chem cryst
Home
-Crystals + Research Contact Lectures + Links + Gallery CSD installation Chemistry Dept Division University of Oxford chem cryst news |
Menu and toolbarChapter 2: The Menus
[Top] [Index] Manuals generated on Wednesday 8 November 2006 2.1: FileNew Working Dir
Choosing this item will display a dialog box allowing you to choose
a new folder to work in. The current dsc file will be closed, and the
working folder will change to the new one. If the new folder contains
an existing crfilev2.dsc, this will be opened.
Open Datafile
Choose this item to open a new CRYSTALS dsc file. The current dsc
file will be closed, and the new one opened. The working directory
will change to the folder containing the new dsc file.
Save Datafile
No action will be taken. The DSC file is constantly updated as operations
are carried out in CRYSTALS, so there is no need to 'save' the current state.
Save Datafile As
A dialog box will allow you to choose a filename to save a copy of the
current dsc file. After the copy has been saved, the current dsc file is
closed, and the new copy is opened.
Open Instruction File (USE file)
Cause CRYSTALS to execute (USE) a pre-prepared text file containing
CRYSTALS commands and/or data lists
Exit Crystals
Closes the program. [Top] [Index] Manuals generated on Wednesday 8 November 2006 2.2: X-ray dataThe X-ray data menu is concerned with the input, export or editing of
experimental X-ray observations and data. Pre-process
Submenu. See section 2.3. Use KCCDIN output
Reads in CRYSTALS format data files produced by the KCCDIN program Use RC93 output
Reads in CRYSTALS format data files produced by the RC93 program Use DIPIN output
Reads in CRYSTALS format data files produced by the DIPIN program Input/Edit Cell
Displays a dialog box for inputing or editing the cell parameters and their associated standard uncertainties. Input/Edit SpaceGroup
Displays a dialog box for entering the space group symbol. It may
either be hand-typed, in which case there must be a space between each
operator, or it may be selected from a list of the most common settings
of every space group.
Input/Edit Cell Contents
Displays a dialog box for entering the type and number of every element
present in the unit cell. Import Shelx file (INS or RES)
Opens a dialog to help import SHELX .ins or .res files. Choose the file name. You will need to know the space group symbol. Import reflection data
Opens a dialog which allows the import of reflection data in a variety
of formats, most commonly, SHELX HKLF4 format. File Export
Enables the creation of text files in various formats Filter reflections
Allows filters to be specified for rejecting certain categories of
reflections. If no filters are present, the dialog will offer a default
of rejecting reflections where I/sigma(I)<3.0 and also some very low angle
reflections. Edit goodies
Allows editing of the 'goodies' - lots of information that is required
for a useful CIF is stored here. This dialog provides a convenient way
to view and edit it. View Reflections
This item will write the current list of reflections to a file and open
that file for you to inspect them. [Top] [Index] Manuals generated on Wednesday 8 November 2006 2.3: X-ray data -> Pre-processRun KccdIn (Kccd data)
KccdIn takes an import.cif file, generated by Nonius Kappa CCD diffractomer software and produces input files suitable for reading into Crystals. Run RC93 (Cad4 data)
RC93 takes cpd.dat and cpd.psi files, generated by Nonius CAD 4 diffractomer software and produces input files suitable for reading into Crystals. Run DipIn (DIP2000 data)
RC93 takes reflection and listing files, generated by DIP2000 diffractomer software and produces input files suitable for reading into Crystals. [Top] [Index] Manuals generated on Wednesday 8 November 2006 2.4: Solve[Top] [Index] Manuals generated on Wednesday 8 November 2006 2.5: StructureUndo
Allows you to step back to any previous model (List 5) stored in the DSC file. All models are stored unless you PURGE the DSC datafile, or explicitly delete them using this dialog. Note: If you use the GUIDE, and automatic purge occurs after you have
checked for extinction - any models marked explicilty as 'to be retained'
will not be PURGED. [Top] [Index] Manuals generated on Wednesday 8 November 2006 2.6: Fourier[Top] [Index] Manuals generated on Wednesday 8 November 2006 2.7: Refinement[Top] [Index] Manuals generated on Wednesday 8 November 2006 2.8: ResultsLikely H-bonds
Finds all X--H distances (X=O or N) where the bond distance falls between 1.5 and 2.2 Angstroms. Also lists the X-H--X angles so that you can decide if the X--H is an acceptable hydrogen bond. Agreement analysis
Displays graphs of four different analyses of variance. Difabs analysis
Creates a contour map of the difabs absorption correction that WOULD BE
applied if you were to run DIFABS. The flatter the map the better. Rotax analysis/twins
Submenu, see section 2.9 Edit CIF goodies
Allows you to edit some of the values that will be put in the final CIF Publication tables
IAllows you to output data in a variety of ways. CIF is probably the most commonly used format. Please note that the standard uncertainties output in CIF files follow the 'Rule of 19', as requesed by Acta Cryst: What it means is as follows.... SU values are quoted to two digits precision if they are <= 19. E.g. rule of 9: 5.548(1) 1.453(2) 3.921(3) 1.2287(8) rule of 19: 5.5483(9) 1.4532(16) 3.921(3) 1.2287(8) rule of 29: 5.5483(9) 1.4532(16) 3.9214(29) 1.2287(9)
