Tutorials and Examples
Automated Single Crystal Structure Solution Using Sir97
Basic run-through of Refining and Quality Checking of an Organic Structure with Sir97
The CCP14 Homepage is at http://www.ccp14.ac.uk
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
The file "atoms.dat" contains:
Specie X Y Z [B]
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
- 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
- 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
- The updated structure is displayed with the now refined anisotropic
thermals. The structure can still be rotated around for better
- 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.