June 2013 - Chimera-dev - RBVI Mailing Lists

Re: [chimera-dev] Chimera/Python sparse matrices
by Greg Couch 06 Dec '13

06 Dec '13

On 8/13/2010 12:06 PM, Forbes J. Burkowski wrote: > What are the steps that need to be taken if the Python used in Chimera is > to have the ability to import functions from SciPy or PySparse? > > Thanks for any advice that you can provide. > > Cheers, > Forbes Burkowski If you want to use prebuilt SciPy binaries with chimera, you need one that is compatible with the version of chimera that chimera is using. Chimera 1.4.x uses Python 2.5, and the daily builds use Python 2.7. You would add those packages to chimera by either (1) given the '--pypath dir' command line option, (2) setting your CHIMERAPTH environment variable (instead of PYTHONPATH, PYTHONPATH is ignored so chimera won't be accidentally broken by other installed Pythons), or (3) add the installation directory to sys.path in Python. If you're not using a daily build on Linux, then you should edit CHIMERA/share/chimeraInit.py and comment out or remove the part that sets the RTLD_GLOBAL flag -- it appears to be no longer needed and its presence breaks SciPy. If you're going to compile from source, which you'll need to do if you're using a daily build, I'd recommend trying PySparse first, since it is a smaller package. Python packages that incorporate C (or C++ or Fortran) code are more difficult than prebuilt binaries because (a) you need a compiler, and (b) if the code calls the Python C API, you need a compatible compiler, ideally the same one as what the rest of Chimera was build with. PySparse needs BLAS and LAPACK libraries and optionally wants UMFPACK and/or SuperLU. On on Redhat and Fedora Linux, you can get the first three libraries by installing the blas-devel, lapack-devel, and suitesparse-devel packages. Chances are you'll be able to install PySparse into chimera's python by running "CHIMERA/bin/pythonXXX setup.py install" in the pysparse source tree (where CHIMERA is the path to where chimera was installed). On Linux, you might have to set the LD_LIBRARY_PATH environment variable to CHIMERA/lib. On Mac OS X, the path to the chimera binary is CHIMERA/Contents/Resources/bin/pythonXXX and the environment variable is DYLD_LIBRARY_PATH. Or you could install PySparse into another Python and use the --pypath/CHIMERAPATH/sys.path approach as given above. Hope this helps, Greg

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volume viewer/mouse
by Dougherty, Matthew T 08 Jul '13

08 Jul '13

I am trying to write some python scripts relating to volume viewer. two things I need to have are: 1) the ability to figure out what dataset is active on the volume viewer. I will manually pick that with the mouse, my python sw will process the active model in volume viewer. 2) on the selected dataset I need to know what the min/max values are. In a unrelated problem: lately I completely avoid changing the camera scale value, I always want it to be 1.0. The mouse scroll wheel changes the scale value, so I am having accidental changes to camera scale values. How do I halt wheel commands from changing scale? under preferences/mouse I have "use mouse scroll wheel" set to false. side note: I just bought a logitech G600 mouse which has 12 buttons on the mouse that can be programmed through mode (3) and shift(2) buttons to have 12*3*2 active buttons that I can set to accelerator commands. So one of my modes will be dedicated to volume viewer controls, another for stereo/dome/camera, the other is general chimera commands. Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine

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Re: [chimera-dev] Rosetta cryoEM model refinement plug-in
by Tom Goddard 18 Jun '13

18 Jun '13

Hi David, Ok, I'll discuss details with Frank. Tom On Jun 18, 2013, at 11:02 AM, David Baker wrote: > Hi Tom, > > thanks for getting back to us so quickly! Ideally perhaps you could write it with our help. We've gotten requests from collaborators that we make our method available in this way. Frank is the expert and has a picture of how this could work – – perhaps the two of you could discuss? > > Best regards, > > David > > > On Jun 18, 2013, at 10:11 AM, Tom Goddard wrote: > >> Hi David, >> >> I develop the EM map tools in Chimera and am happy to discuss making a Rosetta refinement plugin. Could you tell me what setup steps you think would be done in Chimera? I guess the refinement will take minutes to hours. Do you want Chimera to show the progress during the refinement? Is there specific analysis of the refinement result that you want to show in Chimera, e.g. coloring bad fit areas red? Do you plan on writing this plugin with our help or do you want us to write it? And have you published articles on the methodology you want the plugin to follow? >> >> Tom Goddard >> >> >> On Jun 17, 2013, at 4:52 PM, David Baker wrote: >> >>> hello, we are interested in having a rosetta-cryoEM plugin to chimera that would allow users to refine models into maps with Rosetta through a button on chimera (or other simple interface). who would be good to discuss this with? thanks, David and Frank >>> _______________________________________________ >>> Chimera-dev mailing list >>> Chimera-dev(a)cgl.ucsf.edu >>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev >>> >> > >

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(no subject)
by David Baker 18 Jun '13

18 Jun '13

hello, we are interested in having a rosetta-cryoEM plugin to chimera that would allow users to refine models into maps with Rosetta through a button on chimera (or other simple interface). who would be good to discuss this with? thanks, David and Frank

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developing my own trajectory parser
by Dennis N Bromley 03 Jun '13

03 Jun '13

Hi, I apologize if this is a newbie question - I've searched for material but didn't seem to find any answers. I would like to write a plugin that allows chimera to parse up my own trajectory format. I would like it to be seekable rather than loading the whole shebang into memory at once. Is there an example trajectory parser out there or maybe someone could point me in the right direction? I saw charmm.py, which might be a good place to start, but I am not sure of which bits I need to replicate. Any pointers on a good place to begin looking would be very appreciated. thank you! -denny-

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Chimera-dev June 2013