[Chimera-users] Building homology model with built-in Modeller

Elaine Meng meng at cgl.ucsf.edu
Thu Apr 12 15:25:40 PDT 2018

Dear Hieu,
Regarding your first two questions:  Sorry, using the Chimera interface, you can only model a single chain, as mentioned in the manual:
Chimera provides a simplified interface to Modeller and does not include everything you could do if you used Modeller directly.  

For the third question, yes, as long as your protein structure’s sequence is similar enough to the sequence of the target that you can align the two.  In Chimera, with your structure open and the sequence of the target already open in Multalign Viewer (you could open it from a fasta file, for example, or fetch from Uniprot), in the Multalign Viewer menu choose “Edit… Add Sequence”, and then the option From Structure.  If the resulting alignment doesn’t look good enough to you, you would need to use that same Edit menu to delete the sequence you added and then try adding it again with different alignment parameters.  (Of course, you could also use some other method outside of Chimera to make a sequence aligment between your target and template and then open that alignment file in Chimera).

Then you would have the sequence alignment in Multalign Viewer with your structure associated with its own sequence and be able to model the target.

Multalign Viewer:

Summary of different ways to get the inputs needed for comparative modeling with the Chimera-Modeller interface:

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

> On Apr 12, 2018, at 2:35 PM, Nguyen, Hieu T <hn2001 at wildcats.unh.edu> wrote:
> Dear, 
> I am trying to build a few homology models using the sequence of mouse HSP90 alpha and beta, and I have a few questions:
> 	• First I tried to build a model of mouse Hsp90 using its protein sequence and 2CG9 (a dimer) as a template. The proposed model came out as a monomer, which is understandable since the sequence provided is of a monomer. However, I am wondering if there is a way for me to build a dimer using this monomer sequence with a dimer template (write it as a dimer sequence somehow? Or there is a specific option to do this?).
> 	• I also want to build a homology model using 2IOQ as a template. However, on PDB, 2IOQ is displayed as 3 structures (biological assembly 1, biological assembly 2, asymmetrical structure). The structure I desire as a template is biological assembly 2 but when I fetched it by ID, the asymmetrical model came out and is also the template the program used. Is there a way for me to specify the template?
> 	• I have a protein model of my own that is not on PDB. Is there a way for me to use my structure as a template for the sequence? If yes, how would I do so?
> Please let me know as soon as possible. Thank you very much.
> Sincerely,
> Hieu Nguyen 
> Research Assistant - Resident Assistant
> University of New Hampshire '18
> Biochemistry, Molecular and Cellular Biology
> Department of Molecular, Cellular and Biomedical Sciences

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