November 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

4 3

Headtracking software
by Tamás Borsos 17 Nov '10

17 Nov '10

Hi, first of all I would like to thank You all for your work on this project, because we are using your software regularly for short three dimensional presentations to our students at Lorand Eotvos University, Hungary. I am working at the Faculty of Natural Sciences as a software engineer and we have a large stereoscopic projection system and we are just about to finish the development of our head tracking system, which is already able to measure the position and orientation of the viewers head. This way we will be able adapt the viewpoint of the three dimensional software to the viewpoint of the user. In order to completely interface our system with your software we need to modify it or write an additional module. Would you be so kind to help me find a sophisticated (or maybe easy) way to upload/adjust the cameraposition (world transformation) through an interface to your software? Thank you very much in advance. Regards, Thomas Borsos

2 1

Read a file from script
by Elisabeth Ortega 04 Nov '10

04 Nov '10

Dear all, I need to read some parameters that are write in the same file that I have opened. For exemple, I had a python script that parses the author of the PDB file and I want to run it in a chimera script to use it in other part of the script. To open the file I use: from openSave import osOpen f=osOpen("/home/eortega/data.pdb") code .... I want to do that more "polite". I mean, without write the entire route of the file. Saying to chimera that reads the same file that it has open and appears in the screen. Could anyone help me? Thanks Best Elisabeth Ortega Universitat Autonoma de Barcelona

2 1

Programming a Table
by Elisabeth Ortega 03 Nov '10

03 Nov '10

Dear all, I'm trying to do a script that shows in a table an array of numerical values. One little script that shows what I'm trying to do is: from chimera import runCommand as run run("sel") b=[] for a in chimera.selection.currentAtoms(): b=a.serialNumber from CGLtk.Table import SortableTable t=SortableTable(b) t.addColumn("serial", "Serial", format=None) t.setData(b) t.launch() With this little script I'm trying to show in a column of the table the serial number of the atoms of my system. But when I execute that, I got a message in the Python Shell that says: Traceback (most recent call last): File "/home/eortega/intento-tabla.py", line 11, in <module> t=SortableTable(b) File "CHIMERA/share/CGLtk/Table.py", line 489, in __init__ File "CHIMERA/lib/python2.5/lib-tk/Tkinter.py", line 2442, in __init__ Widget.__init__(self, master, 'frame', cnf, {}, extra) File "CHIMERA/lib/python2.5/lib-tk/Tkinter.py", line 1923, in __init__ BaseWidget._setup(self, master, cnf) File "CHIMERA/lib/python2.5/lib-tk/Tkinter.py", line 1901, in _setup self.tk = master.tk AttributeError: 'int' object has no attribute 'tk' And I don't understand it. How can I build successfully my table? Thank you very much Best Elisabeth Ortega Universitat Autònoma de Barcelona

3 2