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

Continuing on from the structure we just solved in solving an organic structure using Sir97.

Answer from Sirware team on the ability to just use Sir97 for structure refinement and ability to import a shelx file

"It is not possible to import a shelx file. What you can do is:
 edit .ins file and create a .sir file like
              %struct
              %job
              %data
               cell      .............
               spacegroup      .......
               content      ..........
               reflections      ......
              %normal
              %fourie
               fragment atoms.dat
               recycle 0
              %menu
              %end
The file "atoms.dat" contains:

      Specie X  Y  Z  [B]
i.e.

ca         .162 .162 .162  
na         .671 .671 .671  
o          .599 .290 .074  
o          .378 .225 .061  
n          .320 .320 .320  
c          .466 .294 .281  
c          .482 .268 .128  

if B is not supplied the Wilson B is used.
The directive "recycle 0" is used to avoid the automatic
L.S procedure. With the %menu command you can use the graphic
interface to refine the structure."

Least Squares Refinement

• It is possible to employ a least squares refinement, setting parameters and options via the menu system.

  Before starting, go into Plot Style and set Ellipsoids for display with atom Labels.

• 

• Go into the Refine option. This leaves a number of options, including refinement; automatic placement of hydrogens; fourier map methods and display of various information relevant to the structure. For example, Th.Fact. checks for any abnormal thermal values.

• 

• To refine the structure, go into L.S.Q.

• 

• Click on Modify, then Isotropic. Crosses indicate atoms that are set to refine isotropically, which in this case are all the Oxygen and Carbon atoms. These can be fixed or released in a variety of ways, including by species, individually, or all.

• 

• To start refining, click on OK until you get back to the Least Squares Refinement window and select GO to start refining.

• 

• You can then go back into Refine, L.S.Q., Modify, Aniso. Then by Species, set the Oxygens and Carbons to refine anisotropically. Then click OK until you get back to the Least Squares Refinement window and select GO to start refining Carbon and Oxygen atoms anisotropically.

• 

• 

• The updated structure is displayed with the now refined anisotropic thermals. The structure can still be rotated around for better view.

• 

• You can then go back into Refine, Hydro, Automatic and let Sir97 try and place hydrogens on the non Oxygen atoms automatically. You can do this manually. You have to option to define H-bonded donor and acceptor atoms.

• 

• Click on L.S.Q., Modify, then Isotropic. Crosses indicate atoms that are set to refine isotropically, in this case the Hydrogen atoms.

• 

• Now click OK back to the Least Squares Refinement menu and press go to refine (summary, carbons and oxygens anisotropically, non-oxygen hydrogens isotropically) to give the following.

• 

• Go into the Refine option. Check using Th.Fact. checks for any abnormal thermal values.

• 

• Other options abound, including constraints/restraints in the L.S.Q, Modify, Equivalence menu option. Options to check Bond Angles, Bond Lengths, etc can be accessed graphically from the main menu system.

  After quitting Sir97, the resulting atom positions will exported to a Shelx *.ins file

  An output file stating exactly what you did with results is also outputted.