[Chimera-users] modeling multimers

Ben Webb ben at salilab.org
Sun Jun 23 19:00:44 PDT 2013

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 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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