Dear Kevin (and others), The symmetry operators are in the "official" pdb in REMARK 290 records, both as text (e.g. x,y,z) and as symmetry (SMTRY) matrices and are even mandatory (see extract below). So far they just have been ignored by the CCP4 and most other crystallographic programs. If the CCP4 would agree to use these matrices or operators, the chaos with space group names and numbers would be solved or at least would not matter any more since they would not be used to get symmetry information.
Best regards, Herman REMARK 290, Crystallographic Symmetry Remark 290 is mandatory for crystalline studies. The remark is generated by PDB. Example 1 2 3 4 5 6 7 1234567890123456789012345678901234567890123456789012345678901234567890 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 1/2-X,-Y,1/2+Z REMARK 290 3555 -X,1/2+Y,1/2-Z REMARK 290 4555 1/2+X,1/2-Y,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 36.30027 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 59.50256 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 46.45545 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 59.50256 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 36.30027 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 46.45545 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: -----Original Message----- From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of Kevin Cowtan Sent: Tuesday, September 07, 2010 12:54 PM To: [email protected] Subject: Re: [ccp4bb] Fd-3m with pdbset George M. Sheldrick wrote: > Perhaps I should mention that with the SHELX method of specifying the > space group symmetry using the symmetry operators, alternative > settings, specified in IT or not, cause no problems. But then we would > not have had this thread (or the H3/R3 and P21221 threads). What George said. (This is the approach used by the CCP4 C libraries and clipper for mtzs and maps, and also for the coot-CNS interchange format, but it is not used for PDB files.) Is anyone who is involved in the new PDB format willing to campaign for the compulsory inclusion of the symops (either full set or a minimal set of generator ops) in the PDB file as a canonical representation of the spacegroup? -- EMAIL DISCLAIMER http://www.york.ac.uk/docs/disclaimer/email.htm
