[Chimera-users] Splitting surfnet surfaces and calculate enclosed volume.

[Jean-Didier Maréchal]

Hi everyone,

I would like to calculate the volume of the main pocket provided by a
surfnet calculation performed on a given selection. The resulting
calculation returns me different pockets of variable sizes. And I have
two small questions:

1. Is there a way to split the resulting surfaces in individual size
ranked entities so that I can calculate the volume of each of them? 
2. What would be the easiest way to call the mv accelerator function
from the python shell (whether by a command emulation or a directly
importing a module)?

Cheers,
JD

On Tue, 2008-03-25 at 12:00 -0700, chimera-users-request at cgl.ucsf.edu
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> Today's Topics:
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>    1. pdb to density map function (Jeff Triffo)
>    2. Re: pdb to density map function (Elaine Meng)
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> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Mon, 24 Mar 2008 20:56:21 -0700
> From: Jeff Triffo <triffo at rice.edu>
> Subject: [Chimera-users] pdb to density map function
> To: chimera-users at cgl.ucsf.edu
> Message-ID: <47E877E5.4020501 at rice.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> 
> hi,
> 
> I think I recall seeing information about a pdb -> density map function 
> (like an MRC density map). is this currently implemented/contained 
> within Chimera? I can use an outside program to do this, but if it is 
> already in Chimera I would prefer to do that.
> 
> thanks,
> 
> -Jeff
> 
> 
> 
> ------------------------------
> 
> Message: 2
> Date: Tue, 25 Mar 2008 09:03:29 -0700
> From: Elaine Meng <meng at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] pdb to density map function
> To: Jeff Triffo <triffo at rice.edu>
> Cc: chimera-users at cgl.ucsf.edu
> Message-ID: <638CF385-92E5-4E11-8875-C5D9682073F5 at cgl.ucsf.edu>
> Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed
> 
> 
> 
> On Mar 24, 2008, at 8:56 PM, Jeff Triffo wrote:
> > hi,
> > I think I recall seeing information about a pdb -> density map  
> > function
> > (like an MRC density map). is this currently implemented/contained
> > within Chimera? I can use an outside program to do this, but if it is
> > already in Chimera I would prefer to do that.
> > thanks,
> > -Jeff
> >
> 
> Hi Jeff,
> Yes, there is a "molmap" command in recent versions:
> http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html
> 
> In addition, the "Fit in Map" tool can use the same functionality to  
> simulate a map from atomic coordinates and then use map-in-map fitting:
> http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/fitmaps/ 
> fitmaps.html
> 
> These features were added after the November production release but  
> are available in recent daily builds:
> http://www.cgl.ucsf.edu/chimera/alpha-downloads.html
> 
> Best,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
> UCSF Computer Graphics Lab 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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> End of Chimera-users Digest, Vol 59, Issue 24
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