Splitting surfnet surfaces and calculate enclosed volume.
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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On Mar 26, 2008, at 11:12 AM, Jean-Didier Maréchal wrote:
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
Hi JD, In recent versions of Chimera (newer than the production release in November 2007... get a daily build), you can measure the surface area and enclosed volume of each separate "blob" with "Measure and Color Blobs": http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/pickblobs/ pickblobs.html It doesn't give you a ranked list, however; you just have to click on each blob you want to measure. The surface area and volume are computed directly from the surface triangle positions. I should mention the new "CASTp fetch" capability: it looks up a structure in the CASTp database and brings up a table of all the pockets, their surface areas and volumes, and pocket mouth measurements. It is most excellent, the main limitation being that not all PDBs are in that database. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/castp.html You can fetch from CASTp with File... Fetch by ID, or with a command such as: open castp:4enl open castp:2gsh.A (the latter showing how to get results for just a particular chain). I will have to leave question #2 to someone else! I hope this helps, 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
Hi JD, You can split the surfnet surface into separate selectable pieces by selecting the whole surface (ctrl-left-button) then using keyboard shortcut "Sc" (split connected pieces). You have to enable keyboard shortcuts with menu entry Tools / General Controls / Accelerators On. After this you can select individual pieces and measure their volumes with the "mv" shortcut. You can select all of the pieces and use "mv" to get a list of volumes for all the pieces. "ma" lists areas. Each piece is numbered and you that number will be shown in a pop-up if you the mouse over it. You can run the measure volumes shortcut (mv) from Python code using: import MeasureVolume MeasureVolume.report_selected_volumes() This code is in your Chimera distribution in chimera/share/MeasureVolume/__init__.py. Tom
Great! Both answers have been useful! Just two small questions: 1. Is it possible to call for an accelerator from the python shell using runCommand? 2. Could I rename the individual surfaces? Cheers! JD On Wed, 2008-03-26 at 12:04 -0700, Tom Goddard wrote:
Hi JD,
You can split the surfnet surface into separate selectable pieces by selecting the whole surface (ctrl-left-button) then using keyboard shortcut "Sc" (split connected pieces). You have to enable keyboard shortcuts with menu entry Tools / General Controls / Accelerators On. After this you can select individual pieces and measure their volumes with the "mv" shortcut. You can select all of the pieces and use "mv" to get a list of volumes for all the pieces. "ma" lists areas. Each piece is numbered and you that number will be shown in a pop-up if you the mouse over it.
You can run the measure volumes shortcut (mv) from Python code using:
import MeasureVolume MeasureVolume.report_selected_volumes()
This code is in your Chimera distribution in chimera/share/MeasureVolume/__init__.py.
Tom
Hi JD, There is no Chimera command to run an accelerator. Would be handy. I'll add that to the requested feature list. There is no user interface to rename surface pieces. You can do it from Python with code like: plist = m.surfacePieces plist[0].oslName = 'filament 3' Here m is a SurfaceModel object and plist is the list of SurfacePiece objects. Setting the oslName changes the name shown in the popup balloon when the mouse is over that surface piece. There isn't any other code that uses surface piece names (e.g. no dialog that lists the surface piece names to allow you to select them, and no way to select a piece using its name). So the names are currently not too useful. Also there is no file format for saving the surface pieces. Lots of limitations. Tom
Hi JD, I enhanced the Chimera command "ac" so you can specify accelerators to run as arguments. For example the command ac ol ce sf will open the last opened file, color by element, and display a molecular surface. This can be used from Python using from chimera import runCommand runCommand("ac ol ce sf") Formerly the "ac" command just enabled typing shortcuts in the main Chimera window and took no arguments. The improved version will be in tonight's daily builds (if they succeed). Tom
participants (4)
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Elaine Meng -
Jean-Didier Maréchal -
Thomas Goddard -
Tom Goddard