August 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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UCSF Chimera Help
by Neil Bugeja 22 Aug '13

22 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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Re: [chimera-dev] Extension to export VTK format files
by Tom Goddard 07 Aug '13

07 Aug '13

Hi Shawn, I opened PDB 1idi, used your code to export it to VTK, and opened it in Paraview 4.0.1 on a Mac. Couldn't get it to show anything. I don't know Paraview and that is probably the issue. Could you tell me something I could do with this Chimera VTK export? I'd like to have an idea of what it is good for before putting it into Chimera. Tom On Jul 26, 2013, at 11:45 AM, Shawn Waldon wrote: > Hi Tom, > > Here is the export code (and the ChimeraExtension.py file). Let me know if there is anything that needs fixing. > > Shawn > > > On Fri, Jul 26, 2013 at 1:15 PM, Tom Goddard <goddard(a)sonic.net> wrote: > Hi Shawn, > > The SketchBio project looks cool. We are trying to make it easy to build hypothetical models of hiv, muscle sarcomeres, fibronectin and all manner of large molecular machinery in Chimera. It is a difficult user interface problem. Graham Johnson, Sam Hertig and I are trying to move this project along. We are happy to help your efforts on this problem. > > Can you send us your Chimera VTK export code and I'll take a look. We don't have a list of coding conventions. I don't really care how you indent your lines, or capitalize your variable names. Mostly I want the user to know when an error occurs what the nature of the problem is (e.g. export can't handle surfaces) without having to ask us. > > Tom > > > > On Jul 25, 2013, at 1:32 PM, Shawn Waldon wrote: > >> Hi Tom, >> >> I don't know exactly how high quality it is. I haven't found any bugs in my latest version, but that doesn't mean they aren't there. I am fairly new to python, so there may be some subtleties that I missed. Also, do you have coding conventions listed somewhere? I have looked, but I haven't found an official list or anything. I am willing to fix it up a bit before submitting it if you can point me to a list of things to fix up. >> >> My use case is that I am writing a higher level modeling tool that uses VTK to do its graphics. I have been calling Chimera as a subprocess to get a surface to render (and now other data). See the project website for more details: http://www.sketchbio.org >> >> Shawn >> >> >> On Tue, Jul 16, 2013 at 10:49 PM, Tom Goddard <goddard(a)sonic.net> wrote: >> Hi Shawn, >> >> That is interesting. We could put it in Chimera if the code is solid. The error reports will come to us so we need high quality code so we have time to do more than reply to bug reports. >> >> What use of molecules in VTK motivated you to write this export code? >> >> Tom >> >> >> On Jul 16, 2013, at 11:30 AM, Shawn Waldon wrote: >> >>> Hello all, >>> >>> As part of a project that I am working on, I recently wrote an extension for Chimera that exports the scene as a .vtk file which can be read into the Visualization Toolkit or Paraview. It exports atoms (points), bonds (lines) and surfaces along with other data associated with them such as the atom and residue names, residue number, position along its chain, b-factor, occupancy, etc. in a format that can be used in VTK-based applications with the default file readers. I think this could be a good thing to add to Chimera itself, so I was wondering if you would like to have the code for the extension to add to Chimera itself. >>> >>> I look forward to hearing from you, >>> -- >>> Shawn Waldon >>> Graduate Research Assistant >>> Department of Computer Science >>> University of North Carolina at Chapel Hill >>> swaldon(a)cs.unc.edu >>> _______________________________________________ >>> Chimera-dev mailing list >>> Chimera-dev(a)cgl.ucsf.edu >>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev >> >> >> >> -- >> Shawn Waldon >> Graduate Research Assistant >> Department of Computer Science >> University of North Carolina at Chapel Hill >> swaldon(a)cs.unc.edu > > > > > -- > Shawn Waldon > Graduate Research Assistant > Department of Computer Science > University of North Carolina at Chapel Hill > swaldon(a)cs.unc.edu > <ExportVTK.zip>

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Chimera-dev August 2013