-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi Tom, Thanks for your interest! I think that a collection of models for the cases where there is more than one assembly is an excellent idea. On a related note, it's a pity that mmCIF files are not more widely used instead of the very limited PDB format. I like the fact that Chimera can handle them. Best regards, Miguel Thomas Goddard escribió:
Hi Miguel,
Adding a fetch by id option for PQS biological assembly PDB files looks like a good idea. I'll put it on the requested features list.
Some of those files reuse atom serial numbers and reuse chain identifiers. For example, satellite tobacco mosaic virus 1a34 which involves 60 copies of the asymmetric unit (4 chains) has more than 200,000 atoms and hundreds of chains. The PDB file format can't handle that correctly. Still the file displays in Chimera although it can be hard to select just a single capsid protein since it shares a chain identifier with other subunits. This is a very small virus. Bigger viruses just don't have PQS entries -- they probably set a size limit. So this isn't a good way to handled icosahedral viruses. But probably most other PDB entries will not have size problems.
Another issue is that PQS has more than one biological assembly for some PDB entries. For example, 1a6v has 3 assemblies, with files called 1a6v_1.mmol, 1a6v_2.mmol and 1a6v_3.mmol. I guess it would make sense to load all of the assemblies as separate Chimera models in those cases.
Thanks for the suggestion.
Tom
- -- Miguel Ortiz Lombardía Centro de Investigaciones Oncológicas C/ Melchor Fernández Almagro, 3 28029 Madrid, Spain Tel. +34 912 246 900 Fax. +34 912 246 976 email: molatwork@yahoo.es www: http://www.pangea.org/mol/spip.php?rubrique2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Le travail est ce que l'homme a trouvé de mieux pour ne rien faire de sa vie. (Raoul Vaneigem) -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.2.2 (GNU/Linux) iD8DBQFGHcb8F6oOrDvhbQIRAoHnAJ952AbA01XpJmKp6ctyWyKrPJEOFwCgpSNu 0riRyAIZrocy+SACVZAiwM8= =mMMB -----END PGP SIGNATURE-----