Hi Mike, The space groups recognized by the Unit Cell tool are defined in the Chimera distribution in file chimera/share/Crystal/space_groups.py (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. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/unitcell/unitcell.h... 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. Tom -------- Original Message -------- Subject: [Chimera-users] Centro-symmetric space groups From: Michael Day To: chimera-users@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
<>< <>< <>< <>< <>< <>< <>< <>< <>< <><