[Chimera-users] question

[Elaine Meng]

Hi Manisha,
Currently Chimera does not do any energy minimization or even  
avoidance/resolution of steric conflicts. However, these are  
definitely under consideration as future developments.
Best,
Elaine

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..
>
>
>
> Regards,
> -Manisha
>
>
>
>
>
>
> -----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:
> http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/
> editing.html
>
> (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:
> http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html
>
> (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,
> Elaine
>
> 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
>                       http://www.cgl.ucsf.edu/home/meng/index.html
>
>
>
>
> _______________________________________________
> 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
                      http://www.cgl.ucsf.edu/home/meng/index.html