- Chimera-dev - RBVI Mailing Lists

Non-standard residues
by Alexander Gawronski 14 Jul '09

14 Jul '09

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Generating images in chimera with the --nogui option
by Davide Baú 09 Jul '09

09 Jul '09

Hi, my name is Davide and I'm currently working on Marc Marti-Renom's group. I'm trying to generate an image using chimera with the --nogui option: chimera --nogui --nostatus --script cmd.py The file cmd.py contains the following lines: from chimera import runCommand > runCommand('open input.cmm') > runCommand('copy file image.png png') but I keep getting the following error message: Traceback (most recent call last): > File "/usr/src/chimera/share/__main__.py", line 65, in <module> > value = chimeraInit.init(sys.argv) > File "CHIMERA/share/chimeraInit.py", line 384, in init > chimera.openModels.open(a, prefixableType=1) > File "CHIMERA/share/chimera/__init__.py", line 1344, in open > File "CHIMERA/share/chimera/__init__.py", line 787, in _openPython > File "cmd.py", line 3, in <module> > runCommand('copy file image.png png') > File "CHIMERA/share/chimera/__init__.py", line 2025, in runCommand > File "CHIMERA/share/Midas/midas_text.py", line 62, in makeCommand > File "CHIMERA/share/Midas/midas_text.py", line 563, in doCopy > File "<string>", line 1, in <module> > File "CHIMERA/share/Midas/__init__.py", line 908, in copy > File "CHIMERA/share/chimera/printer.py", line 1182, in saveImage > AttributeError: '_chimera.NoGuiViewer' object has no attribute 'pilImages' > Error while processing cmd.py: > AttributeError: '_chimera.NoGuiViewer' object has no attribute 'pilImages' > (see reply log for Python traceback info) > cmd.py was generated from within chimera using the "record" command of chimera's "command line". If I delete the line "runCommand('copy file image.png png')", the script execute with no error. Is it possible to generate images using the --nogui option? Thanks a lot for your help! Best regards, Davide ____________ *Davide Baù* Structural Genomics Unit Bioinformatics & Genomics Department, Prince Felipe Research Center Avda. Autopista del Saler, 16 , 46012 Valencia, Spain Tel: +34 96 328 96 80 (ext. 1021) Fax: +34 96 328 97 01 Email: *dbau(a)cipf.es* Web: *http://sgu.bioinfo.cipf.es/dbau*

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Re: [chimera-dev] [Chimera-users] Display Molecule Name
by Greg Couch 02 Jul '09

02 Jul '09

So this is more of a chimera-dev question than a chimera-users question. If you have a Molecule object, m, it's textual "atom specification" would be (in Python): "#%d.%d" % (m.id, m.subid) Normally, if the subid is zero, we leave it out. To find out which molecules are currently being displayed can be harder: for m in chimera.openModels.list(modelTypes=[chimera.Molecule]): if not m.display: continue # molecule displayed, but constituents might not be # if that distinction is important (probably not for # ViewDock), then check bounding box valid, bbox = m.bbox() if not valid: continue # process molecule Hope this helps, - Greg On Thu, 2 Jul 2009, cdlau(a)ucsd.edu wrote: > Hi, > > Thanks for the response. This would not work for my case because I am > writing a plugin for ViewDock for use with a Tiled Wall Display. I was > hoping there was a setting that was available to show the molecule name > (if a setting does exist I can initiate it with runCommand). Does anyone > know if this is possible? > > Thanks, > > Chris > > On Thu, 2 Jul 2009, cdlau(a)ucsd.edu wrote: > > Hi, > > I was wondering if there was a way to display the molecule name that is > being shown in chimera. A simple display such as "molecule #0.10" below > the rendered molecule would be great. > > Thanks for your help, > > Chris > > Just place the mouse over the item you want to know more about and a popup > balloon will tell you about it. The text starts with the model number, > e.g., #0.10, and may or may not have additional information, i.e., for an > atom it includes the residue name and sequence number and the atom name. > > - Greg > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >

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Publishing an extension
by Sébastien Cuendet 29 Jun '09

29 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 29 Jun '09

29 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 22 Jun '09

22 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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a request again...adjust torsion for pseudo bonds
by Jean Didier Pie Marechal 26 May '09

