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. [Top] [Index] Manuals generated on Wednesday 8 November 2006 1.7: General: Who is responsible for it?David Watkin is in charge of most of the code (with the
obvious exception of the SHELXS and SIR92
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. [Top] [Index] Manuals generated on Wednesday 8 November 2006 1.8: General: Where is the manual?The CRYSTALS documentation is currently being revised and updated.
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. [Top] [Index] Manuals generated on Wednesday 8 November 2006 1.9: General: Is there an example to work through?Yes. The distribution contains two old data sets: [Top] [Index] Manuals generated on Wednesday 8 November 2006 1.10: General: Can I prepare commands 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 \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. [Top] [Index] Manuals generated on Wednesday 8 November 2006 1.11: General: 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.) [Top] [Index] Manuals generated on Wednesday 8 November 2006 1.12: General: How can I switch the left and right CRYSTALS windows?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. [Top] [Index] Manuals generated on Wednesday 8 November 2006 1.13: Solving structures: How do I prepare a job for SIR92 or SHELXS? Input the necessary data: Type: \FOREIGN SIR92 or \FOREIGN SHELX [Top] [Index] Manuals generated on Wednesday 8 November 2006 1.14: Solving structures: It failed. How do I prepare a different job? Type: \FOREIGN SIR92 DIFFICULT or \FOREIGN SHELX DIFFICULT [Top] [Index] Manuals generated on Wednesday 8 November 2006 1.15: Solving structures: How do I import the solution back into CRYSTALS?Type \SCRIPT INEMAP and follow the instructions given. (You will be asked which program you used to solve the structure.) [Top] [Index] Manuals generated on Wednesday 8 November 2006 1.16: CAMERON: How do I see a plot of the structure?Type:\SCRIPT PLOT To exit CAMERON, type END or click File/Exit in the menus. [Top] [Index] Manuals generated on Wednesday 8 November 2006 1.17: CAMERON: Can I rotate it and label the atoms?Some basic commands: [Top] [Index] Manuals generated on Wednesday 8 November 2006 1.18: CAMERON: How do I delete atoms?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. [Top] [Index] Manuals generated on Wednesday 8 November 2006 1.19: Fourier: How do I calculate a Fourier map to find missing atoms?You must have already entered the following required information: 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. [Top] [Index] Manuals generated on Wednesday 8 November 2006 1.20: Refinement: What infomation does CRYSTALS need? List 1 - Cell
[Top] [Index] Manuals generated on Wednesday 8 November 2006 1.21: Refinement: Refinement instructionsList 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. [Top] [Index] Manuals generated on Wednesday 8 November 2006 1.22: Refinement: Occupancies of an atom or fragment split over two sites?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: 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: \SCRIPT EDLIST12
\LIST 12 BLOCK SCALE X'S U'S
\ 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)
Step three: 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").
[Top] [Index] Manuals generated on Wednesday 8 November 2006 1.23: Refinement: How do I add restraints?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. \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.
[Top] [Index] Manuals generated on Wednesday 8 November 2006 1.24: Refinement: How do you use Platon's Squeeze from CRYSTALS?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.
