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Tutorials and Examples

Louis Farrugia's WinGX Single Crystal Suite

Solving a structure using fragment searching in Dirdif

(rigid part of the molecule) The CCP14 Homepage is at http://www.ccp14.ac.uk

[Tutorials page] | [WinGX Tutorial Index] | [CCP14 Dirdif for UNIX homepage]

This example assumes you have done the determination of the space group using WinGX in a previous tutorial page..

In this tutorial/run-through, we are going to solve Tetracycline hydrochloride using Fragment searching in Dirdif. This can be a very powerful feature of Dirdif when other methods fail - but a there is a rigid part of the structure that can be used.

Importing the model into WinGX/SXGRAPH

Get a fragment from somewhere. You can either use Dirdif interatively to build the fragment, or get a similar structure from the Cambridge Database, or use a related structure you have previously solved. As the following will show, it is easy in WinGX to trim the fragment down.

In this case, we have a CIF file of a related structure from Cambridge database. We have converted it to a Shelx file (titled import01.ins) using the Model, Import Model facility in WinGX.

Now run SXGRAPH. Use the SXGRAPH menu to select File, Open Shelx File; select *.INS in the Files of type and open the import01.ins file.

Loading the fragment into SXGRAPH

Trimming down the fragment

As an example, get rid of all the hydrogen atoms by selecting from the SXGRAPH menu, Delete, All Type, H Atoms

Then click on Box Selection option and select all the atoms that you think would be in the non-rigid part of the structure. Selected atoms will be highlighted as yellow discs.

Selected atoms

Now from the SXGRAPH menu select Delete, Selected Aoms

Selected atoms have been deleted

Saving the trimmed fragment into Dirdif format (ATMOD file)

To save the fragment into the Dirdif ATMOD file (ready to run Dirdif fragment searching), from the SXGRAPH menu, File, Save ATMOD File. Now exit SXGRAPH.

Saving the Fragment into Dirdif ATMOD format via WinGX's SXGRAPH

Running Dirdif in fragment searching mode - ORIENT

In the WinGX main menu, click on Solve, Dirdif, ORIENT menu option to start to try and automatically solve the structure using Dirdif automatic Patterson methods.

If Dirdif does not solve, look into either contracting the fragment (in the case of possible flexibility in the molecule) or expanding up the fragment to get more scattering power into the fragment.

Running Dirdif in fragment searching mode - ORIENT

Dirdif solving via fragment searching mode - ORIENT

Dirdif solved structure using fragment searching

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