Hello: 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? If already answered, beg pardon. thanks francesco pietra
If not clear, the template here is the fasta file. I wonder where Sali's modeller allows filling residues in a multimer by also taking into account the inetraction between the different subunits. Not seen any example. francesco pietra ---------- Forwarded message ---------- From: Francesco Pietra <chiendarret@gmail.com> Date: Sun, Jun 23, 2013 at 7:17 AM Subject: modeling multimers To: chimera <chimera-users@cgl.ucsf.edu> Hello: 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? If already answered, beg pardon. thanks francesco pietra
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@salilab.org http://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle
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/mod...> 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@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@salilab.org http://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle
participants (3)
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Ben Webb -
Elaine Meng -
Francesco Pietra