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SXGRAPH allows you to easily perform refinements via a graphical interface
without having to know the Shelx commands. Though SXGRAPH will also inform
you of the many of the Shelx commands it is using and you can view the Shelx INS
file to see the effects of using SXGRAPH.
In the following example (a Cesium Titanium Silicate), Dirdif has solved the structure to completion and it is just a matter of completing the refinement using Shelxl97. If there were unfound atoms, SXGRAPH will display these as Shelxl97 generated Q peaks after the cycles of refinement. Note 1: If you find you lose the basic Screen Menu, just select View, Screen Menu to get it back on the screen (or if you have no selected atoms simply right click the graphics screen) Note 2: Many of the SXGRAPH options (restraints, etc) are not available until you have selected some atoms (using the Select menu or left mouse click on atoms). Using the right mouse button after selecting the atoms will bring up the Change Atom/Group Properties Dialog boxes. These allow you to make many changes to the current parameters. Note 3: You do have the option to edit the Shelx INS or RES file manually using the Edit menus. Or using the tradition WinGX Refine menu option. |
Opening Solved Structure in SXGRAPHRun WinGX, load your solved structure, then run SXGRAPH by selecting the SXGRAPH ICON to (in the case of Cesium Titanium Silicate) give you the resulting screen (thicker lines [using View Preferences] and atom labels have been selected as well).
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Refining atoms isotropicallyBy default, all atoms by default are set to refine for position (when allowed by symmetry) and isotropic thermals. Thus do some cycles of refinement in Shelx by selecting Refinement, Run SHELXL-97. When SHELXL is launched from SXGRAPH, there is no text output, but the current status (i.e. cycle number) of the Shelx refinement will be displayed in the status bar at the bottom of the SXGRAPH window. On completion of the refinement cycles, SXGRAPH will present any warnings that Shelx may have generated, the updated structure and resulting Q peaks (for the moment, ignore the EXTI Extinction warning). More detailed examination of the Shelx output is possible via the Refinement, Shelx results menus.
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Refining heavy atoms AnisotropicallyFor the purpose of this demonstration: on this heavy atom structure, it might be best to first refine the heavy Titanium and Cesium atoms; then the lighter Silicon and Oxygen atoms. Remove the Q peaks out of the way with Delete, All Q Peaks. Then select the Cs and Ti atoms by either clicking on them with the mouse or using the Select, All Type menu option.
Click on the Right Mouse Button to bring up the following Change Group Properties menu and select the Set Uijs Anisotropic options box. This will then be applied to the selected Cs and Ti atoms. (If you view the Shelx file, you will see this has added a ANIS CS1 TI2 command).
Select OK and now do another round of refinement via Refinement, Run SHELXL-97 to give the following style of output complete with Q peaks.
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Refining light atoms AnisotropicallyNow that the heavy atoms have been refined, no repeat the same process with the light atoms. Remove the Q peaks out of the way with Delete, All Q Peaks. Then select the Silicon and Oxygen atoms using the Select, All Type menu option for Si and O.
Click on the Right Mouse Button to bring up the following Change Group Properties menu and select the Set Uijs Anisotropic options box. This will then be applied to the selected Cs and Ti atoms. (If you view the Shelx file, you will see this has added a new ANIS command over the selected atoms).
Select OK and now do another round of refinement via Refinement, Run SHELXL-97 to give the following style of output complete with Q peaks.
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Other Refinement OptionsNow could be a good time to refine Extinction (you should have been getting Shelxl generated EXTI warnings - that Extinction was something to look into) Go into the Refinement, Reflections menu. Sellect Use EXTI correction, Apply changes then run Shelxl97 again.
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Viewing the Resulting StructureThis can be done at any time and the structure should be routinely checked to see what is happening. There is no need to exit SXGRAPH (both WinGX and SXGRAPH run as independent processes). Just select your favourite structure viewer under the WinGX Graphics menu option. In this case, you can see that some of the thermals re a bit large. Most of the time Shelx will detect these types of problems but this just misses the usual Shelx Split Atom warning. This could be time for running through Platon as well as doing Difference Fourier Maps. Refer to the main WinGX Tutorial Index for some available options.
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