[Dock-fans] DMS replacement

[Eric Pettersen]

Christian Schudoma wrote:
> I think WriteDMS is a very nice new feature for Chimera.

Thanks!

> Does it run
> with the same default parameters as the original dms?

Since all the DMS parameters except for "-n" (include normals) dealt  
with the the creation of the surface, they are moot in Chimera.  Write  
DMS works off a surface you've created in Chimera -- and such surfaces  
have controls for the same things as the DMS parameters.  Inclusion of  
the normals is controlled by a checkbox on the Write DMS interface.

> Also, I wonder if it would be possible to integrate WriteDMS into the
> DockPrep tool? Maybe add an option there to run surface generation and
> WriteDMS automatically when DockPrepping a molecule?

Since we anticipate people wanting to only write out the DMS  
associated with a binding pocket, and therefore needing to undisplay  
the surface of other areas, we didn't think it really fit into the  
Dock Prep work flow and worked better as a separate tool.

--Eric


                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         http://www.cgl.ucsf.edu


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