[Top] [Index] Manuals generated on Wednesday 8 November 2006 1.25: Refinement: What are parts assemblies and groups?The easy way: type " script xparts" and add new assemblies and groups and then click the atoms that you want to be in those groups. An 'assembly' is a disordered set of atoms, a 'group' is a subset that has the same occupancy (e.g. very simply if a CF3 is has rotational disorder then group 1 might be F(1), F(2),F(3), F(11), F(12), F(13). Group 1 Part 1 might be F(1), F(2), F(3) and group 1 part 2 might be F(11), F(12), F(13). A PART is the value in list 5 used to store this information. PART = ASSEMBLY * 1000 + GROUP Group 1 will not bond to group 2 of the same assembly in the diagram, and in versions of CRYSTALS 12.09 and onwards the bonds and angles in the CIF will also be only between the appropriate atoms. For the refinement itself, you can take shortcuts using a new the PART syntax, e.g. to refine the occupancies: LIST 12 BLOCK SCALE X'S U'S EQUIVALENCE PART(1001,OCC) PART(1002,OCC) WEIGHT -1 PART(1002,OCC) END (Obviously make sure the occ's add up to 1 before you start, same as normal) This stuff is quite new, so try to verify it's doing what you think it's doing! If in doubt send me the .dsc file for checking. [Top] [Index] Manuals generated on Wednesday 8 November 2006 1.26: Structure: How can I adjust a molecule or fragment to have ideal coordinates?We find a nice orthoxylene molecule (eg. CSD entry WAFKOD) and we want to correct our rather poor orthoxylene molecule which is numbered C101-C108 starting on one methyl and ending on the other, going the long-way around the ring. That atoms we want to correct are specified on the TARGET directive. The coordinates of atoms of the ideal molecule are given on ATOM directives, following a SYSTEM directive with the cell parameters of the structure that the ideal molecule is taken from. \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
[Top] [Index] Manuals generated on Wednesday 8 November 2006 1.27: Analysis: Find the angle between a plane of atoms and a bond\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
[Top] [Index] Manuals generated on Wednesday 8 November 2006 1.28: Analysis: Calculate intermolecular distances\dist select range=limits limit 2.0 4.0 2.0 4.0 include N(6) O(8) end
e.s.d yes
include O
[Top] [Index] Manuals generated on Wednesday 8 November 2006 1.29: Analysis: Find LIKELY H-BONDS with donors or acceptors other the O and NThe instruction that is executed is: \dist out mon=all select range=limits limit 1.5 2.2 0.7 2.2 pivot H bonded O N end
[Top] [Index] Manuals generated on Wednesday 8 November 2006 1.30: Analysis: How do I use ROTAX to test for twin laws?1. Choose Analyse-> Rotax Analysis/Twins-> ROTAX from the menu. 2. In the ROTAX dialog box, leave settings as 180 degree rotation and show F.O.M. less than 5.0. Click OK. 3. On the results dialog there will be (possibly) some numbers in a listbox below where it says "Choose a figure of merit:". Any which are exactly zero correspond to possible merohedral twin laws If there are any non-zero numbers then these are likely merohedral twin laws. Click one of the numbers to see the twin-law matrix. If you like the look of a twin-law (lowest non-zero FOM) then click the button "Apply Twin Law", then "Apply Twin Laws" on the next dialog. 4. To test the twin law Choose Refinement-> Setup and Refine and check the "Twin Element Scales" box. Then do some cycles of refinement. The R-factor should drop substantially if the twin law is correct, and typing \PARAM END
[Top] [Index] Manuals generated on Wednesday 8 November 2006 1.31: Analysis: How do I add hydrogen atoms to water molecules?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
\HYDROGEN DISTANCE 0.9 HBOND O(6) O(21) END
[Top] [Index] Manuals generated on Wednesday 8 November 2006 1.32: Publication: Editor wants completeness of the data at 25 degreesIs 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:
[Top] [Index] Manuals generated on Wednesday 8 November 2006 1.33: Publication: What's the difference between _theta_max and _theta_full?_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. [Top] [Index] Manuals generated on Wednesday 8 November 2006 1.34: Publication: Diagram shows wrong enantiomer. What to do?
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.
\edit transform -1 0 0 0 -1 0 0 0 -1 all end
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
[Top] [Index] Manuals generated on Wednesday 8 November 2006 1.35: References: What References should I know about?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 Watkin, D.J. Prout, C.K., Pearce, L.J. (1996). CAMERON, Chemical Crystallography Laboratory, University of Oxford, Oxford, UK.
RC93 Watkin, D.J., Prout, C.K., Lilley, P.M.deQ. (1994), RC93, Chemical Crystallography Laboratory, University of Oxford, Oxford, UK.
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 Carruthers, J.R. and Watkin, D.J. (1979), (Chebychev Weighting) Acta Cryst, A35, 698-699
SHELXS86 Sheldrick, G.M. (1986). SHELXS86. Program for the solution of crystal structures. Univ. of Gottingen, Federal Republic of Germany.
DIFABS Walker, N., and Stuart, D. DIFABS. Acta Cryst, A39, 158-166
[Top] [Index] Manuals generated on Wednesday 8 November 2006 1.36: Miscellaneous: Environment variablesCRYSTALS 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.
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© Copyright Chemical Crystallography Laboratory, Oxford, 2006.
Comments or queries to David Watkin -
david.watkin@chem.ox.ac.uk Telephone +44 1865 285019.
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