[Chimera-users] Dock?

Eric Pettersen pett at cgl.ucsf.edu
Thu Oct 19 11:24:35 PDT 2006

Hi Josh,
	We don't currently have plans to make a comprehensive Chimera  
frontend to DOCK, where you never have to leave Chimera to start your  
DOCK run.  Something like that would require extremely close  
coordination between the Chimera and DOCK teams, since every change  
or addition to DOCK input parameters or status messages would need to  
be reflected in the frontend (and undoubtedly explained in the  
frontend documentation as well).  What we have done to date and will  
continue to do is develop tools to assist in the preparation of DOCK  
input and assessment of DOCK output.  Right now the Dock Prep tool  
cleans up, protonates, and assigns charges to a receptor for use in a  
DOCK run, and ViewDock allows you to browse through and analyze your  
DOCK results.
	Improvements we anticipate making in the nearer term include:  using  
a rotamer library to fill out missing side chains (they are currently  
truncated to glycine/alanine) and optionally minimize them; have  
Chimera create the MS surface file (with normals) directly so that  
using DMS is no longer necessary; and making a tool to visualize  
sphgen output and allow interactive pruning of unwanted spheres and  
writing a new sphere file.
	Some of these capabilities aren't necessarily DOCK-specific.  For  
instance, Dock Prep's result is a Mol2 file that could be used in a  
variety of programs.


                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         pett at cgl.ucsf.edu

On Oct 19, 2006, at 12:49 AM, S Joshua Swamidass wrote:

> Hello,
> Are there any plans to develop a gui frontend for DOCK using chimera?
> Josh
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

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