[Chimera-users] Homology modelling with Chimera/Modeller

Y Y yong.yin at staidsonbio.com
Tue Feb 16 10:22:14 PST 2021

Hi Elaine:

Thanks very much for your explanation.

Indeed, I am trying to model a Fc fusion protein with two chains.  Besides
Fc having 3D structures, the other receptor and ligand have their 3D
complex structures. In such a case, can the Modeller (eg. Modeller 9.24
version) alone do the modeling job?

I highly appreciate your help.

Best regards


On Tue, Feb 16, 2021 at 9:31 AM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi TW,
> The Chimera interface to Modeler is simplified so you cannot necessarily
> do any type of modeling that might be possible if you used Modeller
> directly.  I'm not completely sure either of the following would work, but
> possible things to try:
> (A) open all the separate template structures and if they don't associate
> automatically, use the Multalign Viewer (sequence viewer window)
> associations dialog to manually associate all of the structures to your
> single long fusion sequence.  Then you can choose all of them as templates.
> However, the modeling may not pay attention to the current relative
> positions of these domains in the structures.  They might be modeled in
> different orientations not interacting with each other.
> (B) If the PDB structures are already the correct sequences and all you
> are trying to do is connect them with linkers without moving them relative
> to each other, a different approach to try would be to first combine all
> the parts you want in your fusion into a single chain in a single model
> (e.g. see Model Panel function copy/combine).  Then associate that single
> chain (which will have missing segments, the linkers) with your long fusion
> sequence.  Then use the "missing loops" option of the Chimera Modeller
> interface to try to fill them without moving the existing parts relative to
> each other.
> If I misunderstood you and you are actually trying to model a complex of
> more than one chain (not just one single fusion chain), you can't use the
> Chimera interface for Modeller for that.  The interface only models single
> chains.
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> > On Feb 13, 2021, at 2:38 PM, StaidsonBio <yong.yin at staidsonbio.com>
> wrote:
> >
> > Hi:
> >
> > I am trying to do homology modelling with Chimera/Modeler for a Fc
> fusion protein, which contains three domains, one is Fc, one is receptor
> and the 3rd is ligand. Fc has many PBD structures in PDB database and the
> receptor has couple of 3D structures with the ligand as well. I used the
> fusion protein sequence to do blast in Chimera and it gave matched sequence
> files to Fc domain only, no sequence files for the receptor-ligand complex,
> even it already has couple of solved 3D crystal structure files in PDB
> database. Is there any suggestion about this issue? Can I do separately,
> use Fc domain alone as search sequence for its template and use
> receptor-ligand sequences as search sequence for its template? If it is ok,
> there are two template files. How to make them into one template file for
> modelling late?
> >
> > Thanks very much for your suggestion.
> >
> > Sincerely
> >
> > TW
> >
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