[Chimera-users] Suggestion on biological assembly load

[Miguel Ortiz Lombardia]

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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 at yahoo.es
www: http://www.pangea.org/mol/spip.php?rubrique2
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