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:[log in to unmask]] On Behalf Of
Kevin Cowtan
Sent: Tuesday, September 07, 2010 12:54 PM
To: [log in to unmask]
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
|