January 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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Add new Amber parameters
by Elisabeth Ortega 22 Jan '13

22 Jan '13

Dear Chimera dev. team, I have to use my own set of Amber99 parameters because I'm working with transition metals. I'm testing if I can minimize a benchmark system that contains one copper atom coordinated to 6 water molecules. To do it, I don't use any script, I use directly the tool "minimize" present in Tools-> Structure Editing. To do so I edited the frcmod.ff99SB file with the atom, bond, dihedral... all the fields that frcmod.ff99SB ask to me. That didn't work (Element "Cu" is not currently supported by MMTK). Then I followed the instructions here: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.… and I put a file called "cu" with the required data in: lib/python*/site-packages/MMTK/Database/Atoms I tried again, and the same problem. In the same webpage, there are instructions of how can we edit the Amber parameters files present in: bin/amber11/dat/leap/parm I put my parameters in frcmod.ff99SB and I also tried to put it in frcmod.ff03, but it fails again. How can I solve this problem and perform the minimizations? I'm using both windows(x64) and linux(x86) versions of Chimera 1.6.2 (build 36855) but I planned to finish the testing with Chimera 1.7 that contains by default the Amber12 package. At the bottom of the message there is the mol2 file and the parameters that I'm testing. Thanks in advance for your time. Elisabeth O.-C. My mol2 file is: @<TRIPOS>MOLECULE cuh2o.mol2 19 12 1 0 0 SMALL AMBER ff99SB @<TRIPOS>ATOM 1 CU 0.0581 0.0224 0.0049 CU 1 UNK 2.0000 2 OH -2.2040 0.0438 0.0019 O.3 1 UNK -0.8230 3 OH -0.0067 -0.2388 2.1919 O.3 1 UNK -0.8370 4 OH 0.0041 0.2849 -2.1820 O.3 1 UNK -0.8450 5 OH 2.2006 0.0021 0.0073 O.3 1 UNK -0.8270 6 OH -0.0248 -2.4186 -0.2871 O.3 1 UNK -0.8330 7 OH 0.0202 2.4645 0.2971 O.3 1 UNK -0.8420 8 H15 -2.6953 -0.0699 0.6640 H 1 UNK 0.4010 9 H16 -0.6665 -0.1584 2.6929 H 1 UNK 0.4170 10 H18 -0.6618 0.2534 -2.6804 H 1 UNK 0.4330 11 H19 2.6899 -0.0779 -0.6612 H 1 UNK 0.4240 12 H20 0.6422 -2.9163 -0.2996 H 1 UNK 0.4180 13 H14 0.6417 2.9769 0.0874 H 1 UNK 0.4200 14 H17 -2.6936 -0.1186 -0.6513 H 1 UNK 0.4180 15 H22 0.6497 -0.1530 2.6964 H 1 UNK 0.4220 16 H21 0.6504 0.1511 -2.6890 H 1 UNK 0.4130 17 H13 2.6872 -0.2103 0.6483 H 1 UNK 0.4060 18 H24 -0.6602 -2.9263 -0.1105 H 1 UNK 0.4160 19 H23 -0.6488 2.9572 0.3459 H 1 UNK 0.4200 @<TRIPOS>BOND 1 18 6 1 2 14 2 1 3 10 4 1 4 9 3 1 5 8 2 1 6 19 7 1 7 6 12 1 8 17 5 1 9 16 4 1 10 15 3 1 11 13 7 1 12 5 11 1 @<TRIPOS>SUBSTRUCTURE 1 UNK 1 RESIDUE 4 A UNK 0 ROOT And my initial trial of parameters that I write in the mod file is (I put the same than Fe atom parameters written in the file frcmod.heme_ff94 only to test if that works): MASS CU 63.55 BOND CU-OH 200.00 2.0 ANGLE CU-OH-HO 35.00 120.00 OH-CU-OH 50.00 90.00 DIHEDAL X-OH-CU-X 1 0.00 0.00 2.0 NONBON CU 1.2 0.05 0.00 -- Elisabeth Ortega Carrasco, Ph.D. Student Molecular Modelling of Transition Metal Systems Group Lab. C7/153, Chemistry Department Universitat Autonoma de Barcelona Tel.: +34935812857 email.: ortega.elisabeth(a)qf.uab.cat

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new Programmer's Example
by Eric Pettersen 15 Jan '13

15 Jan '13

The examples in the Programmer's Guide now include one that discusses the basics of how to measure various atomic-level quantities. http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Examples/index.html --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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How to install? - continued
by pythonchemia Gazeta.pl 14 Jan '13

14 Jan '13

hi, Mr Eric and Greg I would like to thank you for your valuable suggestions. In fact, it would be better to use the Chimera 1.6. 2 or 1.7. Thank you Mr. Greg and Eric. Yours sincerely - Janusz Grabowski

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Re: [chimera-dev] [Chimera-users] How to install ?
by Greg Couch 10 Jan '13

10 Jan '13

And it would help to use a more recent version of Chimera, either version 1.6.2 or the 1.7 release candidate. The newer releases have newer versions of Python and MMTK embedded in them with the associated improvements and bug fixes. -- Greg On 01/10/2013 11:30 AM, pythonchemia Gazeta.pl wrote: > > I have Chimera 1.5 with Python IDLE v 2.7 and Windows XP and MinGW.

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Re: [chimera-dev] [Chimera-users] How to install ?
by Eric Pettersen 10 Jan '13

10 Jan '13

Hi Janusz, Chimera has its own self-contained Python environment, so in order to install these packages so that you can use them from within Chimera you will need to use Chimera's Python whenever the installation procedure for a package calls on you to execute a Python script. For a script with no arguments that would be: chimera --nogui installation-script.py and for scripts with arguments: chimera --nogui --script "installation-script.py argument1 argument2 ..." On non-Mac platforms you can find the chimera executable in: <your chimera installation>/bin On Macs it is in: Chimera.app/Contents/Resources/bin While the 1.5 version of Chimera is nice enough, I would encourage you to upgrade to the 1.7 release candidate, which has many improvements. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Jan 10, 2013, at 11:30 AM, pythonchemia Gazeta.pl wrote: > Dear Chimera Team ! > > I intersted in chemistry. I use chimera 1.5 software for personal purposes, non - commercial. > Chimera is a very usefull Tool. I like it :). I know Python language a little. I'm beginner programmer. > I have Chimera 1.5 with Python IDLE v 2.7 and Windows XP and MinGW. My website is pythonchemia.aq.pl > I have some questions: > > 1 - How to install pDynamo library ? from https://sites.google.com/site/pdynamomodeling/home for Chimera 1.5 automatically or manually ? > > 2 - How to install OpenBabel library ? from openbabel.org/wiki/Main_Page for Chimera 1.5 automatically or manually ? > > 3 - How to install Biopython library ? from http://biopython.org/wiki/Main_Page for Chimera 1.5 automatically or manually ? > > Please help me ! - I wait on answer. > Sorry for my english > > Yours sincerely - Janusz Grabowski > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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Chimera-dev January 2013