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Tutorials and Examples

Automated Single Crystal Structure Solution Using Sir2002

Using Sir2002 to solve large polymeric inorganics involving pseudo-symmetry - R-factor stop and RELAX Procedure

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

[CCP14 Tutorials page] | [Sir97/2002 Tutorial Index] | [EXPO]
[WinGX] | [Crystals] | [Platon/System S]

Sir97 (and soon for Sir2002) can be spawned transparently from the following single crystal suites (freely available for students and academics) :

Note: a feature of Sir97 and Sir2002 that may not be obvious is that if it fails to solve on the first trial, you should just leave it run. Sir2002 by default goes through the first 200 Trials.

However, if you have a nasty structural problem, some non-defaults may be required. In this case of a large polymeric inorganic (structure not yet published - and originally solved manually using model building and knowledge of the crystal chemistry), there is not only the problem of solving (where there may be many low false minima), but recognising that the structure has been solved. Thus for some structural problems, you may have to play around a bit with the defaults.

  • The first problem may be that you need to use the RELAX procedure if a default run gives no decent or recognisable solutions. If a "low" R-factor solution is found but does not seem to make sense; try and resolve with the RELAX procedure. This is changed via the Modify, Setup menu.

  • The second problem with this polymeric inorganic structure may be that the default "Stop when R% is less than" may be set too high. Found solutions using the default of 25% do not make that much sense, but lowering this to 20% (and using the RELAX procedure) finds a solution that make more sense and can be refined up. Lowering the default "Stop when R% is less than" is changed via the Modify, Setup menu.

If the structure is not solving, Sir2002 may also give a hint that the RELAX Procedure could be worth trying if you receive the message that there are psuedotranslational effects as per the following screen image.

Be wary that Sir2002 assumes you have put in the correct chemistry (or close to the correct chemistry). When in doubt, perform an elemental analysis. It is not that uncommon for other elements to be present in inorganic crystals, especially if a flux of different composition has been used to grow the crystals (or purity of starting materials may not be as advertised).

Obtaining the data

Structure is presently unpublished. Will distribute data when structure is in print.

Starting out with Sir2002

Copy over an existing Sir2002 *.sir file. Open the file in your favourite text editor and modify the cell, hkl file, spacegroup and contents information as per the following. By default, Sir2002 assumes F-square data. While the "Fosquare" command used in Sir97 is now redundant in Sir2002, it will not cause any harm having it in.

%structure    blah
%job   from Ian Grey
         Cell     18.9141  18.9141  45.5111   90.000   90.000  120.000
         Space   R 3
         Content   XX 3 YY 117 ZZ 180 AA 480
         Reflections   r3.hkl
         Format  (3i4,2f8.2)

Changing the defaults

From the top menu, select Modify, Setup and select the RELAX Procedure and change the "Stop when R% is less than" to 20%.

Now running Sir2002 with the non-defaults - solves on Trial 17

From the top left menu select, File, Load and Go. Select the *.sir file and then select the Go ICON. You can edit the information before trying to solve the structure by selecting the Edit ICON.

Where as Sir2002 may have had difficulties on the defaults, it can now solve the structure. In this case on Trial 17. It may still require much work to refine up the structure and figure out what is going on.

[CCP14 Tutorials page] | [Sir97/2002 Tutorial Index] | [EXPO]
[WinGX] | [Crystals] | [Platon/System S]

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