November 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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adjust contour to mass
by Martin Turk 26 Nov '13

26 Nov '13

Hi, I am trying to write a simple python script that will iterate over opened volumes and adjust the contour level to a certain mass. This shouldn't be more than ~10 lines. However, I can't find chimera's python library reference to look up the class structure and operator names. Does someone know how, for example, set volume level to 0.01 would look like in python? in the command line it would be for all models: volume #0-99 level 0.01 for models I've found chimera.openModels and then you can list over them, but that's about it. Thanks, Martin Turk

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FYI: Chimera crashes X-Server (solved - Nvidia driver problem)
by Wolfgang Lugmayr 19 Nov '13

19 Nov '13

Hi, Probably you know already, but I found nothing like this in the list archive. Short version: Use Nvidia driver version 319.49 on Linux when running Chimera. Long version: I've setup a new PC with Scientific Linux 6.4 and the latest Nvidia driver v319.60. Simple configuration (no stereo). When running Chimera (official builds 1.8 and 1.8.1) the X-Server crashed and logged me out somewhere after the first pop-up window (Loading Tix ...). I recompiled the latest SVN version (1.9_b39272), but still the same effect. Running the program with --debug-opengl showed no pop-up window on my system as on other older Linux PCs. Debugging the program led to a section in Tkinter/Togl part until the server crashes and gives me the login screen. So I assumed it has more to do with Tk than with Chimera. I've made a gdb remote debug session with my X-Server (see screenshot). Based on this info I made a Internet search and more programs have a similar problem with newer versions of the Nvidia driver. All infos recommend the stable 319.49 version. After this driver installation and a reboot - everything (official and my builds) work now fine. Cheers, Wolfgang -- Besuchen Sie uns auf: www.uke.de _____________________________________________________________________ Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg Vorstandsmitglieder: Prof. Dr. Martin Zeitz (Vorsitzender), Prof. Dr. Dr. Uwe Koch-Gromus, Joachim Prölß, Rainer Schoppik _____________________________________________________________________ SAVE PAPER - THINK BEFORE PRINTING

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Intersurf QUESTION
by niko 05 Nov '13

05 Nov '13

Hello, I use CHIMERA since several years. Thank you very much for this excellent program MY QUESTION : Is it possible to save the ASCII file of the histogram generated by the "intersurf" calculation between two molecules ? Thank you very much Nicolas Papageorgiou.

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Chimera-dev November 2013