August 2010 - 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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Re: [chimera-dev] [Chimera-users] WIngware for Chimera?
by Eric Pettersen 31 Aug '10

31 Aug '10

On Aug 27, 2010, at 8:53 AM, Forbes J. Burkowski wrote: > Hi: > > At the risk of being a heretic, I would like to ask the following > question: > > Is it possible to use the Wingware Python IDE instead of IDLE to > edit and > execute Python scripts for Chimera? > > More information about Wingware can be found at wingware.com. > > I suppose that if Wingware is given the appropriate pathnames it could > import chimera and other needed packages. So, it could be used as > Python script editor. However, I am hoping that it could also be > used to > run and debug scripts that interact with the Chimera window. Would > this > be possible? First off: heretic! ;-) Second, the new face in our lab, Darren Weber, has developed a wiki page describing how to get the Eclipse IDE to work with Chimera: http://plato.cgl.ucsf.edu/trac/chimera/wiki/ChimeraEclipse Perhaps some of the information there could be adapted to getting Wingware to interface with Chimera. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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Query about writing extensions in Chimera
by Arun Prasad Pandurangan 24 Aug '10

24 Aug '10

Dear Chimera Developers Team, Would like to know whether its possible to develop a custom application that can be added as a plug-in inside Chimera (For example like the recent program Ringer)? If so, is there any expert advice or tutorials available to develop such a custom application that depends on Chimera? Thank you. With kind regards, Arun Prasad

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adding python packages to chimera environment
by Darren Weber 20 Aug '10

20 Aug '10

This an example of getting some packages installed into the Chimera python environment. In my case, I was interested in using the spyder IDE within the Chimera python installation. http://packages.python.org/spyder/ First, get the setuptools (easy_install) package: $ sudo -i # export PATH=$PATH:/opt/UCSF/Chimera64-2010-08-05/bin/ # export LD_LIBRARY_PATH=/opt/UCSF/Chimera64-2010-08-05/lib # sh /home/dweber/Downloads/setuptools-0.6c11-py2.7.egg --prefix=/opt/UCSF/Chimera64-2010-08-05/ That gets 'easy_install' working with the Chimera python installation. Now for the spyder IDE. It requires PyQt4, so it's not trivial, but the following seems to build and install OK (against an Ubuntu package install for Qt4, not a custom build of Qt4 in foreign; the wget commands fetch linux-specific downloads): $ sudo -i # wget http://www.riverbankcomputing.co.uk/static/Downloads/sip4/sip-4.10.5.tar.gz # tar zxvf sip-4.10.5.tar.gz # cd sip-4.10.5 # /opt/UCSF/Chimera64-2010-08-05/bin/python2.7 configure.py # make # make install # cd .. # wget http://www.riverbankcomputing.co.uk/static/Downloads/PyQt4/PyQt-x11-gpl-4.7… # tar zxvf PyQt-x11-gpl-4.7.4.tar.gz # cd PyQt-x11-gpl-4.7.4 # update-alternatives --config qmake #select qmake-qt4 option # /opt/UCSF/Chimera64-2010-08-05/bin/python2.7 configure.py --no-designer-plugin --qmake=/usr/bin/qmake-qt4 ...<snip>... The PyQt Python package will be installed in /opt/UCSF/Chimera64-2010-08-05/lib/python2.7/site-packages. PyQt is being built with generated docstrings. PyQt is being built with 'protected' redefined as 'public'. The PyQt .sip files will be installed in /opt/UCSF/Chimera64-2010-08-05/share/sip/PyQt4. pyuic4, pyrcc4 and pylupdate4 will be installed in /opt/UCSF/Chimera64-2010-08-05/bin. ...<snip>... #make #make install That should satisfy the deps for spyder. Then use easy_install to get spyder installed, like so: # /opt/UCSF/Chimera64-2010-08-05/bin/easy_install spyder Then to run spyder with a chimera-like env, the following seems to work: # export CHIMERA=/opt/UCSF/Chimera64-2010-08-05 # export LD_LIBRARY_PATH="$CHIMERA/lib/" # export TCL_LIBRARY="$CHIMERA/lib/tcl8.6" # export TCLLIBPATH="{$CHIMERA/lib}" # unset TK_LIBRARY # unset TIX_LIBRARY # export LD_PRELOAD=libotf.so # export PATH=$PATH:$CHIMERA/bin # unset PYTHONHOME # unset PYTHONPATH # $CHIMERA/bin/spyder Within the spyder interactive console, it reports running python 2.7 and I see: >>> import sys >>> sys.path ['', '/opt/UCSF/Chimera64-2010-08-05/bin', '/opt/UCSF/Chimera64-2010-08-05/lib/python2.7/site-packages/setuptools-0.6c11-py2.7.egg', '/opt/UCSF/Chimera64-2010-08-05/lib/python2.7/site-packages/spyder-1.1.4-py2.7.egg', '/opt/UCSF/Chimera64-2010-08-05/lib/python2.7/site-packages/pyflakes-0.4.0-py2.7.egg', '/opt/UCSF/Chimera64-2010-08-05/lib/python2.7/site-packages/rope-0.9.3-py2.7.egg', '/opt/UCSF/Chimera64-2010-08-05/lib/python27.zip', '/opt/UCSF/Chimera64-2010-08-05/lib/python2.7', '/opt/UCSF/Chimera64-2010-08-05/lib/python2.7/plat-linux2', '/opt/UCSF/Chimera64-2010-08-05/lib/python2.7/lib-tk', '/opt/UCSF/Chimera64-2010-08-05/lib/python2.7/lib-old', '/opt/UCSF/Chimera64-2010-08-05/lib/python2.7/lib-dynload', '/opt/UCSF/Chimera64-2010-08-05/lib/python2.7/site-packages', '/opt/UCSF/Chimera64-2010-08-05/lib/python2.7/site-packages/PIL'] >>> This is not quite the right path (and maybe LD_LIBRARY_PATH etc.), but a few tweaks get it working, i.e.: >>> sys.path.append('/opt/UCSF/Chimera64-2010-08-05/share') >>> sys.path.append('/opt/UCSF/Chimera64-2010-08-05/lib') >>> import chimera >>> chimera.version.version 'alpha version 1.5 (build 31152) 2010-08-05 19:55:24 GMT' This may not be a complete config/setup, but it's close. The spyder interface provides autocompletion, auto help-inspection, debug facilities, workspace, etc. If anyone finds a better way to do this, please let me know. There may be better ways to do this with virtualenv, see http://clemesha.org/blog/2009/jul/05/modern-python-hacker-tools-virtualenv-… Best, Darren -- Darren L. Weber, Ph.D. Programmer/Analyst on Chimera Development Team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco Mission Bay Campus (MC 2240), Genentech Hall (Room N453) 600 16th Street, San Francisco, CA 94158-2517 dweber[at]cgl.ucsf.edu, 415-439-0619 (google voice) http://www.cgl.ucsf.edu/chimera/

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asynchronous running of Chimera extensions
by Marcin Pawlowski 19 Aug '10

19 Aug '10

Dear Chimera developers. Me and of my students are developing a chimera extension to deal with protein structures. Unfortunately, the execution of our plunging last at least 5 minutes, so during this time the chimera program is hinged. We would like to execute the program in an asynchronous way. Is it possible? Please do not hesitate to contact us if you require further information about our project. Best regards, Marcin Pawlowski

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(no subject)
by Reza Heidari 16 Aug '10

16 Aug '10

Hi, How can i display just some of residues (in form sphere) on a protein (in form ball & stick), for example: Trp38, Val66, Ala80. Please help me, thanks a lot.

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