August 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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Using Pmw widgets
by Mateusz Dobrychłop 01 Sep '11

01 Sep '11

Dear Chimera Dev Team, I am writing a Chimera extension and I use the Pmw toolkit in my GUI. I had no problems testing it and it worked great until I decided to reinstall my OS (Windows 7). After that, I installed Chimera 1.5.3, imported my extension and didn't face any problems at first. But then, after closing the viewer and running it again, an error occured right after importing the extension's gui: Traceback (most recent call last): File "<pyshell#5>", line 1, in <module> b=Pmw.EntryField(a,labelpos="w",label_text="asd") File "C:\Program Files (x86)\Chimera 1.5\bin\lib\site-packages\Pmw\Pmw_1_3\lib\PmwEntryField.py", line 73, in __init__ sequences = root.bind_class(tag) File "C:\Program Files (x86)\Chimera 1.5\bin\lib\lib-tk\Tkinter.py", line 1012, in bind_class return self._bind(('bind', className), sequence, func, add, 0) File "C:\Program Files (x86)\Chimera 1.5\bin\lib\lib-tk\Tkinter.py", line 947, in _bind return self.tk.splitlist(self.tk.call(what)) TclError: bad window path name ".94327912.94328912" I didn't change anything since the last succesful testing of my extension - something happened after closing Chimera for the first time, and I have no idea what it is. After that, I tried reinstalling Chimera, installing older versions - it's always the same story; everything works great on the first run, but after I close the viewer for the first time, I am not ever able to use Pmw anymore. The code that causes this error is simple: a=Tkinter.Tk() b=Pmw.EntryField(a,labelpos="w",labeltext="c") I tried to type the same thing in IDLE and I got the exact same error. Thank you for any help, best, Mateusz

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Re: [chimera-dev] Chimera-dev Digest, Vol 90, Issue 1
by Jean Didier Pie Marechal 29 Aug '11

29 Aug '11

HI everyone, just a small suggestion. When opening the match ->aling tool. All the models present in the session are selected. Could we have a pushing button somewhere for select all/none action? or that mouse sliding would select or unselect series of models. Thanks a lot JD Dr. Jean-Didier Maréchal Lecturer The Computational Biotechnological Chemistry Team Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal(a)uab.es www: http://asklipio.qf.uab.es ----- Missatge original ----- De: chimera-dev-request(a)cgl.ucsf.edu Data: Dimarts, Agost 16, 2011 9:00 pm Assumpte: Chimera-dev Digest, Vol 90, Issue 1 > Send Chimera-dev mailing list submissions to > chimera-dev(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev > or, via email, send a message with subject or body 'help' to > chimera-dev-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimera-dev-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-dev digest..." > > > Today's Topics: > > 1. Residue.uniprotIndex (Eric Pettersen) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Tue, 16 Aug 2011 11:42:15 -0700 > From: Eric Pettersen <pett(a)cgl.ucsf.edu> > Subject: [chimera-dev] Residue.uniprotIndex > To: UCSF Chimera Mailing List <chimera-users(a)cgl.ucsf.edu>, > chimera-dev BB <chimera-dev(a)cgl.ucsf.edu> > Message-ID: <1235B56D-4D54-4ED8-9F5A-BD981304D475(a)cgl.ucsf.edu> > Content-Type: text/plain; charset="us-ascii" > > I thought some of the script writers out there might want to know > that > in the latest daily builds residues have a "uniprotIndex" attribute > > which gives the position of the residues relative to their UniProt > sequence, if the correspondence can be determined. To determine > the > correspondence the structure must have valid PDB HEADER and SEQRES > records, and the PDB web site must be reachable (to use their > UniProt > mapping service). > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > > >

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Residue.uniprotIndex
by Eric Pettersen 16 Aug '11

16 Aug '11

I thought some of the script writers out there might want to know that in the latest daily builds residues have a "uniprotIndex" attribute which gives the position of the residues relative to their UniProt sequence, if the correspondence can be determined. To determine the correspondence the structure must have valid PDB HEADER and SEQRES records, and the PDB web site must be reachable (to use their UniProt mapping service). --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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