[Chimera-users] question

Goel, Manisha MAG at stowers-institute.org
Mon Jun 26 09:41:49 PDT 2006

Hi Elaine,

I too have been looking for a good protein-protein docking program, so I
am jumping on the bandwagon ..
Just small question regarding point 2 in the mail ..
Does chimera do any minimization/optimization of the complex after we
manually dock the two protein together ?
Thanks a lot for your help..


-----Original Message-----
From: chimera-users-bounces at cgl.ucsf.edu
[mailto:chimera-users-bounces at cgl.ucsf.edu] On Behalf Of Elaine Meng
Sent: Monday, June 26, 2006 11:34 AM
To: Jaya Bhatnagar
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] question

Dear Jaya,
(1) Chimera will display whatever coordinates and residue names are  
present in the input file.  It does not matter if the residues or the  
atoms in them are standard or not.  However, you cannot define new  
residues to be built by Chimera with the "swapaa" or "addaa" commands.

We have recently added a Build Structure tool (Structure Editing  
category) that lets you add arbitrary atoms and bonds to structures  
interactively.  It is in the early stages of development, however,  
and is likely to change in the future.  If you use this, you may want  
to check the bond lengths and adjust them in the "Set Bond Length"  
section of the Build Structure tool.  The man page for Build Structure:

(2) Chimera does not do any automated docking.  However, you can  
manually/interactively dock structures by moving one relative to the  
other (to freeze a structure and move only the others, you would  
uncheck its Active button in the Model Panel or its checkbox under  
the Command Line).
The man page for the Model Panel:

(3) I believe there is no limit on the number of amino acids present  
in the protein.  There may be limitations due to the input file  
format (that is, the residue number column can only be a certain  
width in the input file format, usually PDB).  However, in  
combination with use of different chain IDs this limit is quite  
high.  For example, ribosome structures can be viewed in Chimera,  
although it may take a while for the structure to load.

I hope this helps,

On Jun 23, 2006, at 8:06 AM, Jaya Bhatnagar wrote:

> Hi,
> Is it possible in chimera to define a new amino acid residue? Also,
> what
> algorithms does it support involving docking of two proteins? And  
> is there
> a limit on number of amino acids present in the protein?
> thanks a lot,
> Jaya
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu 
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

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