[Chimera-users] Chimera and docking (original subject: Command File)

[Muhammad ALi]

Hisir very very much thanx for help and i have don a lot of with chimera.., i have an other question that can we make a DNA model with chimera??? if we can then how?? m waiting ,,,,,

--- On Thu, 4/4/13, Elaine Meng <meng at cgl.ucsf.edu> wrote:

From: Elaine Meng <meng at cgl.ucsf.edu>
Subject: Chimera and docking (original subject: Command File)
To: "Muhammad ALi" <muh.ali741 at yahoo.com>
Cc: "chimera" <chimera-users at cgl.ucsf.edu>
Date: Thursday, April 4, 2013, 10:03 PM

Hello,
ViewDock is for viewing results from a docking calculation.  It is interactive and does not require any command file.  However, it does require results (an output file) from docking.  It will read output from a few different docking programs, including DOCK, Autodock, GOLD, Glide, etc. as described in the ViewDock manual page:
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/viewdock/framevd.html>

See also the ViewDock tutorial, which includes an example output file from the DOCK program:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/vdtut.html>

If you are actually trying to do a docking calculation, you will need to look at the website of some docking program instead of Chimera.  For example, DOCK is available for download, and it also has tutorials:
<http://dock.compbio.ucsf.edu/index.html>
<http://dock.compbio.ucsf.edu/DOCK_6/tutorials/index.htm>

Chimera 1.7 includes an AutoDock Vina tool that does docking using a web service, but it is limited to finding only a few positions of a single ligand:
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html>

* Before trying to do docking you should probably spend some time learning how to use Chimera (or any molecular graphics and analysis program), because if you don't understand what is in the input structures, or do not prepare them correctly for docking calculations, the docking results may not be meaningful. *

For learning how to use Chimera, see here:
<http://www.cgl.ucsf.edu/Outreach/Tutorials/GettingStarted.html>
... and the tutorials in the User's Guide (Chimera menu: Help... Tutorials), also visible here:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/frametut.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 4, 2013, at 3:24 AM, Muhammad ALi wrote:

> AOA 
>   
>  Sir kindly tell me how to make a command file (containing required commands) for viewdock

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