[Chimera-users] Crystal contacts tool

Miguel Ortiz-Lombardia molatwork at yahoo.es
Thu Jan 18 13:28:22 PST 2007

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Hi Tom,

I agree that the first tool would be better. But I liked the spheres
representation for having a quick idea of the symmetry-related molecules
interacting. It's also extremely useful for pedagogical purposes. The
proportionality between the number of contacts and the radii of the
cylinders is such a clever idea! I will try to make a version where the
maximum radius will be assigned to the maximum number of contacts so the
differences are enhanced for crystals of proteins with a lot less
contacts than proteins in virus capsides.

I'll be waiting for that new tool, but I can understand it's not on the
top of the list ;-)

Thank you for your help!
Best regards,


En/na Thomas Goddard ha escrit:
> Hi Miguel,
>   I agree that the term non-crystallographic symmetry (NCS) can be
> confusing.  The crystal contacts Chimera tool was developed specifically
> for fixing the MTRIX records in virus entries in the PDB so the
> description uses terminology that makes sense for virus crystal structures.
>   I think the crystal contacts tool could be adapted so that the spheres
> represent individual PDB chains.  This would be similar to your earlier
> request for a tool that just displays contacting chains.  But I think
> the tool you described earlier would be better (only displays contacting
> chains from entire crystal, shows them as atomic models) and is just as
> easy to implement.  Not sure if I will have time to work on it in coming
> weeks or months -- I haven't yet scheduled it into my long list of
> projects.
>     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
e-mail: molatwork at yahoo.es
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