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[ccp4bb]: Summary: converting Xplor to PDB coordinate files
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> Is it the case that PDBSET keyword ELEMENT no longer works after v 3.3?
> If so, how do people convert Xplor/CNSv0.1 files to standard
> pdb format for sfall? My irons are all changing to flourines!
No one contended that the keword ELEMENT still works. I guess it
was felt not worthile to maintain, since once the element field is
misplaced there is no logical way of determining whether, for example,
CA is C-alpha or Calcium; CD is C-delta or Cadmium. And the new format
adopted since vers 3.3 puts element names in #77-78. But it is still
in the documentation. And it was useful for FE, provided you have no
As for converting Xplor to PDB:
S.Ravichandran uses Dave Schuller's PDB Pipeline:
Schuller, D.J. (1996), "The PDB pipeline", PDB newsletter, 76, 8-9.
Dave Schuller recommended using 4-letter atom names in Xplor (FE+3), which
if right-justified in #13-16 will put the element in #13-14. This
requires editing the topology/parameter files for consistancy.
Another possibility is to keep a copy of pdbset version 3.3, where the
ELEMENT keyword works, and use this as the first step after Xplor to
fix elements in #13-14. Then when CCP4 version 4 sees it in subsequent
steps, the correct element will be added in #77-78.
Edward A. Berry, MailStop 3-250
Lawrence Berkeley National Laboratory
1 Cyclotron Road, Berkeley, CA 94720
Jfax +1-530-323-9836 (you send fax, I receive email)