[Chimera-users] Doubt

Elaine Meng meng at cgl.ucsf.edu
Fri Apr 19 10:35:28 PDT 2013


Hi Victor,
Sorry, you cannot use the Chimera-Modeller interface to model-build more than one chain at a time.  The interface is relatively simple and only connects to a subset of the many calculations that Modeller can perform.

<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/modeller.html#comparative>
"Currently, only a single protein chain or subunit can be modeled at a time."

You could either do it in two separate steps, or if the dimer is very symmetrical simply model the monomer and then copy it symmetrically to make the dimer.  To do it in two separate steps, you already did the first step.  For the second step: from the sequence alignment window use Structure... Associations to change the association of the target sequence to the other chain, and then repeat the modeling.

See the "sequence-structure association" section in:
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/framemav.html>

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 Apr 19, 2013, at 3:11 AM, Víctor J. Gallardo López wrote:

> Good Morning Mr./Ms.,
> 
> I have a bit problem with the molecular modeling. I have a dímer (the two chains of this protein are the same sequence) and I want to put 34 residues at the N-terminal in each chain. I load my fasta (with this residues addition) in chimera and I blast a protein structure in the PDB that has the same residues as my protein without this addition. When I modeller (homology) my fasta, the programm only gives me one of the chain with this addition but I need the whole protein (with the two chains and with this residue addition for each chain as well). How  can I do it? I hope you resolve my problems. Thanks you for you attention.
> Sincerely,
> 
> Víctor J. Gallardo




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