[Chimera-users] [Fwd: Re: [Dock-fans] DMS replacement]

[Elaine Meng]

Hi Christian,
We're glad you like the "Write DMS" tool in Chimera!
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/dms.html#writedms>

Note that it does not run a surface calculation, but simply converts  
the molecular surface already shown in Chimera into the DMS format for  
output.  Thus it effectively uses whatever parameters you had used to  
calculate the molecular surface in Chimera.  That is currently done  
with MSMS (included with Chimera), a different program than DMS with  
different heuristics, so even with the most similar parameters  
possible I don't think the dots would be in exactly the same places  
even though the surfaces would basically coincide.  More about  
molecular surfaces in Chimera:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/representation.html#surfaces 
 >

If you used Chimera defaults for surface calculation, the probe radius  
is the same as the DMS default (1.4 Angstroms), but the atomic radii  
and dot density are different.

The dms man page says the default density gives about 5 dots per  
square Angstrom.
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/dms1.html>
You could set the Chimera molecular surface vertex density to 5  
(instead of the default 2) to be similar to the dms default.  To  
change an existing surface, Ctrl-click to select it and then  for  
"MSMS surface" in the Selection Inspector (Actions... Select) change  
the "vertex density" value.  If you want to change the Chimera  
defaults so that future surfaces will be created with that density,  
choose Favorites... Preferences, go to the "New Surfaces" category,  
change the value, click Save.
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/preferences.html#New%20Surfaces 
 >

Default atomic radii in Chimera:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vdwrad.html>
I don't believe the old DMS default radii are necessarily better than  
the Chimera default atomic radii, but if you really wanted to set the  
radii in Chimera to these values, it can be done with the "Define  
Attribute" tool or the command "defattr" along with the attribute  
assignment file dmsrad.txt attached below (it is a very small, simple  
text file).
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defineattrib.html 
 >

I personally favor having Write DMS as a separate tool from Dock Prep  
because I think people should display the surface, adjust which part  
is displayed (since there is a nice option to only write what is  
displayed), and possibly change the surface calculation parameters  
rather than clicking a single button on Dock Prep to just do  
everything and write the whole surface without tailoring it to the  
situation.
Best,
Elaine
-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html

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>
> From: Christian Schudoma <schudoma at mpimp-golm.mpg.de>
> Date: October 2, 2008 5:48:57 AM PDT
> To: "dock-fans at docking.org" <dock-fans at docking.org>
> Subject: Re: [Dock-fans] DMS replacement
>
> I think WriteDMS is a very nice new feature for Chimera. Does it run
> with the same default parameters as the original dms?
>
> 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?
>
> Thanks & best regards,
> Christian
>