February 2012 - 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] IDE
by Eric Pettersen 08 Feb '12

08 Feb '12

On Feb 6, 2012, at 6:33 PM, Elnaz Rezaei wrote: > I need to know what are the functions and properties of "atom > object" do in chemira. > I searched but I could not find! Hi Elnaz, In IDLE you can type "dir(chimera.Atom)" to see the names of all methods/attrs of Atom, or "help(chimera.Atom)" to get a longer but somewhat more readable listing. We do have some information in the Chimera Programmer's Guide: Chimera Programmer's Guide but an encyclopedic listing of Atom attrs/methods isn't part of it. If you said what you were looking to accomplish I could probably offer better advice. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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Re: [chimera-dev] [Chimera-users] associating multiple structures and sequences
by Eric Pettersen 07 Feb '12

07 Feb '12

On Feb 6, 2012, at 7:01 PM, Uppal, Karan wrote: > Hi, > > I am writing a custom extension based on MultiAlign Viewer that > highlights regions in a multiple sequence alignment based on > numerical values stored in an external file. I modified the > RegionBrowser.py script, and added a function that works just like > "showSS". There may be ways to accomplish what you modification does without changing the MAV code. Just using an imported MAV rather than your custom mod has the advantage of gaining any additional functionality and bug fixes that MAV gets in later releases. One possibility is for you to use "sequence coloring files" that MAV already reads (they can also optionally color associated structures). The format is documented here: JEvTrace File Formats Such files can be read programatically with the MAViewer.loadScfFile method. Another possibility is to directly create the new regions you want with the MAViewer.newRegion method. The 'blocks' argument to that method is a series of 4-tuples describing the rectangles composing the region: (top-seq, bottom-seq, left, right) where left/right are zero- based sequence indices. > It works fine for one structure and sequence combination. However, I > am trying to associate multiple copies of the same protein structure > and its sequence. So, the structures are identical and so are the > sequences in the sequence alignment, but each copy represents > different information. My problem is that the sequences in the > alignment viewer dialog box are highlighted in a random fashion. > And, I want the sequences to be highlighted in an ordered fashion > starting from first sequence to last sequence since we want to be > able to map the highlighted regions back to the external file. > > Is there a way to control the order in which the sequences are > highlighted in the alignment viewer dialog? Or is there a way to get > the model # associated with a particular sequence and using the > model # to highlight the alignment viewer? I'm not 100% sure what "highlighted" means here, but I presume the problem is that your first structure isn't necessarily associating with your first sequence, since the structure and alignment sequences are all identical? If that's the issue, then you need to explicitly control the structure association rather than allowing automatic association to occur. You do that by providing the argument 'autoAssociate=False' to the MAViewer constructor. Then you need to call the MAViewer's 'associate' method for every structure association you want to set up. Now, there's a big doc string for that method, but briefly you want to call associate like so: mav.associate(mseq, seq=aseq) where mseq is the Sequence from the structure you want to associate and aseq is the Sequence in alignment you want to associate with. You get the Sequences from a model with: mol.sequences() or, if you know the chain ID you want (e.g. 'A'): mol.sequence('A') --Eric P.S. I cc'ed this to chimera-dev and set replies to go there since this seems like much more a developer topic than a user topic. Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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IDE
by ELNAZ REZAEI 06 Feb '12

06 Feb '12

Hello, Is it possible to use other python IDE (e.g. komodo) with Chimera? Thanks, ELnaz

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