April 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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Trajectory and MD Movie GUI
by Alex 18 Apr '13

18 Apr '13

Dear all, I'm developing a plugin and would like to add frames to a model on the fly and being able to use the trajectory (MD Movie) GUI to navigate among the frames. Unfortunately, I can't find a way to instanciate the dialog MovieDialog (Movie/gui.py) with a model already opened. It seems that I have to use an Ensemble object (Trajectory/__init.py__) but its constructor requires another ensemble, and the Ensemble objects seem to be created inside MovieDialog's constructor. I'm rather confused right now and would appreciate some help on the matter. Thank you in advance, Best regards, Alex Tek --------- Alex Tek, Phd Department of Cell and Molecular Biology BMC Box 596 SE-751 24 Uppsala Sweden

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ligand
by Muhammad Ali 16 Apr '13

16 Apr '13

sir When I retrieve a ligand structure in SDF files from PDB site, it contains many ligand, how to get a single ligand ??? also ligand files are why not available in PDB files ?? I have to covert them in Chimera.....

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IDLE : code completion under MAC OS X
by Benjamin SCHWARZ 12 Apr '13

12 Apr '13

Hello, I started to develop simple python/chimera scripts. The manual is rather poor on these aspects (btw, is there a doxygen somewhere ?), and therefore the code completion in the chimera IDLE shell is particularly useful… Unfortunately, on my MAC (OS X), it appears to be messy : the TAB key triggers the usual "completion scrollable list window" on both my windows and linux (debian) machines, but not on my MAC. Note that I am still able to scroll through the "invisible" choices by pressing TAB and then using the up and down arrows, it is just that I cannot see the list, which is a bit annoying to have a clear view at once. I guess this has more something to do with the IDLE configuration than with chimera itself, but I don't know how to dig that up, so if you have any idea how to solve this I'd be pleased to read from it. --Ben

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Pseudobonds and gap detection
by Ibai Gazpio 10 Apr '13

10 Apr '13

Dear, We are developing a chimera extension and I would like to know if there is a way to detect or select those models which have an internal sequence gap, represented by the program as a pseudobond in order to distinguish them from those who haven't. Is there a function to do that? Thank you very much and congratulations for the program. Sincerely Ibai

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3dconnexion
by Dougherty, Matthew T 03 Apr '13

03 Apr '13

Hi, I am starting to build a matrix of USB HID devices using controllermate on a mac. I am planning to use two 3dconnexion devices. one to handle 6D translation/rotation, and the other to manage color/lighting; or maybe left hand for trans and right for rotation, etc. . The current driver in chimera only sees one device. If I touch the first USB 3dconnexion device plugged in, it behaves as expected. Touching the second device, chimera acts as though it is the first device. So the driver is not keeping track of the number of devices. In controllermate I can see both devices and can program them independently. For example, I will be able to remap these signals to my choosing and pass it on to a chimera extension I am developing. The second problem I am having is when chimera starts up it exclusively grabs the low level driver, ignoring the the high level driver which incorporates context management. Consequently controllermate is unable to intercept and modify the signal before passing it on. A good reason to do this would be creating deadband zones, or a user defined response curve, or integration with multibutton panel like the logitech g13 so that I can modulate the response (eg, 0.1x,1x,10x,100x, etc). How do I disable 3dConnexion so that it will not load in chimera? I could wipe out the code, but would prefer minimally screwing with chimera base code which is a headache for daily builds and has a risk factor of unforeseen consequences. Something in preferences would be helpful. In a related question on preferences, the scroll wheel is tied to camera zoom. I would like to remap that as a movement in z. Generally I like to keep my scale factor at 1; I find heavy or casual use tends to get me into camera problems. Is this possible? at the moment I disable the scroll wheel. Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine

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Chimera-dev April 2013