- 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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Numpy multiarray import problem
by Mateusz Dobrychłop 05 Dec '13

05 Dec '13

Dear Chimera Team, I am working on my own Chimera Extension. After succesful installation of BioPython using Chimera's Python copy, I've encountered another BioPython - related problem, that is also related to the numpy library. I'm trying to import something from the BioPython library, and BioPython is trying to import from numpy. I recieve a following error: RuntimeError: module compiled against API version 8 but this version of numpy is 7 ... File "/home/mateusz/pyry4.4/Modules/Trans/ComponentRepresentation.py", line 6, in <module> from Bio.PDB import PDBParser, PDBIO, NeighborSearch File "/home/mateusz/.local/UCSF-Chimera64-1.8.1/lib/python2.7/site-packages/Bio/PDB/NeighborSearch.py", line 10, in <module> from Bio.KDTree import KDTree File "/home/mateusz/.local/UCSF-Chimera64-1.8.1/lib/python2.7/site-packages/Bio/KDTree/__init__.py", line 10, in <module> from KDTree import KDTree File "/home/mateusz/.local/UCSF-Chimera64-1.8.1/lib/python2.7/site-packages/Bio/KDTree/KDTree.py", line 20, in <module> from Bio.KDTree import _CKDTree <type 'exceptions.ImportError'>: numpy.core.multiarray failed to import I tried to install numpy the same way I installed BioPython (using Chimera's Python copy), but this does not solve the problem. I also tried to import numpy.core.multiarray directly in Chimera's IDLE and it did import. I'm using Chimera 1.8.1 on Ubuntu 12.10 (64 - bit). Is there anything I can do to make it work? Best wishes, Mateusz

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Re: [chimera-dev] camera positions
by Tom Goddard 05 Dec '13

05 Dec '13

Hi Matt, Take a look at the _savePosition() routine in chimera/share/Midas/__init__.py that defines the contents of each position: return ( viewer.scaleFactor, viewer.viewSize, cam.center, cam.nearFar, cam.focal, xforms, clips, om.cofrMethod, cofr, viewer.clipping, cam.fieldOfView, ) These are the fields you see in the session file. Notice it has the camera focal plane position (cam.focal) but no eye separation parameter. Tom On Dec 5, 2013, at 5:09 AM, "Dougherty, Matthew T" wrote: > Hi Tom, > > I was looking at a typical savepos as it is saved as a session file, below > > Can you tell me how to interpret it contents? Trying to understand what parameters are kept. > > > Matthew Dougherty > National Center for Macromolecular Imaging > Baylor College of Medicine > > > > def restoreMidasBase(): > formattedPositions = {'cPos': (1.0, 5.706403395613076, (105.314, 50.822, 41.951), (43.72859999036789, 40.17340000963211), 41.951, {(0, 0): ((0.0, 0.0, 0.0), (0.0, 0.0, 1.0, 0.0))}, {(0, 0, 'Molecule'): (False, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, False, 5.0)}, 4, (105.314, 50.822, 41.951), False, 7.8352333034904085)} > import Midas > Midas.restoreMidasBase(formattedPositions) >

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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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Interfacing with Chimera
by Bernard Lieberman 21 Oct '13

21 Oct '13

Hello, I'm presently writing an application that I'd like to interface with Chimera. Essentially my program will be capable of loading a specific python session with the appropriate model and then select, stylize, etc. specific residues. I'm able to generate the commands required but I'm wondering if it's best to find a way to hook the Chimera command line or if I should be going the route of editing my source py file? I'm essentially looking for the best method to have my VB6 application interface with Chimera and was looking for some suggestions if others have done this in the past. Any tips or suggestions are greatly appreciated. Thanks! *Bernard Lazarus Lieberman*

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declaring an integer to be used for the model and select command
by Moses Adenaike 08 Oct '13

08 Oct '13

Hello there! I am trying to write a python script for chimera to rotate one molecule then translate another molecule to the right. I can get the code to work when I say use select 0 and model 1. But I want to define functions Rotate and Translate and be able to parse an integer value for the model numbers: Example def Rotate (0) where 0 would be the value of a variable called model inetger then later the function would have the code runCommand("move x -1 model #modelinteger") but when I try to compile chimera says model integer is not defined. I define it outside the function as modelinteger=0 but still the same error message shows. Basically how do I get chimera to understand that my variable modelinteger is indeed an integer?

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UCSF Chimera Help
by Neil Bugeja 21 Aug '13

21 Aug '13

Dear Sir/Madam I am a student at the University of Malta and I am currently using your software to carry out homology modelling for my thesis. I have a slight problem figuring out how to dock a ligand into a receptor on the program...Is this possible or do I need to install another software? I tried looking through the available tutorials but cannot find any so far Thank you for your help Regards -- Neil Bugeja B.Pharm (Hons) IV Year Faculty of Medicine & Surgery University of Malta

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Re: [chimera-dev] Extension to export VTK format files
by Tom Goddard 08 Aug '13

08 Aug '13

Hi Shawn, Thanks, I've added your VTK export to the Chimera daily builds. Will be in tonight's builds. Tom On Aug 8, 2013, at 12:19 PM, Shawn Waldon wrote: > Hi Tom, > > Thanks for the code tips and locations! I changed my code so that it works with Multiscale surfaces and the MSMSModel surfaces. I also handle the case where a multiscale surface piece doesn't have atoms (because it was generated as part of the biological unit) now using some helper functions from the msc command. > > As far as exporting things twice, the code does technically process the molecule twice. Once, which the model it is processing is the molecule itself, it creates points for atoms and lines for bonds and gives it some model number. Then when it is processing the surface it exports the geometry and the data for the closest atom to each point (that is relevant to that surface piece, thanks for that tip), but assigns this a different model number. In VTK it is relatively straightforward to threshold on this model num and just get the data that is of interest. > > I've attached the new version of the code. Let me know if anything else needs fixing. > > Shawn > > > On Wed, Aug 7, 2013 at 1:46 PM, Tom Goddard <goddard(a)sonic.net> wrote: > Hi Shawn, > > The solvent excluded surfaces produced by the surface command or menu Actions / Surface / Show are instances of Python class MSMSModel defined in share/MolecularSurface/msurf.py. They are a subclass of SurfaceModel and the only type of Chimera surface which has a direct association between surface vertices and nearest atoms. That association is given by s.atomMap which maps vertex number (0 based) to Python atom object. > > The MultiScale surfaces are a plain SurfaceModel. I'd suggest adapting your current code to use > > > for piece in m.surfacePieces: > if hasattr(m, 'surfacePieceAtomsAndBonds'): > atoms, bonds = m.surfacePieceAtomsAndBonds([piece], create = False) > # Now export associated atom (closest among atoms) for each vertex. > … > # Now add triangles for surface piece even if it has no associated atoms > > > I didn't study your code closely but it seems you will handle molecules that belong to multiscale surfaces twice. Not sure if that will create duplicates in your vtk output. > > Tom > > > > -- > Shawn Waldon > Graduate Research Assistant > Department of Computer Science > University of North Carolina at Chapel Hill > > <ExportVTK.zip>

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