need some scripts from chimera source code
Hi all I am working on a project that requiring some program scripts concerning with 1) Compute Amber Energy Function 2) Read rotamer information from the Dunbrack Backbone-dependent Rotamer library 3) Read in Electron Density Map and get the density value for each 3-D point in the crystal I did check some related python files in the source code folder and can understand them to some extent, but for running these files, some modules (e.g. Chimera, Rotamers) are needed. However, I don't know how to install these modules, or maybe I should recompile Chimera from source code first(If so, then how, because I don't know the procedure either. BTW, my platform is mac osx)? Could someone show me which files I should use for the above mentioned three subjects and what kinds of modules I should install and how? Thank you so much and sorry for disturbing others. Yang
On Jun 19, 2009, at 6:04 PM, ylei@ecs.umass.edu wrote:
Hi all
I am working on a project that requiring some program scripts concerning with
1) Compute Amber Energy Function 2) Read rotamer information from the Dunbrack Backbone-dependent Rotamer library 3) Read in Electron Density Map and get the density value for each 3-D point in the crystal
I did check some related python files in the source code folder and can understand them to some extent, but for running these files, some modules (e.g. Chimera, Rotamers) are needed. However, I don't know how to install these modules, or maybe I should recompile Chimera from source code first(If so, then how, because I don't know the procedure either. BTW, my platform is mac osx)?
Well, Chimera is itself a Python interpreter. So if you open a Python script (ending in .py) with either File->Open or with the "open" command then Chimera will run that script. The script can import any of the modules provided by Chimera (e.g. "import chimera" or "import Rotamers"). If you need to run a script without Chimera's interface coming up or need to provide arguments to your script, see the "-- nogui" and "--script" arguments (respectively) documented here: http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/options.html
Could someone show me which files I should use for the above mentioned three subjects and what kinds of modules I should install and how?
For (1), we would need more details. What are you trying to do? Compute charges? Minimize structures? For (2) you would use the Rotamers module, probably either the getRotamers function or the useBestRotamers function, depending on your needs. For (3) I think we would need a better description of what you are trying to accomplish, but you can certainly open a density map with: from chimera import openModels density = openModels.open("map_file_name_with_proper_suffix")[0] I'm not an expert on how to get the density value at a point, but maybe Tom Goddard from our lab (who wrote the volumetric data code) will chime in on how to do that. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
There is a Chimera tool called "Values at Atom Positions" which interpolates density map values at atom positions and can use those values to color the atoms or select only those in high density. That code is all in Python and is a good example of how to interpolate density values at specific points. Look at the Python code in any Chimera distribution in chimera/share/AtomDensity/__init__.py in particular the set_atom_volume_values() routine. On the Mac this file will be in Chimera.app/Contents/Resources/share/AtomDensity. Tom Eric Pettersen wrote:
On Jun 19, 2009, at 6:04 PM, ylei@ecs.umass.edu <mailto:ylei@ecs.umass.edu> wrote:
Hi all
I am working on a project that requiring some program scripts concerning with
1) Compute Amber Energy Function 2) Read rotamer information from the Dunbrack Backbone-dependent Rotamer library 3) Read in Electron Density Map and get the density value for each 3-D point in the crystal
I did check some related python files in the source code folder and can understand them to some extent, but for running these files, some modules (e.g. Chimera, Rotamers) are needed. However, I don't know how to install these modules, or maybe I should recompile Chimera from source code first(If so, then how, because I don't know the procedure either. BTW, my platform is mac osx)?
Well, Chimera is itself a Python interpreter. So if you open a Python script (ending in .py) with either File->Open or with the "open" command then Chimera will run that script. The script can import any of the modules provided by Chimera (e.g. "import chimera" or "import Rotamers"). If you need to run a script without Chimera's interface coming up or need to provide arguments to your script, see the "--nogui" and "--script" arguments (respectively) documented here: http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/options.html
Could someone show me which files I should use for the above mentioned three subjects and what kinds of modules I should install and how?
For (1), we would need more details. What are you trying to do? Compute charges? Minimize structures?
For (2) you would use the Rotamers module, probably either the getRotamers function or the useBestRotamers function, depending on your needs.
For (3) I think we would need a better description of what you are trying to accomplish, but you can certainly open a density map with:
from chimera import openModels density = openModels.open("map_file_name_with_proper_suffix")[0]
I'm not an expert on how to get the density value at a point, but maybe Tom Goddard from our lab (who wrote the volumetric data code) will chime in on how to do that.
--Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
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participants (3)
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Eric Pettersen -
Thomas Goddard -
ylei＠ecs.umass.edu