[CCP14 Home: (Frames | No Frames)]
CCP14 Mirrors: [UK] | [CA] | [US] | [AU]

(This Webpage Page in No Frames Mode)


Tutorials and Examples

CRYSTALS Single Crystal Suite

Refining an Inorganic Structure using Crystals

The CCP14 Homepage is at http://www.ccp14.ac.uk

[Tutorials page] | [Crystals Tutorial page]

Run Crystals, select File, New and go to the directory where the HKL data and Dirdif solution is located.

Select Structure, Input, Shelx File (INS or RES) to import the Dirdif solution which is in a Shelx format. Crystals will prompt for the space group [C 2/c] (which is not part of the Shelx format), then will continue in importing the information from the Shelx file. If Crystals has a problem with a kosher Shelx file, it could be you inserted the Space Group file in the wrong format.

As Crystals can do DLS refinement, reflection data is an option you need to explicitely set. Thus to insert the Fsquare reflection data, select X-ray Data, Reflection Data to import the HKL Intensity file.

Select Refinement, Guided Automatic to start the refinement. Crystals will do a few cycles of refinement, then the Supervisor Dialog will then come up to guide you through the refinement.

Calling up the Guided Refinement from the Menu

Guide Refinement Supervisor GUI

Crystals screen with Guide Refinement Supervisor GUI

At this point, Crystals recommends we refine position and isotropic thermal parameters. Click OK to do this. Crystals will then to a cycles of refinement.

Crystals now recommends that you continue on with anisotropic refinement but before doing this, it would be best to check out the thermals and other nuances in the Cameron Structure Viewing program as blown up thermals may reveal spurious peaks that were assigned as atoms.

Close the Guided Refinement dialog and select Cameron from the top menu. Selecting Ellipses shows that one of the Oxygen thermals has blown up, implying it is a spurious peak that should be deleted.

In the Cameron Command line box (it is still retained for accessing all the complex and simple functionality of Cameron) type exclude and click on the offending atom (in this case O14). Then type View to view the result.

  • Exit Cameron using File, Exit Cameron. Crystals will prompt whether you wish to apply the changes performed by Cameron. In this case Yes is the answer.

    It should be noted that you can graphically apply commands to the structure in the Crystals Window (such as deleting, constraints and restraints), but Cameron is required for closer examination of the structure, looking at packing, etc.

  • Select Refinement, Guided Automatic to restart the guided refinement. The Supervisor Dialog will then again come up to guide you through the refinement, in this case advising you to refine the atomic positions and anisotropic thermals. click OK to make this happen.

    At this point, Crystals now recommends you Check Extinction. So continue on with this.

    Crystals now would like to optimise the weighting scheme. Thus continue on and select "optimal" for weighting scheme determination and go with the defaults.

    At this point, it may be good to check things out again with Cameron. The large Oxygen thermals are worth checking out with the Crystals Fourier Contour Map facility as this may be a split atom problem. But that will be the subject of another separate tutorial/run-through.

    It is again pointed out that traditional Crystals users and people who want to issue manual commands can still do this with the bottom right hand command line dialog box. In this case, we will finish off the refinement by issuing the manual script command \script routine. To get out of a script, just type direct at any time.

    You can then interact with Crystals in the traditional manner with the added advantage of being able to use the scroll bar to evaluate all the text output.

    CIF files have now been produced and you can exit and restart Crystals at any time and continue where you left off in the refinement.

    [Tutorials page] | [Crystals Tutorial page]

    [CCP14 Home: (Frames | No Frames)]
    CCP14 Mirrors: [UK] | [CA] | [US] | [AU]

    (This Webpage Page in No Frames Mode)

    If you have any queries or comments, please feel free to contact the CCP14