26 May '09

Dear all, sorry to bother you again. I want to perform a conformational search rotating residues around their chelation bond with a metal. With the adjust torsion tool, I can't rotate around pseudo bond, and I actually need to transform the different pseudo bonds in bonds. Could you authorize pseudo bonds to be rotated around? (in the contrary I'll continue with transforming pseudo bonds in bonds, but I thought that remaining with pseudo bonds is better especially when you do "add hydrogens" or other stuffs afterwards ) All the best, JD Dr. Jean-Didier Maréchal Lecturer Computational Biotechnological Chemistry @ Transmet 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 ----- Missatge original ----- De: chimera-dev-request(a)cgl.ucsf.edu Data: Dimecres, Maig 13, 2009 9:00 pm Assumpte: Chimera-dev Digest, Vol 64, Issue 5 > Send Chimera-dev mailing list submissions to > chimera-dev(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.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. [Chimera-dev] Compiling chimera from source code (christopher > lau) 2. Re: [Chimera-dev] Compiling chimera from source code > (Greg Couch) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Tue, 12 May 2009 21:15:56 -0700 > From: christopher lau <chris.d.lau(a)gmail.com> > Subject: [chimera-dev] [Chimera-dev] Compiling chimera from source > code > To: chimera-dev(a)cgl.ucsf.edu > Message-ID: > <f2026a300905122115w3cd5df71mdc8090670593ad94(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Dear Madam/Sir, > > I am currently involved in a project which requires compiling the > Chimerasource code from scratch. I have been using: > > http://www.cgl.ucsf.edu/chimera/sourcecode.html > > for reference, and I understand that surfacing library is not > availabledue to licensing issues. Because I am not interested in > using this > feature, I wanted to know if it was still possible to compile the > Chimerasource code. I know that it will be difficult but any > knowledge or past > experience that may help me would be greatly appreciated. > > Thanks in advance, > > Chris >

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[Chimera-dev] Compiling chimera from source code
by christopher lau 12 May '09

12 May '09

Dear Madam/Sir, I am currently involved in a project which requires compiling the Chimera source code from scratch. I have been using: http://www.cgl.ucsf.edu/chimera/sourcecode.html for reference, and I understand that surfacing library is not available due to licensing issues. Because I am not interested in using this feature, I wanted to know if it was still possible to compile the Chimera source code. I know that it will be difficult but any knowledge or past experience that may help me would be greatly appreciated. Thanks in advance, Chris

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Re: [chimera-dev] scripting rotation around a bond
by Jean Didier Pie Marechal 06 May '09

06 May '09

Hi Eric, thanks a lot that is what I wanted. One question though: How do you inverse the part of the molecule you want to rotate? (The reverse in the GUI). Best JD Dr. Jean-Didier Maréchal Lecturer Computational Biotechnological Chemistry @ Transmet 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 ----- Missatge original ----- De: Eric Pettersen <pett(a)cgl.ucsf.edu> Data: Dimecres, Abril 29, 2009 9:16 pm Assumpte: Re: [chimera-dev] scripting rotation around a bond > On Apr 29, 2009, at 3:34 AM, Jean Didier Pie Marechal wrote: > > > Dear all, > > > > I'd like to generate from my script an ensemble of structures > > obtained by the rotation of a subgroup of the molecule around a > > given bond. Said in another way, I want to do something similar > to > > the adjust torsion tools without getting to the interfase but > > defining myself the value of the angle I want to test. > > I can't figure out what is the module to load and how to use it > and > > it seems there is no command line for this (rotation seems to > accept > > only the atom specification for the bond as an argument). Could > you > > give me a hand on this? > > Hi JD, > Basically, given a bond you want to rotate around, you create a > BondRot instance to do it: > > br = chimera.BondRot(bond) > > Then you can change it by a delta (in degrees) from it's > _original_ > (not current) position with the angle() method. You also have to > specify which side of the bond doesn't move: > > br.angle = (10, br.biggerSide()) > > You can get back to the original position with br.reset() (or with > a > delta of zero). Make sure to dispose of the BondRot with > br.destroy() > when you're done with it. > You probably want to use a daily build here, otherwise the bond- > rotation GUI will pop up as you work with the BondRot. Which can > be > kind of cool as the adjustment dial flies around like a movie clock > in > a fast-forward sequence. > > > By the way, I wanted to get the to the programmers's guide but I > > can't. You removed it from your server correct? > > > > All the best, > > JD > > The Programmer's Guide is still there, it's just not a direct link > off > the home page. Instead you have to click on the "Documentation" > link > and it's in the list on the resulting page. We removed the auto- > generated reference section since it was very big and of little > utility. > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > >

