June 2009 - Chimera-dev - RBVI Mailing Lists

Publishing an extension
by Sébastien Cuendet 30 Jun '09

30 Jun '09

Hi, At the Molecular Modelling Group (http://www.molecular-modelling.ch/) in Lausanne, Switzerland, we've developed a Chimera extension with 3 functionalities: * GUI for CHARMM setups: inspect, clean up and prepare molecules for use with CHARMM * GUI for the EADock docking software: setup a receptor, a ligand, choose the docking parameters that suit your needs, and run your docking * access to the S3DB database, a database containing more than 250 manually curated complexes The extension is reaching the end of the test phase and we plan on releasing it soon. However, coming closer to the release day brought up several questions: 1) We needed a slightly modified version of the writeMol2 function (in writeMol2.py), and had to include a modified version of the writeMol2 and midas package in our extension. Of course we're not claiming any intellectual property on any of those two modified files, but is it a problem to integrate them into our extension? 2) More or less the same situation appears for the rotamers window, from which we took a part to integrate it in part of our extension that allows a user to fix residues with missing atoms. We basically copied and pasted the code we needed. The problem is slightly different since this isn't a built-in function of Chimera, as opposed to writeMol2, for example. But again, is that a problem? 3) We plan to add some features to the awesome ViewDock extension that is already part of Chimera. However, we really only want to implement shortcut commands that are helpful when using EADock, but since ViewDock is already so complete, it makes no sense to start from scratch. We see two options: either extend the ViewDock extension with our features, or inherit a large part of the ViewDock extension and customize it in our own extension. Option 1 seems possible only if the owner of the ViewDock extension agrees to integrate our features in his extension and brings up questions of supporting/updating those features, whereas option 2 brings up the question already mentioned above. Could someone let us know what the standard policy is to deal with those issues? Thanks, Sébastien Cuendet

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Re: [chimera-dev] [Chimera-users] modeldisp
by Eric Pettersen 30 Jun '09

30 Jun '09

Hi Chris, I don't know how you opened your file, but if you opened it with chimera.openModels.open() then the return value is a list of models from that file, so... models = chimera.openModels.open("myfile.mol2") for i in range(len(models)): ... though perhaps more direct would be: models = chimera.openModels.open("myfile.mol2") for m in models: m.display = False for i, m in enumerate(models): ... setup stuff m.display = True ... more stuff m.display = False --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Jun 29, 2009, at 5:11 PM, cdlau(a)ucsd.edu wrote: > Hi, > > I am currently using the modeldisp command on the command line to > hide and > view various molecules within a single mol2 file. I was wondering > how I > would be able to access how many total molecules there were in a > single > mol2 file. For example, if the mol2 file is loaded into model 0, I > would > be using > > modeldisp #0.$i > > etc in a large loop where $i is changing. What command can I use to > return a value for the total number of molecules in the mol2 file so > I can > have this be the upper limit of $i? > > Thanks for your help, > > Chris > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

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need some scripts from chimera source code
by ylei＠ecs.umass.edu 23 Jun '09

23 Jun '09

Hi all I am working on a project that requiring some program scripts concerning with 1) Compute Amber Energy Function 2) Read rotamer information from the Dunbrack Backbone-dependent Rotamer library 3) Read in Electron Density Map and get the density value for each 3-D point in the crystal I did check some related python files in the source code folder and can understand them to some extent, but for running these files, some modules (e.g. Chimera, Rotamers) are needed. However, I don't know how to install these modules, or maybe I should recompile Chimera from source code first(If so, then how, because I don't know the procedure either. BTW, my platform is mac osx)? Could someone show me which files I should use for the above mentioned three subjects and what kinds of modules I should install and how? Thank you so much and sorry for disturbing others. Yang

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need some scripts from chimera source code
by ylei＠ecs.umass.edu 19 Jun '09

19 Jun '09

Hi all I am working on a project that requiring some program scripts concerning with 1) Compute Amber Energy Function 2) Read rotamer information from the Dunbrack Backbone-dependent Rotamer library 3) Read in Electron Density Map and get the density value for each 3-D point in the crystal I did check some related python files in the source code folder and can understand them to some extent, but for running these files, some modules (e.g. Chimera, Rotamers) are needed. However, I don't know how to install these modules, or maybe I should recompile Chimera from source code first(If so, then how, because I don't know the procedure either. BTW, my platform is mac osx)? Could someone show me which files I should use for the above mentioned three subjects and what kinds of modules I should install and how? Yang

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FW: [Chimera-users] Electrostatics
by Gawronski, Alexander 18 Jun '09

