[Chimera-users] modeling multimers

Elaine Meng meng at cgl.ucsf.edu
Mon Jun 24 09:45:00 PDT 2013


Hi Francesco,
The Chimera-Modeller interface does not handle modeling multiple chains, only one chain at a time. This is mentioned in the documentation:

<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/modeller.html#comparative>

As Ben mentioned, you can model multimers using Modeller directly (outside of Chimera). The Chimera interface is meant to be relatively simple, and only handles a subset of what Modeller can do.
Best,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jun 23, 2013, at 7:00 PM, Ben Webb <ben at salilab.org> wrote:

> On 6/22/13 10:17 PM, Francesco Pietra wrote:
>> Modeling a trimer (all three chains present, though missing residues and
>> atoms) with chimera and modeller installed locally.
>> 
>> The default is modeling each chain, one at a time. The chains are
>> identical in sequence but the X-ray structure shows different localized
>> conformations. Question: is modeller modeling by taking the other two
>> chains into account?
> 
> The Modeller mailing list would be more appropriate for such a question (unless it's specific to the Chimera Modeller interface). If you want to model a trimer using a trimer template, you don't need to do anything special (just include the entire sequence of each trimer, with '/' chain break characters where appropriate). Modeller will consider all interatomic distances. (If the Chimera Modeller interface isn't doing this, the Chimera people may want to comment further.)
> 
> If you want Modeller to model (e.g.) chain A using structural information from each of chains A, B, and C, that's just multiple template modeling (using A, B, and C as templates for A).
> 
> 	Ben
> -- 
> ben at salilab.org                      http://salilab.org/~ben/
> "It is a capital mistake to theorize before one has data."
> 	- Sir Arthur Conan Doyle




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