April 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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Monitor lines
by moneal＠notes.cc.sunysb.edu 19 Apr '11

19 Apr '11

Hello, We just purchased a Zcorp 650, http://www.zcorp.com/en/Products/3D-Printers/ZPrinter-650/spage.aspx and would like to begin building models of proteins. As you probably know, when you print a physical model of a protein @ 100,000x scale on one of these printers, it is very fragile. To help support the model, one must place "Struts" in key locations. We currently use Jmol because it has a strut algorithm built into the software. The algorithm is open source, written originally by George Phillips and adapted by Bob Hanson (see email below). But Stony Brook faculty are begging us to train our students on Chimera and not JMol because (not surprisingly) most faculty at SBU use Chimera and not JMol. My question: would you be willing to incorporate this algorithm into Chimera (or does it already exist)? This would allow Chimera to output pdb files that are ready for rapid prototyping, a blossoming field: http://www.economist.com/node/18114327?story_id=18114327&CFID=162504503&CFT… I look forward to your response, Marvin Marvin H. O'Neal III, Ph.D. Undergraduate Biology 108 CMM/BLL Stony Brook University Stony Brook, NY 11794-5110 Phone: (631) 632-1326 Fax: (631) 632-1680 Sure, why not! It's not my algorithm, though. See http://jmol.svn.sourceforge.net/viewvc/jmol/trunk/Jmol/src/org/jmol/modelse… 125 // 126 // Struts calculation (for rapid prototyping) 127 // 128 /////////////////////////////////////////////////////////// 129 /** 130 * 131 * Algorithm of George Phillips phillips(a)biochem.wisc.edu 132 * 133 * originally a contribution to pyMol as struts.py; 134 * adapted here by Bob Hanson for Jmol 1/2010 135 * 136 * Return a vector of support posts for rapid prototyping models 137 * along the lines of George Phillips for Pymol except on actual molecular 138 * segments (biopolymers), not PDB chains (which may or may not be 139 * continuous). Bob On Thu, Apr 14, 2011 at 9:57 AM, <moneal(a)notes.cc.sunysb.edu> wrote: Bob, I teach introductory biology labs at Stony Brook and use physical models to introduce students to research. I have used Ras-Mol but recently switched to Chimera. I would like to share your strut algorithm with the Chimera group in hopes that they will incorporate it into the software. Would you be willing to work with me on this? Marvin Marvin H. O'Neal III, Ph.D. Undergraduate Biology G-05 CMM/BLL Stony Brook University Stony Brook, NY 11794-5110 Phone: (631) 632-1326 Fax: (631) 632-1680 -----Forwarded by Marvin O'Neal/CAS on 04/14/2011 10:45AM ----- To: "moneal(a)notes.cc.sunysb.edu" <moneal(a)notes.cc.sunysb.edu> From: "Franzen, Margaret" <franzen(a)msoe.edu> Date: 04/13/2011 01:56PM Subject: RE: strut algorithm (See attached file: Bob Hansen.vcf) Hi, Marvin! Your earlier question now makes sense! Bob Hansen is the Jmol guru who teaches Chemistry at St. Olaf – and breathes life into all things Jmol. His contact is below: Margaret From: moneal(a)notes.cc.sunysb.edu [mailto:moneal@notes.cc.sunysb.edu] Sent: Wednesday, April 13, 2011 12:51 PM To: Franzen, Margaret Subject: RE: strut algorithm Hey Margaret, My question about the Strut command in Jmol was specific to the math of the algorithm. I was looking for the equation that runs in the background when a student types this command. I couldn't find it in the documentation guide. Do you have Bob's email? There seem to be several Bob Hanson's on the internet. Marvin Marvin H. O'Neal III, Ph.D. Undergraduate Biology G-05 CMM/BLL Stony Brook University Stony Brook, NY 11794-5110 Phone: (631) 632-1326 Fax: (631) 632-1680

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minimize in IDLE and command line
by Elisabeth Ortega 07 Apr '11

07 Apr '11

Dear Chimera Dev. Team, I have a problem when I'm trying to launch "minimize" in the Python IDLE. If I write in the IDLE: >>> import MMMD >>> MMMD.base.Minimizer(chimera.openModels.list(modelTypes=[chimera.Molecule]),nsteps=0) I get (in the IDLE): <MMMD.base.Minimizer instance at 0x9e0978c> But if I write in the command line: minimize nsteps 0 I get (in the IDLE and in the message bar): >>> Initial energy: 475.211926 Anybody has any idea about that? Kind regards. Elisabeth Ortega - Carrasco Ph.D. Student @ Universitat Autònoma de Barcelona

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Molecular energy
by Elisabeth Ortega 05 Apr '11

05 Apr '11

Dear Chimera Dev. Team, I'm trying to add energy calculations in my script. To do so, I started with the class Minimize, defining nsteps as 0 but I think that it is not so tidy. In chimera/share/MMMD/MMTKinter.py I found the function minimize and a line that says: msg = "Initial energy: %f" % self.universe.energy() . My question is... How can I invoke this self.universe.energy() in order to get the energy? I tried to write a new class in MMMD/base.py and a new function in MMMD/MMTKinter.py in order to obtain a function like "MMMD.base.energy()" to write in my script but I think that I am doing it more complex that it is... Anyone has any idea for doing it successfully? Thanks, Elisabeth Ortega-Carrasco Ph.D. Student @ Universitat Autònoma de Barcelona.

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Chimera-dev April 2011