July 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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Re: [chimera-dev] Extension to export VTK format files
by Tom Goddard 07 Aug '13

07 Aug '13

Hi Shawn, I opened PDB 1idi, used your code to export it to VTK, and opened it in Paraview 4.0.1 on a Mac. Couldn't get it to show anything. I don't know Paraview and that is probably the issue. Could you tell me something I could do with this Chimera VTK export? I'd like to have an idea of what it is good for before putting it into Chimera. Tom On Jul 26, 2013, at 11:45 AM, Shawn Waldon wrote: > Hi Tom, > > Here is the export code (and the ChimeraExtension.py file). Let me know if there is anything that needs fixing. > > Shawn > > > On Fri, Jul 26, 2013 at 1:15 PM, Tom Goddard <goddard(a)sonic.net> wrote: > Hi Shawn, > > The SketchBio project looks cool. We are trying to make it easy to build hypothetical models of hiv, muscle sarcomeres, fibronectin and all manner of large molecular machinery in Chimera. It is a difficult user interface problem. Graham Johnson, Sam Hertig and I are trying to move this project along. We are happy to help your efforts on this problem. > > Can you send us your Chimera VTK export code and I'll take a look. We don't have a list of coding conventions. I don't really care how you indent your lines, or capitalize your variable names. Mostly I want the user to know when an error occurs what the nature of the problem is (e.g. export can't handle surfaces) without having to ask us. > > Tom > > > > On Jul 25, 2013, at 1:32 PM, Shawn Waldon wrote: > >> Hi Tom, >> >> I don't know exactly how high quality it is. I haven't found any bugs in my latest version, but that doesn't mean they aren't there. I am fairly new to python, so there may be some subtleties that I missed. Also, do you have coding conventions listed somewhere? I have looked, but I haven't found an official list or anything. I am willing to fix it up a bit before submitting it if you can point me to a list of things to fix up. >> >> My use case is that I am writing a higher level modeling tool that uses VTK to do its graphics. I have been calling Chimera as a subprocess to get a surface to render (and now other data). See the project website for more details: http://www.sketchbio.org >> >> Shawn >> >> >> On Tue, Jul 16, 2013 at 10:49 PM, Tom Goddard <goddard(a)sonic.net> wrote: >> Hi Shawn, >> >> That is interesting. We could put it in Chimera if the code is solid. The error reports will come to us so we need high quality code so we have time to do more than reply to bug reports. >> >> What use of molecules in VTK motivated you to write this export code? >> >> Tom >> >> >> On Jul 16, 2013, at 11:30 AM, Shawn Waldon wrote: >> >>> Hello all, >>> >>> As part of a project that I am working on, I recently wrote an extension for Chimera that exports the scene as a .vtk file which can be read into the Visualization Toolkit or Paraview. It exports atoms (points), bonds (lines) and surfaces along with other data associated with them such as the atom and residue names, residue number, position along its chain, b-factor, occupancy, etc. in a format that can be used in VTK-based applications with the default file readers. I think this could be a good thing to add to Chimera itself, so I was wondering if you would like to have the code for the extension to add to Chimera itself. >>> >>> I look forward to hearing from you, >>> -- >>> Shawn Waldon >>> Graduate Research Assistant >>> Department of Computer Science >>> University of North Carolina at Chapel Hill >>> swaldon(a)cs.unc.edu >>> _______________________________________________ >>> Chimera-dev mailing list >>> Chimera-dev(a)cgl.ucsf.edu >>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev >> >> >> >> -- >> Shawn Waldon >> Graduate Research Assistant >> Department of Computer Science >> University of North Carolina at Chapel Hill >> swaldon(a)cs.unc.edu > > > > > -- > Shawn Waldon > Graduate Research Assistant > Department of Computer Science > University of North Carolina at Chapel Hill > swaldon(a)cs.unc.edu > <ExportVTK.zip>

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Extension to export VTK format files
by Shawn Waldon 26 Jul '13

26 Jul '13

Hello all, As part of a project that I am working on, I recently wrote an extension for Chimera that exports the scene as a .vtk file which can be read into the Visualization Toolkit <http://www.vtk.org> or Paraview<http://www.paraview.org>. It exports atoms (points), bonds (lines) and surfaces along with other data associated with them such as the atom and residue names, residue number, position along its chain, b-factor, occupancy, etc. in a format that can be used in VTK-based applications with the default file readers. I think this could be a good thing to add to Chimera itself, so I was wondering if you would like to have the code for the extension to add to Chimera itself. I look forward to hearing from you, -- Shawn Waldon Graduate Research Assistant Department of Computer Science University of North Carolina at Chapel Hill swaldon(a)cs.unc.edu

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installing python module
by Ibai Gazpio 19 Jul '13

19 Jul '13

Hi all, I would like to install an external module for python called paramiko in order to perform a ssh connection in one of my applications. How could be possible to achieve that? How is the procedure to install this kind of packages? Thanks, Ibai

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Coordination bonds treated as covalent
by Jean Didier Pie Marechal 19 Jul '13

