meng at cgl.ucsf.edu
Mon Jun 26 09:48:02 PDT 2006
Currently Chimera does not do any energy minimization or even
avoidance/resolution of steric conflicts. However, these are
definitely under consideration as future developments.
On Jun 26, 2006, at 9:41 AM, Goel, Manisha wrote:
> 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
> (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:
>> Is it possible in chimera to define a new amino acid residue? Also,
>> 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,
>> Chimera-users mailing list
>> Chimera-users at cgl.ucsf.edu
> 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
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
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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