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Re: [chimera-dev] [Chimera-users] unable to install on SLES 11
by Greg Couch 05 May '09

05 May '09

On Tue, 5 May 2009, Rajendra P. OJHA wrote: > Dear Users, > It gives the segmentation fault and icon disappear. How to rectify > the problem. > Thanks > Ojha Please send me more information. Which version of chimera did you try, which operating system are you using, and which graphics driver do you have installed? - Greg

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add h
by Virginie Lafont 01 May '09

01 May '09

Hi, I am a new user of chimera and I already have a question. I have an protonated aspartic acid in my protein and I was wondering, is it possible to add hydrogen atom to aspartic acid with chimera? Thanks Virginie

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scripting rotation around a bond
by Jean Didier Pie Marechal 29 Apr '09

29 Apr '09

Dear all, I'd like to generate from my script an ensemble of structures obtained by the rotation of a subgroup of the molecule around a given bond. Said in another way, I want to do something similar to the adjust torsion tools without getting to the interfase but defining myself the value of the angle I want to test. I can't figure out what is the module to load and how to use it and it seems there is no command line for this (rotation seems to accept only the atom specification for the bond as an argument). Could you give me a hand on this? By the way, I wanted to get the to the programmers's guide but I can't. You removed it from your server correct? All the best, JD Dr. Jean-Didier Maréchal Lecturer Computational Biotechnological Chemistry @ Transmet 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 ----- Missatge original ----- De: chimera-dev-request(a)cgl.ucsf.edu Data: Divendres, Abril 24, 2009 9:00 pm Assumpte: Chimera-dev Digest, Vol 63, Issue 7 > Send Chimera-dev mailing list submissions to > chimera-dev(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.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. Re: stereo: Linux, nvidia Quadro FX 5600 (Randy Heiland) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Fri, 24 Apr 2009 13:45:42 -0400 > From: Randy Heiland <heiland(a)indiana.edu> > Subject: Re: [chimera-dev] stereo: Linux, nvidia Quadro FX 5600 > To: Greg Couch <gregc(a)cgl.ucsf.edu> > Cc: "chimera-dev(a)cgl.ucsf.edu" <chimera-dev(a)cgl.ucsf.edu> > Message-ID: <9CE3734E-31AE-45C3-B5DC-80BC2D67856C(a)indiana.edu> > Content-Type: text/plain; charset="us-ascii" > > Just thought I'd add to this thread, in hopes that it may save > others > some time... > > On Apr 24, 2009, at 11:22 AM, John Matthews wrote: > > > Hello Randy, > > > > Unfortunately, the CE3s are not compatible with the new 120Hz LCDs > > from Viewsonic and Samsung. We are currently looking at a few > > possible solutions. When we have something, we'll post it on our > > website. > > > > Thanks, > > > > > > John Matthews | Sr. Engineer > > RealD > > 5335 Sterling Drive > > Boulder, CO 80301 > > (P) 303.545.5843 x121 | (F) 303.448.9573 | jmatthews(a)reald.com > > www.reald.com > > > > > > > > > > -----Original Message----- > > From: Randy Heiland [heiland(a)indiana.edu] > > Sent: Friday, April 24, 2009 9:19 AM > > To: Real D Support > > Cc: Heiland Randy > > Subject: CrystalEyes and Viewsonic FuHzion > > > > Hello, > > > > I'd like to know if the CrystalEyes (CE-3) should work with the > > Viewsonic Fuhzion (120Hz) monitor? Just looking at the monitor thru > > them, it is very dark. Running glxgears in stereo does not work. > > > > If they should indeed work, then perhaps I need a different nvidia > > driver. > > > > Linux-x86_64 > > nvidia driver version: 180.29 > > GPU 0 (Quadro FX 5600) > > > > thanks, Randy Heiland > > > On Apr 17, 2009, at 12:46 PM, Greg Couch wrote: > > > I don't remember how we configured our Linux machine for stereo, > but > > the > > alternative to using the GUI to configure the X server for > stereo, > > is to > > read the documentation that came with the NVidia driver in > > /usr/share/doc/NVIDIA_GLX-1.0/README.txt and configure xorg.conf > > with a > > text editor. Look in "Appendix D. X Config Options" for the > > "Stereo" and > > "AllowDFPStereo" options. > > > > Good luck, > > > > Greg > > > > 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 > >> > >> _______________________________________________ > >> Chimera-dev mailing list > >> Chimera-dev(a)cgl.ucsf.edu > >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev > >> > >

