[Chimera-users] Suggestion on biological assembly load

[Miguel Ortiz-Lombardia]

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Dear all,

I have small suggestion to make that I would find helpful if implemented
in chimera:

I think it would be great if the "biological assembly" could be fetched
by ID from the File menu, just as it goes now for the pdb coordinates
file from the RCSB site.

Such assemblies are kept at the PQS database at the EBI (Cambridge). The
links there follow this syntax:

http://pqs.ebi.ac.uk/pqs-doc/macmol/<ID>.mmol

where <ID> is obviously that of the PDB structure.

Despite the extension, it is a plain PDB file. The CRYST1 record (for
crystallographic structures) of such coordinates files has been modified
to space group P1, since the crystallographic operations of the original
structure don't hold. A potential problem if these files is that they
don't seem to care about having duplicated atom numbers...

These assemblies are most often correct and validated by experiments.
However, you might want to add a caveat or, even better, an intermediate
window with a link to the place where the PQS explains how that
particular oligomer was generated and why it is considered biologically
relevant:

http://pqs.ebi.ac.uk/pqs-bin/macmol.pl?filename=<ID>


Best regards,



Miguel
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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
e-mail: molatwork at yahoo.es
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Et ainsi ne pouvant faire que ce qui est juste fût fort, on a fait que
ce qui est fort fût juste.
                                                Blaise Pascal, Pensées
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