January 2011 - 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] [Chimera-users] Surface electrostatic and hydrophobicity.
by Miguel Ortiz Lombardia 29 Jan '11

29 Jan '11

Le 28/01/2011 20:37, Elaine Meng a écrit : > and there is nothing like a "hydrophobic potential" Dear Elaine, In fact, such a thing does exist, have a look here: http://biop.ox.ac.uk/www/lj2000/noble/noble_02.html and here: http://www.moldiscovery.com/docs/vsplus/grid.html I tried long ago to import GRID maps to Chimera but faced two problems: 1/ GRID did not provide a real "volume object", but one that would actually have non-zero values only on grid points corresponding to the solvent accessible surface, which is not implemented in Chimera (and the vdwdefine +1.4 trick is not good enough here) 2/ Eventually, GRID became part of a big package that needed a big licence fee... How this potential is calculated was published long ago (see the second web page above and Goodford's cite in the first one) It would be truly useful if it was implemented in Chimera (if you still have slots in your wish-list) I can enter a feature request if you want... Best regards, -- Miguel Architecture et Fonction des Macromolécules Biologiques (UMR6098) CNRS, Universités d'Aix-Marseille I & II Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France Tel: +33(0) 491 82 55 93 Fax: +33(0) 491 26 67 20 mailto:miguel.ortiz-lombardia@afmb.univ-mrs.fr http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.

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menubar
by Elisabeth Ortega 25 Jan '11

25 Jan '11

Dear Chimera Dev Team, I created a new item in the menu bar but my question now is how can I put options in the new bar? As you know, to put any option in the menu 'Tools' we "only" have to copy the new folder in chimera/share/ . I'm trying to do the same with my new item but the only way that I found to do so is modifying the ChimeraExtension.py file of VolumeMenu. Exists any other possibility much easier than that? Thanks. Elisabeth Ortega Universitat Autònoma de Barcelona (UAB)

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Re: [chimera-dev] modify the menu bar
by Eric Pettersen 21 Jan '11

21 Jan '11

Hi Elisabeth, I guess my recommendation is to structure your code like an extension, so that Chimera will execute a ChimeraExtension.py file at startup that you've written. Normally, you put code into a ChimeraExtension.py file to do all the stuff to get your extension into the Tools menu, add a command version, etc.. but the code in that file can actually be almost anything. Just put your code to add your top-level menu in there instead of normal extension-adding code. Let me know if you need more details. --Eric On Jan 21, 2011, at 10:58 AM, Elisabeth Ortega wrote: > Hi Eric, > > I'm testing the two options. Your option works only when I execute > ">>chimera mymenu.py" .How can I auto-execute your code when I start > Chimera? > > Thanks > > 2011/1/21 Eric Pettersen <pett(a)cgl.ucsf.edu> > Hi Elisabeth, > As Tom says, the code he refers to is really more complex than you > need. Just do this: > > from chimera.tkgui import addMenu > myMenu = addMenu(label="menu name") > > to create a top-level menu that you can add items to. An example of > its use in Chimera itself is in the _getAliasMenu() function in > Midas/midas_text.py. > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > &nbsp p; http://www.cgl.ucsf.edu > > On Jan 21, 2011, at 9:20 AM, Tom Goddard wrote: > >> Hi Elisabeth, >> >> There is some code in Chimera that makes a new top-level menu >> called >> Volume that is a copy of the Tools / Volume Data submenu. That >> Volume >> menu is displayed using menu entry Tools / Volume Data / Volume >> Menu on >> Menubar and if you show it it is remembered in the Chimera >> preferences >> file so it will appear every time you run Chimera. This is a more >> complex than you need. But the main routine that would be useful to >> study is called create_toplevel_volume_menu() in file >> >> chimera / share / VolumeMenu / __init__.py >> >> in your Chimera distribution. It would be easy to make a similar >> Ch a toplevel Scripts menu and simply read all >> the files in one of your directories and made menu entries which >> caused >> the file to be opened in Chimera. If you need more help with >> writing it >> ask. >> >> Tom >> >> >>> Dear Chimera Dev Team, >>> >>> >>> I'm trying to put other option in the menu bar (File, Select, >>> Actions, >>> ... , myOption, Help) to store my own scripts. I'm doing a deep >>> search >>> on your python and C++ codes but I don't find which is the code >>> that I >>> have to modify. >>> I know that is easy to store my scripts in the Tools menu, but I >>> prefer to put my scripts in a new option of the menu bar. >>> >>> >>> Thanks a lot for taking the time to reply. >>> >>> >>> >>> Elisabeth Ortega >>> Autonomous University of Barcelona (UAB) >> >> _______________________________________________ >> Chimera-dev mailing list >> Chimera-dev(a)cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev > > > > >

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modify the menu bar
by Elisabeth Ortega 21 Jan '11

21 Jan '11

Dear Chimera Dev Team, I'm trying to put other option in the menu bar (File, Select, Actions, ... , myOption, Help) to store my own scripts. I'm doing a deep search on your python and C++ codes but I don't find which is the code that I have to modify. I know that is easy to store my scripts in the Tools menu, but I prefer to put my scripts in a new option of the menu bar. Thanks a lot for taking the time to reply. Elisabeth Ortega Autonomous University of Barcelona (UAB)

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Creating graphics objects from Python code
by Konrad Hinsen 12 Jan '11

12 Jan '11

Hi everyone, I would like to add non-molecular graphics objects to my molecules for illustration. The obvious way to do so is to load a BILD or VRML file, but since I create these objects in Python scripts, I'd prefer to a direct Python interface rather than write a temporary file and load it. Is there a reasonably stable interface for doing this? Thanks in advance, Konrad. -- --------------------------------------------------------------------- Konrad Hinsen Centre de Biophysique Moléculaire, CNRS Orléans Synchrotron Soleil - Division Expériences Saint Aubin - BP 48 91192 Gif sur Yvette Cedex, France Tel. +33-1 69 35 97 15 E-Mail: research AT khinsen DOT fastmail DOT net ---------------------------------------------------------------------

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Chimera-dev January 2011