[Chimera-users] Dimer construction from a monomer generated using Modeller

Markl, Prof. Dr. Juergen markl at uni-mainz.de
Fri Mar 19 12:17:52 PDT 2010

I solve comparable problems as follows:
First I store the new trimer in Chimera as a single pdb file, but it would open as three sub-files which is not accepted by Modeler as template.
I open the pdb file in a text editor and delete the "model 1", "model 2" etc lines als well as the "ENDMDL" lines from the pdb text file, in order to obtain a pdb file of the trimer that opens in Chimera as a true single file.
I use this new pdb file of the  trimer as template to remodel (in Modeller) the sequence of the trimer (i.e. the three consecutive sequences of the monomers). In the resulting homology model, all secondary structures are unchanged, but the loops at the interfaces do not overlap any more, because Modeller prevents this. 
Of course the true conformation of these loops remaines unknown. However, we use such molecular models for fitting them into cryoEM densities, and the latter hopefully give us information about the shape of the loop.
Best regards

Von: chimera-users-bounces at cgl.ucsf.edu [chimera-users-bounces at cgl.ucsf.edu] im Auftrag von Elaine Meng [meng at cgl.ucsf.edu]
Gesendet: Freitag, 19. März 2010 18:58
An: akshita kumar
Cc: chimera-users at cgl.ucsf.edu
Betreff: Re: [Chimera-users] Dimer construction from a monomer generated        using Modeller

Dear Akshita,
I don't think this is something you can handle effectively with
Chimera.  Instead, it might be possible to:

(a) from the trimer of the model you have now, re-model just the loops
using Modeller so they don't conflict with each other
- OR -
(b) instead of modeling a monomer from the template monomer, use
Modeller to model a trimer starting from a template trimer, which
might also the loops more sensibly

However, I don't know either of these things can be done, or how to do
them, since I don't have direct experience.  You might try asking on
the Modeller forum:

Good luck,
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Mar 19, 2010, at 3:33 AM, akshita kumar wrote:

> Dear Members,
> Using 1T3D as template, we have generated a homology model via
> Modeller. As the biological unit is a trimeric structure we need to
> generate trimer of the model too. Therefore we undertook structural
> alignment of the model and individual template 1T3D chains ("a, b ,
> c"). However in our model the loop region that falls at the
> interface between two dimers is much  longer and as a result the
> loops between dimer overlap each other.
> Can anybody please suggest a solution for generating a dimer/trimer
> from the monomer built using homology modelling.
> Thanks
> Akshita
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