[Dock-fans] resend: rotation angles in DOCK?

Trent E. Balius tbalius at aol.com
Mon Mar 4 07:49:45 PST 2013


 Hi Chinh

DOCK6 does not output this information.  You could modify the source code to have it print this information.

I would suggest that you output the orients (write_orientations yes) or write out the growth trees (write_growth_tree yes) and calculate the translation rotation matrix using a different program by performing an alignment: I believe that Chimera will calculate this.

See the following for more information:

http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#LigandFileOutput
http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#GrowthTreeAndStatistics
http://www.cgl.ucsf.edu/pipermail/chimera-users/2007-August/001744.html


I hope that this helps,

Trent

 

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Trent E. Balius, PhD
Shoichet Lab – Dept. of Pharm Chem,
University of California, San Francisco
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           San Francisco, CA 94158     
Office: Byers Hall, Rm 509
URL: http://docking.org/~tbalius
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-----Original Message-----
From: Chinh Su Tran To <chinh.sutranto at gmail.com>
To: dock-fans <dock-fans at docking.org>
Sent: Mon, Mar 4, 2013 2:02 am
Subject: [Dock-fans] resend: rotation angles in DOCK?


Hi, 




I'm sorry for this duplicate email (if it is) since the previous email was failed to deliver.


I'd like to ask if it is possible to obtain the rotation angles and translation of my docking.
In the dock results which came as mol2 format, I could not obtain these infor.


Could anyone please show me any references/suggestion how to do those as I could not find any similar thread in the archive?


Thank you.
Chinh



 
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