On Tuesday 02 June 2009 15:00:23 Edward Miller wrote: > I see now that the last atom COOT reads in is atom number 99999. > > > Perhaps, I fear, this is a problem with the PDB format - that the column > width for atom numbers can not accommodate more than 99999 atoms. > > Ed >
Yes. This is one of many limitations of the PDB format. We've had this discussion before, and the rational option (abandon it in favor of something better) has been nixed by the Powers That Be. Note that the current PDB standard http://www.wwpdb.org/documentation/format32/sect9.html states "If a collection contains more than 99,999 total atoms, then more than one entry must be made" And, in fact, the PDB splits such large models into more than one PDB file upon deposition if you haven't already done so before hand. Nevertheless, many [most?] programs deal happily with this nonsense by ignoring the sequence field altogether. What earthly good does it do you to know what was the seqeunce number for atom NZ of Lys Z34 in a particular version of your model, given that it was almost certainly different after being processed by the next program used in the course of refinement or model-fitting. The situation is somewhat different for non-protein atoms, since the sequence number is used by the CONECT records. So I'll make a modest proposal to give all protein atoms sequence number 1, at leave the other 99,998 available integers for ligands :-) -- Ethan A Merritt Biomolecular Structure Center University of Washington, Seattle 98195-7742
