Hi, Jut to expand on Charles's answer a bit,
On Oct 3, 2007, at 4:22 AM, R.M. van der Werf wrote: > Hi, > > Perhaps this is a stupid question, but I do wonder why > - Xplor cannot read PDBs as provided by the protein databank? > - Xplor output is not PDB standard as required for submission to the > protein databank. The two major differences between xplor-standard PDBs and PDB-standard PDBs are the atom names and the absence of the segid field in the PDB standard. Xplor has used nonstandard atom names for a long time because they greatly facilitate atom selections. The PDB's standard atom names for, for example, leu delta protons are 1HD1, 1HD2, etc. Xplor's are HD11, HD12, etc. With xplor's atom names, you can do selections like (resn leu and name h*) that cover all the atoms in the residue. As an aside, lots of our scripts (in Python, TCL, and in the classic xplor language) are dependent upon the xplor atom naming convention. So changing naming conventions would require changes to a lot of stuff. The second major difference between xplor and PDB-standard PDB files is xplor's addition of the segid field. As far as I can tell, Axel added the segid because the PDB standard's chainID is only one character long. As Charles said, we have some pretty good tools for reading and writing PDB-standard PDB files, but we're always looking for cases where xplor's tools don't yet work. So please email us if you find such a case. --JK
