[Chimera-users] Centro-symmetric space groups

Tom Goddard goddard at cgl.ucsf.edu
Fri Aug 28 15:41:34 PDT 2009

Hi Mike,

  The space groups recognized by the Unit Cell tool are defined in the 
Chimera distribution in file


(On the Mac this is 
Chimera.app/Contents/Resources/share/Crystal/space_groups.py.)  That is 
Python code and you can look at it in any text editor.  Look at the 
table at the end of the file.  A few years ago I made this file and I 
tried to include every space group listed in a Protein Databank entry 
though I may not have succeeded.  Are the non-centrosymmetric groups 
used by the PDB?

  A fallback is to just specify exactly the symmetries that build the 
unit cell from the asymmetric unit using PDB REMARK 290 SMTRY records.  
Can be inconvenient, but if those symmetries are already present in a 
different PDB entry you can copy and paste them.

  More detail on Unit Cell is in the User's Guide.


If you have suggestions for how to improve it, tell me.  I have to warn 
you that we've really focused on electron microscopy density map 
analysis in Chimera and our x-ray map capabilities are rough.


-------- Original Message --------
Subject: [Chimera-users] Centro-symmetric space groups
From: Michael Day
To: chimera-users at cgl.ucsf.edu
Date: 8/28/09 3:25 PM
> How do you get Chimera to recognize centrosymmetric space groups.
> If I include the space group on the CRYST1 card of the PDB file all is 
> well for non-centrosymmetric groups but when a center of symmetry 
> enters the picture all bets are  off.
> I'm using Tool->Higher-Order Structure->Unit cell
> For example adding the space group in column 56 of the PDB
> P1 as P 1 - all's good
> P-1 as P -1 - complete nonsense although it recognizes there are two 
> symmetry elements
> P2 as P 1 2 1 - all's good
> P21 as P 1 21 1 - all's good
> P212121 as P 21 21 21 - no problem
> But;
> P21/c as P 1 21/c 1 - no recognized symmetry elements and no unit cell 
> expansion.
> Cheers,
> Mike
> <<< 
> ------------------------------------------------------------------------>>>
> Dr. Michael W. Day
> Director - X-ray Crystallography Lab & Molecular Observatory
> California Institute of Technology
> Mail Code 139-74
> Pasadena, CA 91125
> <>< <>< <>< <>< <>< <>< <>< <>< <>< <><

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