[Chimera-users] Problem for docking result analysis

[Elaine Meng]

Hi Bishwajit,
Chimera tools for looking at interactions include the following (in menu under Tools... Structure Analysis):

FindHBond
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbond.html>
Find Clashes/Contacts
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclash.html>
Distances
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#distances>

The "Structure Analysis and Comparison" tutorial uses these tools and does other things to analyze binding:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html>

When you say docking results, I don't know if you mean a large number of different ligands or positions, or just one.  The tools mentioned above are useful in both situations, but we also have a tool, "ViewDock" that makes it much more convenient to look through large numbers of docking results and mark the ones that are the most interesting.  However, it depends on which program you used for docking as to whether the format of results can be read directly into this tool.  It takes multi-model PDB or multi-Mol2 as output by the program DOCK.  If you used some other program for docking, you may be able to reformat the output so it can be read into this tool.

Here is the information for ViewDock, and a ViewDock tutorial that includes sample data:
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/viewdock/framevd.html>
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/vdtut.html>

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 Apr 12, 2011, at 4:19 AM, Bishwajit Das wrote:

> Hi,
>   I load a docking results in .pdb format,now how can i view inter-molecular bonding information with chimera.
> please help me.
> BISHWAJIT DAS
>    KOLKATA