[Chimera-users] [chimera-dev] Loop refinement in chain A and Chain B

[Elaine Meng]

Hi Aashish,
The address for questions about using Chimera is chimera-users at cgl.ucsf.edu (CC’d here).  Chimera-dev is for programming questions.

It sounds like you did find the “model/refine loops” dialog for using the Modeller web service.  

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

In that dialog, you would need to choose either “non-terminal missing structure” (if the missing residues are in the middle) or “all missing structure” (if some of the missing residues are in the termini), and also enter a license key for running Modeller.

However, I have no idea what you mean by “not running,” so I can’t give any more help than that.  

Also, be aware that in Chimera using this dialog, you can only model one chain at a time.  I.e. when it is adding the residues to chain A it does not care if they are in a bad place relative to chain B, and vice versa.

Our newer program ChimeraX has the advantage that you can sensibly model the dimer using the Modeller web service, with the two chains “seeing” each other.   However, to use that you would have to download and learn a different program. 
<http://www.rbvi.ucsf.edu/chimerax/index.html>
<http://www.rbvi.ucsf.edu/chimerax/download.html>
<http://www.rbvi.ucsf.edu/chimerax/docs/user/tools/modeller.html#comparative>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On May 6, 2019, at 5:39 AM, Aashish Bhatt <aashish.ph16221 at inst.ac.in> wrote:
> 
> Dear Sir/ Ma'am
> 
> I have dimer PDB structure in which 40 amino acid is missing in both chain A and B.
> Is it possible to make a model with a chimera? I have tried the same with chain A and but it is not running.
> 
> Can you please give me an idea of how to build the complete structure?
> 
> Best regards
> 
> Aashish 
> INST-Mohali
> India