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

Nguyen, Hieu T hn2001 at wildcats.unh.edu
Thu Apr 12 14:35:15 PDT 2018


I am trying to build a few homology models using the sequence of mouse HSP90 alpha and beta, and I have a few questions:

  1.  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?).
  2.  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?
  3.  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.


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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