ADL: Rotating Grid Box and Sensitivity Tweaks

Jeffrey Dyason j.dyason at griffith.edu.au
Mon Aug 6 14:21:43 PDT 2007


Andrew,
        I've not found any easy way to rotate the orientation of the grid 
box but the tedious way is to change the coordinate space of your protein 
in a modelling program (I've used InsightII) by aligning it to a 
particular view and then saving the transformed coordinates.


Bye Jeff.
-----------
Jeff Dyason                                    e-mail: 
J.Dyason at griffith.edu.au
Institute for Glycomics http://www.griffith.edu.au/glycomics
Griffith University                          (Gold Coast Campus)  
PMB 50 Gold Coast Mail Centre       Tel: +61 7 5552 7028
Queensland 9726 Australia              Fax: +61 7 5552 8098



Andrew Fant <fant at moleculargeek.com> 
Sent by: autodock-bounces at scripps.edu
07/08/07 06:18 AM
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autodock at scripps.edu; Please respond to
fant at moleculargeek.com


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Subject
ADL: Rotating Grid Box and Sensitivity Tweaks






Good Afternoon All,
   I have two autodock questions that I could appreciate some feedback on, 
one
relatively simple, and one I fear that may not be.

Is there an easy, graphical method to rotate the orientation of the grid 
box
that is set up in ADT?  I realize that this might be non-trivial because 
by this
point the pdbqt files for receptor and ligand have already been set up 
using
that coordinate frame, but it would be nice if possible.  I have a model 
of a
receptor with a long rectangular binding region that naturally runs along
essentially the diagonal of a binding cube, and I spend a lot of time 
doing dock
searches in areas that aren't particularly useful.





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