19 Jul '13

Hi guys, I am preparing a movie in which I want an organometallic compound linked to an organic one to rotate around the bound between both moieties. Do to so, I need the whole first coordination sphere of the metal and the metal itself to behave as a unique block. If I generate bonds with chimera (covalent) I can do that. Unfortunately, if I keep the session and open back, the bonds have been changed by pseudo bonds (which is actually A LOT BETTER!) but pseudo bonds does not allow the first coordination sphere to behave as a block. I wonder what is the best to solve this problem? Can atoms related by pseudobonds be set (even from the python shell) to be rigid? All the best, JD Dr. Jean-Didier Maréchal Associate Professor 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

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Re: [chimera-dev] camera dialog
by Tom Goddard 11 Jul '13

11 Jul '13

Hi Matt, The ViewerDialog() call always constructs a new viewer. So if you want to use this code to position your two viewer and only create the second one on the first time instead of d2 = viewing.ViewerDialog(viewer = viewer) use code that checks if you already created the second viewer like this if hasattr(chimera, 'viewer2'): d2 = chimera.viewer2 else: d2 = viewing.ViewerDialog(viewer = viewer) chimera.viewer2 = d2 Tom On Jul 10, 2013, at 12:52 AM, "Dougherty, Matthew T" wrote: > here is what I have implemented. > > the first time it executes, everything is fine. > second time it executes D2 begins stacking up viewer dialog windows. > > > from chimera import dialogs > from chimera import viewing, viewer > > d = dialogs.find('View Editor', create = 1) > d.enter() > top = d.uiMaster().winfo_toplevel() > top.autoposition = False > s = top.wm_geometry() > top.wm_geometry('%dx%d+%d+%d' % (400,350,420,30)) > d.nb.raise_page('pCamera') > > d2 = viewing.ViewerDialog(viewer = viewer) > d2.enter() > top2 = d2.uiMaster().winfo_toplevel() > top2.autoposition = False > s2 = top2.wm_geometry() > top2.wm_geometry('%dx%d+%d+%d' % (400,350,10,30)) > d2.nb.raise_page('pSideView') > > > Matthew Dougherty > National Center for Macromolecular Imaging > Baylor College of Medicine > ________________________________________ > From: Tom Goddard [goddard(a)sonic.net] > Sent: Tuesday, July 09, 2013 1:51 PM > To: Dougherty, Matthew T > Cc: chimera-dev(a)cgl.ucsf.edu > Subject: Re: [chimera-dev] camera dialog > > Hi Matt, > > The following Python will bring up a second viewing dialog with the camera and side view tabs. They both work in some simple tests with the current daily build. For some reason the second one does not have the Lighting tab. There may be other problems. It is unlikely the dialog positions and shown tabs would be saved in a session. > > from chimera import viewing, viewer > d = viewing.ViewerDialog(viewer = viewer) > > Tom > > > On Jul 8, 2013, at 3:29 PM, "Dougherty, Matthew T" <matthewd(a)bcm.edu> wrote: > >> using python is it possible to put up two camera dialogs? >> would like to have camera & sideview up at the same time, or lighting and camera up at the same time. >> >> >> Matthew Dougherty >> National Center for Macromolecular Imaging >> Baylor College of Medicine >> _______________________________________________ >> Chimera-dev mailing list >> Chimera-dev(a)cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev >> > >

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volume viewer features/suggestion
by Dougherty, Matthew T 09 Jul '13

09 Jul '13

I have starting using feature display as my default setting, putting in other features depending on project and available display space. when selecting a feature it can be difficult to get a handle on what is being presented; the window expands or reduces, feature blocks are being inserted/deleted throughout the dialog. would suggest a horizontal black line separating the feature blocks, to make the visual grouping easier to pick out. or a vertical line down the left using color to differentiate feature groups. Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine

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camera dialog
by Dougherty, Matthew T 09 Jul '13

09 Jul '13

using python is it possible to put up two camera dialogs? would like to have camera & sideview up at the same time, or lighting and camera up at the same time. Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine

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volume viewer/mouse
by Dougherty, Matthew T 08 Jul '13

08 Jul '13

I am trying to write some python scripts relating to volume viewer. two things I need to have are: 1) the ability to figure out what dataset is active on the volume viewer. I will manually pick that with the mouse, my python sw will process the active model in volume viewer. 2) on the selected dataset I need to know what the min/max values are. In a unrelated problem: lately I completely avoid changing the camera scale value, I always want it to be 1.0. The mouse scroll wheel changes the scale value, so I am having accidental changes to camera scale values. How do I halt wheel commands from changing scale? under preferences/mouse I have "use mouse scroll wheel" set to false. side note: I just bought a logitech G600 mouse which has 12 buttons on the mouse that can be programmed through mode (3) and shift(2) buttons to have 12*3*2 active buttons that I can set to accelerator commands. So one of my modes will be dedicated to volume viewer controls, another for stereo/dome/camera, the other is general chimera commands. Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine

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Trouble with Saving New Atom Attributes
by Juliette Cao 05 Jul '13

05 Jul '13

Hi All, I was successfully able to change a few atom types using the setattr command. I checked to see that the atoms I changed were correct (by selecting the atoms and then then clicking the IDATM type option.) I saved the .pdb file When I opened up the saved .pdb file and checked the atom types, they had reverted back to their original type. Is there a specific way to save files after using setattr command? Regards, Juliette Cao University of Houston

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