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Re: [ccp4bb] pdb-l: Stop the new PDB format! |
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CCP4bb navigationCCP4bb <-- 2007 <-- August 2007 <-- 01 August 2007Subject: Re: pdb-l: Stop the new PDB format! From: Joe Krahn krahn {- at -} NIEHS {- dot -} NIH {- dot -} GOV Date: 2007-08-01 > On Jul 21, 2007, at 11:12 AM, Joe Krahn wrote: > >> Another problem is that the original meaning of HET groups continues to >> be corrupted. ATOM records are for commonly occurring residues from a >> list of standard residues. > > No, they're for commonly occurring _polymer_ residues. Two consecutive > residues contained in ATOM records are implied to connected to each > other barring an intervening TER card. I imagine this is the principal > reason that water residues use HETATM records. > > --Eric > The idea that ATOM is only for _polymer_ residues was not part of the original format, and is specifically one of the changes that I am asserting as wrong. The original PDB format stated that ATOM is for "standard residues" which are defined by a list of residue names given in the PDB format documentation, and the "list of standard residues" included water. Non-standard residues must define themselves with extra HET records. With RCSB's database, HETs must be completely defined as well, which makes it easy for them to forget that the whole idea of HETATM is to allow unknown residue types to be displayed. RCSB has added the concept of HET's being non-polymers, but also keeps this concept mixed up by not including Se-Met (MSE) which is certainly enough not to be a HET group. So, the idea that ATOM implies some polymerization linkage is dysfunctional. What the PDB format should include is an INIT record that is the counterpart of the TER record. The bigger point of my post, however, was that the interests of the non-database user community are, in my opinion, being ignored, particularly with the PDB format. Structural biology is so diverse that it really needs input from the whole community to do the right thing. The problem is that when the PDB 3.0 format was announced 3 months ago, it was done with the intent of intentionally not allowing time to consider problems and alternatives posed by the user community. Joe Krahn CCP4bb navigationCCP4bb <-- 2007 <-- August 2007 <-- 01 August 2007 |
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