[Chimera-users] Suggestion on biological assembly load
Miguel Ortiz Lombardia
molatwork at yahoo.es
Wed Apr 11 22:43:24 PDT 2007
-----BEGIN PGP SIGNED MESSAGE-----
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
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.
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 at yahoo.es
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 v18.104.22.168 (GNU/Linux)
-----END PGP SIGNATURE-----
More information about the Chimera-users