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@cgl.ucsf.edu wrote:
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Today's Topics:
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@rice.edu> Subject: [Chimera-users] pdb to density map function To: chimera-users@cgl.ucsf.edu Message-ID: <47E877E5.4020501@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
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Message: 2 Date: Tue, 25 Mar 2008 09:03:29 -0700 From: Elaine Meng <meng@cgl.ucsf.edu> Subject: Re: [Chimera-users] pdb to density map function To: Jeff Triffo <triffo@rice.edu> Cc: chimera-users@cgl.ucsf.edu Message-ID: <638CF385-92E5-4E11-8875-C5D9682073F5@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@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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