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Tutorials and Examples

Automated Single Crystal Structure Solution Using Sir97

Basic run Through of Solving an Organic Structure with Sir97

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

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

Sir2002 is now released and has solved structures with up to 2000 atoms in the asymmetric unit. Refer to the main page for more information

Sir direct methods structure solution software can be spawned transparently from the following single crystal suites (freely available for students and academics) :

Note: a feature of Sir97 that may not be obvious to people solving routine solvable structures (or who have mainly used Sir92) is if Sir97 states that an adequate solution has not been found after Fourier cycling (R factor too high); it will automatically continue until it either solves the structure, or exhausts its strategy options.

The following organic example uses the default example file that comes with the Sir97 distribution.

From either an Icon in MS-Windows (or typing sir97 on UNIX command line), run sir97.

  • This brings up the following screen

  • Click on OK and you are then prompted to open up a sir97 control file. It would be best to have each structure in a separate directory.

  • The file we are going to look at relates to the Cesium Titanium Silicate. Following is the information inside the file that you would be expect to edit manually and is described in the Sir97 manual. Though, using previous sir97 files as a template is an easy option.

    [Click here for the Sir97 manual in PDF format]

    %structure loganin
    %job test structure: loganin
      cell  8.187 14.277 15.693 90 90 90
      space   p 21 21 21
      cont c 68 h 104 o 40
      refl loganin.hkl
(if you are using Fsquares, add the following line below refl, Fosquared)
  • Click on the browse file and click on the loganin.sir file.

  • Click on OK to confirm your selection.

  • Then click OK again to let Sir97 go through its stuff (this is the fun to watch bit). Following we see sir97 much up the hkl data.

  • Sir97 munches on relentlessly - it feels no pain, it isn't human, IT CAN'T BE REASONED WITH!

  • Has done the phasing and is now up to the fourier.

  • After the Fourier, Sir97 tries to optimise what it things would make the best starting structure.

  • A further optimisation cycle.

  • Sir97 now attempts to assign most likely atom types. Red is Oxygen and C is carbon.

  • A further cycle of optimising a likely structure.

  • Sir97 now presents what it considers to be the best structure it can suggest from the data.

  • By clicking and dragging with the mouse, you can rotate the structure around the screen for alternative screen views.

  • By going into Plot Style you can change the looks of the atoms, including adding atom labels.

  • By clicking on the Contour menu option, (in this case also selecting an X Section) you can view the Fobs electron density map, with overlapping, labelled atom positions. Use the left and right arrow icons to go up and down the sections of the contour map.

  • You can also look at the electron density map on different on a different plane. In this case a Y section.

  • You can scroll up the sections, again seeing overlayed atoms and bonds.

  • You can change the labelling options so the atom types are displayed. It is possible to reassign elements to physically reasonable assignments. In this case, we have entered the Refine menu system to optimise, explore the structure.

Examining the Electron Density Maps

  • To see where other pieces of electron density exist that might be due to unassigned atoms, we have various options for generating electron density maps.

  • Here, Sir97 is computing the fourier map

  • Sir97 reports 5 new peaks and prompts the user to see if these new peaks make physical sense.

  • The user can see these peaks in relationship to the other atoms, obtain distance and angle information, delete these or accept these as atoms. (Atom options was set back to simple)

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

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