New 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.

Guided Import

Starts up "The Guide".
The Guide tries to suggest a strategy for working with 'routine' structures.

Diffractometer cifs

Submenu. See section 2.3.

Use Pre-processed

Submenu. See Section 2.4

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 HKLF4 data

Opens a dialog which allows the import of reflection data in a variety of formats, most commonly, SHELX HKLF4 format.

Import HKLF5 data

Converts a Shelx HKLF5 file into CRYSTALS format. Gives the opportunity to enter the twin law matrices

Import "cif" files

Opens a dialog which allows the import of data from "cif" and "fcf" files.

If the "cif" file contains more than one structure, the data from each may either be put into separate CRYSTALS format files, or into one single file. If there is a single file, it can be imported directly into CRYSTALS. If the "cif" file contians a Z'=2 structure, the two molecules can be 'matched', ie tested for similarity.

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.

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.

Run Generalised cif input

May eventually replace other options listed below.

Run Agilentin (Oxford Diffraction data)

Agelentin in processes Oxford Diffraction data.

Run 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.

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

Undo

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.

Likely 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 2.10

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.

ROTAX

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).

Cameron Graphics

Starts Cameron, a program for visualising crystals structure packing and producing publication diagrams

Special

Submenu. See section 2.12.

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 2.6).

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 2.6).

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.

Cameron (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.

Atoms

Submenu. See section 2.14.

Model

Submenu. See section 2.15.

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.

Covalent

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).

Update 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