[o-info] RE: o-info Digest, Vol 47, Issue 11

warren@delsci.com

> anyone got opinions on this?

You bet!  *PDB notwithstanding, the existing segi field would seem the
obvious incremental solution to the problem that a single-letter chain
ID is no longer sufficient for describing today's systems.  

Let us all simply agree that a segment can have any composition of
chains, and a chain, any composition of residues. 

Even with the 1-character segment ID seemingly implied by O's 6
character "residue" field, you have immediately created at least 26-fold
more capacity.  If can imagine raising that limit from 6 to 9 to
encompass the full 4-character segi field, then you would have several
orders of magnitude additional headroom.

Cheers,
Warren

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> Today's Topics:
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>    1. MOI v11 feature in pdb_read & some loose talk (Alwyn Jones)
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> ----------------------------------------------------------------------
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> Message: 1
> Date: Fri, 23 Feb 2007 13:46:53 +0100
> From: Alwyn Jones <alwyn@xray.bmc.uu.se>
> Subject: [o-info] MOI v11 feature in pdb_read & some loose talk
> To: o-info o-info <o-info@o-info.bioxray.dk>
> Message-ID: <59CBCB2E-D630-45DA-BD3D-3D3F5C411860@xray.bmc.uu.se>
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> 
> i've got another v11 'feature' to report, courtesy of lothar esser.
> 
> if in pdb_read you want cns segid's, do not want to 
> concatenate the residue name and segid, and if the chain and 
> seg IDs are the same 1 character, THEN on pdb_write you will 
> loose the chain id character.
> 
> i've already fixed it and will recompile things over the weekend.
> 
> i have had a look at what the ePDB is planning this summer, 
> http:// remediation.wwpdb.org/ i checked the various test PDB 
> files there too. overall, i think the biggest hiccup will 
> come from the atom name changes and nucleic acid residue type 
> changes. i think this is GOOD, but it will need updating of 
> my dictionaries. i don't know if cns, ccp4 are planning a 
> switch to fit in with the wPDB timetable. it could be a 
> period of 'interesting' times with conflicting coordinates 
> and dictionaries.
> 
> the remediated (nice word) files have a remark record in them 
> indicating that they have the new changes. i intend to make 
> use of this, and PDB files that O generates will contain a 
> similar record.
> 
> as you probably know, o forms a 6 character residue name out 
> of the contents of columns 22-27, removing spaces, 
> capitalizing and shifting left. this has been called 'a gross 
> simplification to the pdb format'  
> but i still sleep moderately well at night. in v11 i tried to 
> help people working on structures with very many chains by 
> allowing the concatenation of residue names with SEGIDs. 
> this, of course, causes problems when trying to cram long 
> SEGIDs and names into just 6 characters. wPDB are not 
> planning on using SEGIDs, but they've put out the suggested 
> use of PART/PRTEND cards for discussion. i could support this 
> by generating separate O-style molecules for everything 
> between each set of PART/PRTEND cards. anyone got opinions on this?
> how about creating a new molecule each time the CHAINID not 
> equal to SEGID? i could support this with some limitations on 
> SEGID width to help form the molecule's name, or by some 
> other naming ploy.
> 
> Alwyn Jones
> alwyn@xray.bmc.uu.se
> http://xray.bmc.uu.se/alwyn
> 
> 
> 
> 
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