18 Jun '09

Hello, I sent an email to Eric Pettersen about automating coloring by electrostatics (see below). He told me to direct further questions to the chimera-dev list. So my question is, in the function colorESP(surf, rgbas, potVals) what should rgbas and potVals be specifically? Is there additional information on this functionality that I can look at? Thanks! Alex Gawronski -----Original Message----- From: Eric Pettersen [mailto:pett@cgl.ucsf.edu] Sent: Thu 6/18/2009 2:50 PM To: Gawronski, Alexander Cc: chimera-users(a)cgl.ucsf.edu Subject: Re: [Chimera-users] Electrostatics Hi Alex, In theory this is doable. In practice, this will not work for some of structures in the PDB until our next release. This is because the MSMS surfacing library that we're currently using will fail for a small fraction of the structures in the PDB. Of course, a "small fraction" of the entire PDB is still probably hundreds of structures. Our next release (1.4) will include a new surfacing library that will be more stable -- though it might not be as fast as MSMS. My best guesstimate of when the 1.4 release will be available is September, though there's a slight chance it could be earlier. Do you intend to compute electrostatics using some Poisson-Boltzmann solver? If so, then doing that for the entire PDB seems like a Herculean task. Certainly Chimera can show the output once you've computed it, but it won't be much help in automating the computation. An alternative is that the current daily build includes the Coulombic Surface Coloring tool, which unsurprisingly performs the somewhat cruder coulombic electrostatics computation for a structure and then colors a surface appropriately. Although Poisson-Boltzmann is a more accurate computation it has been our experience that qualitatively the results are quite similar. You can see an informal comparison here: http://tinyurl.com/mzopva There is no command line version of Coulombic Surface Coloring, so you would have to use the Python API. Given a surface, RGBA values, and corresponding potential values, something like: from ESP import colorESP colorESP(surf, rgbas, potVals) and to get a surface object (assuming exactly one is open): import chimera, _surface surf = chimera.openModels.list(modelTypes=[_surface.SurfaceModel])[0] As to how to call Chimera commands from a Python script: from chimera import runCommand runCommand("surf") To run a Python script without bringing up the Chimera GUI, look at the --nogui and --script arguments documented here: http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/options.html Further questions should probably be sent to the chimera-dev mailing list rather than the chimera-users list. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Jun 18, 2009, at 7:02 AM, Gawronski, Alexander wrote: > Hello, > > I'm a student at Carleton University and I need to create meshes > with electrostatic coloring for all the proteins in the pdb. I need > a way of automating this process with scripts but I can't figure out > how. Is this possible to do this through command line? How do I call > chimera commands from a script? > > Any help would be greatly appreciated! > > Thanks, > Alex Gawronski > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users No virus found in this incoming message. Checked by AVG - www.avg.com Version: 8.5.339 / Virus Database: 270.12.56/2162 - Release Date: 06/18/09 05:53:00

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Re: [chimera-dev] stereo: Linux, nvidia Quadro FX 5600
by Dave Rager 05 Jun '09

05 Jun '09

Hello, I recently experienced this same problem with a similar card. I haven't seen the exact fix posted anywhere but this thread pointed me in the right direction so I figured I'd post what I needed to do to fix this... With glxgears I'd get: glxgears -stereo Error: couldn't get an RGB, Double-buffered, Stereo visual With http://astronomy.swin.edu.au/~pbourke/opengl/stereogl/pulsar.c: ./pulsar -s ERROR: Internal error <Visual with necessary capabilities not found> in function fgOpenWindow >From the /usr/share/doc/NVIDIA_GLX-1.0/README.txt: o Workstation overlays, stereo visuals, and the unified back buffer (UBB) are incompatible with Composite. These features will be automatically disabled when Composite is detected. Simply running: "nvidia-xconfig --no-composite" fixed it. Looks like it added the following to xorg.conf: Section "Extensions" Option "Composite" "Disable" EndSection Hopefully this helps anyone else with this problem... Thanks, Dave. *************************** On Fri, 17 Apr 2009, Randy Heiland wrote: Hello again gang, I'm guessing someone there can help me get past this - I know Greg has offered advice elsewhere. My subject line says it all - I want to get stereo working on this machine. Trying something more basic than chimera: $ glxgears -stereo Error: couldn't get an RGB, Double-buffered, Stereo visual $ glxinfo -v|grep stereo bufferSize=32 level=0 renderType=rgba doubleBuffer=1 stereo=0 bufferSize=32 level=0 renderType=rgba doubleBuffer=1 stereo=0 ... It's not obvious to me where/how one enables stereo via System->Prefs- >More Prefs->nvidia x server settings The specs: Linux-x86_64 nvidia driver version: 180.29 GPU 0 (Quadro FX 5600) mem 1536 MB PCI Express 16x X screens: Screen 0 Display: Apple Cinema HDDisplay (DFP-1) GPU 1 (Quadro NVS 290) 256 MB PCI Express 16x X screens: none Display: none with an Apple 30" Cinema HDDisplay currently attached (and a ViewSonic Fuhzion, 120Hz as something else to experiment with). Currently have CrystalEyes. I'd welcome any advice you might have. thanks, Randy

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Chimera-dev June 2009