[Chimera-users] creating multimeric units

[Elaine Meng]

Hi Alexander, 
It depends on the information in the PDB file: there may be various matrices in the header that describe how to generate the biological multimer (BIOMT), or copies related by crystallographic symmetry (SMTRY or CRYST1), or copies related by noncrystallographic symmetry (MTRIX).  

If information of one of those types is present and describes the dimer, you can make the dimer in Chimera with Multiscale Models or Unit Cell (both are under Tools... Higher-Order Structure) or the command "sym"
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html>
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/unitcell/unitcell.html> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multiscale/framemulti.html> 

If the structure is in the PDB but symmetry information is not included in the file, you could try using Chimera's File... Fetch by ID, PQS option (predicted quaternary structure database) or getting the biological unit directly from the PDB website.

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

On Jul 24, 2011, at 5:03 AM, ALEXANDER MUCHUGIA wrote:

> Hi, 
> My name is Alexander Muchugia, I am a Bioinformatics student at Rhodes University, South Africa and I am working on modelling HIV protease.
> It is a dimer but Its modelled as a monomer. I was trying to look for software than can convert it as a dimer. I am enquiring if it is possible to use chimera to do it and how can I do it.
>  
> Regards.
>  
> Alexander.
>  
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