The object of this approach is to provide a more consistent distribution of precision across all values. Summary file
Produces a human-readable summary file of the crystal structure Acta checks
Performs some basic validation checks on a complete or almost complete
structure, to try to catch any problems remaining. Checkcif on the web
Just a link to the IUCr cif checking website. Platon
Writes files for and runs Platon, if you haven't run it before, you
will be asked to browse for the PLATON.EXE file on your hard disk. [Top] [Index] Manuals generated on Wednesday 8 November 2006 2.9: Results -> RotaxROTAX
Runs the Rotax procedure for looking for twin-laws. Output consists of a selection of possible twin laws with associated figures-of-merit. Figures closer to zero are best, but beware figures of exactly zero (corresponding to exact lattice overlap), since they are probably just part of the point group symmetry of your structure. You may choose a twin law to be applied Input twinned structure
Allows you to give a known twin-law. The ROTAX option above is probably
easier to use, even if you already know the twin law. Remove twin laws
Removes the twin laws (List 25), removes the twin scales from the model (List 5) and reverts to the original reflection listing. (Saved during the application of the twin-law). [Top] [Index] Manuals generated on Wednesday 8 November 2006 2.10: GraphicsCameron Graphics
Starts Cameron, a program for visualising crystals structure packing and
producing publication diagrams Special
Submenu. See section 2.11. Import last Cameron output
Reads in the model which Cameron wrote at the end of its last run. Could be useful if you've trashed the model since then (although, see also: Structure -> Undo, section 2.5). Import last Cameron input
Reads in the model which CRYSTALS last wrote to send to Cameron. Could be useful if you trashed the model in Cameron and then accidentally brought it back into CRYSTALS. (Although, see also: Structure -> Undo, section 2.5). View CHIME file
If you have saved a CHIME file whilst in CAMERON, this opens it. If you
don't have a .pdb viewer installed, you will get a 'Choose Program' dialog
instead. [Top] [Index] Manuals generated on Wednesday 8 November 2006 2.11: Graphics -> SpecialCameron (use existing input files)
Starts Cameron without writing new input files for it. Useful if you have an external program that produces cameron.ini and cameron.l5i files. [Top] [Index] Manuals generated on Wednesday 8 November 2006 2.12: AppearanceAtoms
Submenu. See section 2.13. Model
Submenu. See section 2.14. Auto scale (zoom off)
Restores the model to its original view, if it has been zoomed. Set Text Font
Allows you to choose a font for the text output window. I recommend Lucida Console, or Courier - in any case use a fixed/monospaced font, otherwise the output of tables will not make much sense. Set Input Font
Lets you choose a font for the input editbox. Might be useful if
you are demonstrating command line features on a high-res screen. [Top] [Index] Manuals generated on Wednesday 8 November 2006 2.13: Appearance -> AtomsCovalent
Sets radius of atoms displayed in the main model window to be 1/4 of
their covalent radius. Van der Walls
Sets the radius of atoms displayed in the main model window to be
the VDW radius. Thermal
Displays atoms as either ellipse representation of ADPs, or sphere
representing U[iso]. Quarter size
Set radius to 1/4 of given value (either covalent, vdw or thermal). Half size
Set radius to 1/2 of given value (either covalent, vdw or thermal). Full size
Set radius to given value (either covalent, vdw or thermal). [Top] [Index] Manuals generated on Wednesday 8 November 2006 2.14: Appearance -> ModelUpdate model
If automatic update is disabled, this command updates the model Auto update OFF
Disables auto update. Useful for big structures where the drawing is
significantly slowing the program Auto update ON
Enables auto update of the model window. Set wallpaper
Experimental feature. Allows you to set the background of the model
window with a bitmap. The bitmap is stretched or shrunk to fit the window.
Significantly slows the drawing on slower machines. Also, the width of
the bitmap in pixels must be a multiple of 4. No wallpaper
Removes the model background if present [Top] [Index] Manuals generated on Wednesday 8 November 2006 2.15: DevelopmentThis menu contains items that are currently under development. They
are not documented yet, and you should not need to use them. If you
wish to experiment, please make a copy of your structure and experiment
on the copy. Feedback is welcome.
|
© Copyright Chemical Crystallography Laboratory, Oxford, 2006.
Comments or queries to David Watkin -
david.watkin@chem.ox.ac.uk Telephone +44 1865 285019.
This page last changed on Wednesday 8 November 2006.
The website was re-generated on Wednesday 8 November 2006.
Choose your nearest mirror for faster access:
[ Original
|
CCP14 UK Mirror
|
CCP14 Canadian Mirror
|
CCP14 USA Mirror
|
CCP14 Australian Mirror
]
Authorised people, edit:
this file,
news,
tree,
template,
stylesheet.
Rebuild website.