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.
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.
Now from the SXGRAPH menu select Delete, Selected Aoms
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.
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.