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stereo: Linux, nvidia Quadro FX 5600
by Randy Heiland 24 Apr '09

24 Apr '09

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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Re: [chimera-dev] [Chimera-users] [Chimera-Users] help with IDLE
by Eric Pettersen 21 Apr '09

21 Apr '09

Hi Chris, I don't know if it works the same on all platforms, but on my mac if I copy text from somewhere I can paste it into IDLE with IDLE's Edit- >Paste menu item. --Eric On Apr 20, 2009, at 7:25 PM, christopher lau wrote: > Thanks Eric, > > Is there any way to paste commands copied from another application > or script into the IDLE shell? > > -Chris > > On Mon, Apr 20, 2009 at 10:36 AM, Eric Pettersen <pett(a)cgl.ucsf.edu> > wrote: > On Apr 19, 2009, at 5:57 PM, cdlau(a)ucsd.edu wrote: > >> Dear Sir/Miss, >> >> I am using the IDLE extensively and I have noticed I cannot paste >> text or >> <arrow up> to run previous commands. I was wondering if anyone >> knew how >> to change these features or if it is possible. I explored the >> options>configure IDLE, but haven't found any preference changes that >> change these problems I am having. Thanks for your help in advance. > > Hi Christopher, > To reuse/edit a command, either up-arrow to or mouse-click into the > command you want and hit return. A copy of the command will appear > at the current Python prompt. You can then edit it with the arrow > keys or the mouse and then hit Return to execute the modified command. > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > > >

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Re: [chimera-dev] [Chimera-users] [Chimera-Users] help with IDLE
by Eric Pettersen 20 Apr '09

20 Apr '09

On Apr 19, 2009, at 5:57 PM, cdlau(a)ucsd.edu wrote: > Dear Sir/Miss, > > I am using the IDLE extensively and I have noticed I cannot paste > text or > <arrow up> to run previous commands. I was wondering if anyone knew > how > to change these features or if it is possible. I explored the > options>configure IDLE, but haven't found any preference changes that > change these problems I am having. Thanks for your help in advance. Hi Christopher, To reuse/edit a command, either up-arrow to or mouse-click into the command you want and hit return. A copy of the command will appear at the current Python prompt. You can then edit it with the arrow keys or the mouse and then hit Return to execute the modified command. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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Using chimera.BondRot
by Frederic RODRIGUEZ 16 Apr '09

16 Apr '09

Dear Chimera developers We want to generate structures (ligand+protein) in which we impose a variation (0 to 360 degrees, with step of 1 or 5, 10 degrees) of one or two dihedrals of the ligand. We want to use Chimera to select interactively, a list of dihedrals, and launch a script which do the rotations, produce PDB structures, save them. After we want to do another processing but using our own code (and perhaps including a new extension GUI, python, we work under Windows XP). We want to use BondRot functions, so we have explored module StructMeasure (and other related files ... BondObject.h) in order to understand how we can use this feature. We have done some experiments using a modified version of this extension so that we can select and rotate dihedrals as we want. If we make a script or a new extension, and let original StructMeasure module in place, we have problems. When we add a bond rotation using an expression such as: br = chimera.BondRot(bond) the panel AdjustTorsions of StructMeasure is always loaded. We would like to know if we can do our task without the use of chimera.BondRot , or if we can use it independently of StructMeasure dialog. thanks, Fred Rodriguez, Mansi Trivedi -- Frédéric Rodriguez Laboratoire de Synthèse et Physicochimie de Molécules d'Intérêt Biologique UMR 5068 CNRS / Université Paul Sabatier 118 Route de Narbonne 31062 TOULOUSE cedex 9, France vce: 05.61.55.85.66 - fax: 33 (0)5.61.55.60.11 elm: build(a)chimie.ups-tlse.fr

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Re: [chimera-dev] [Chimera-users] PDB data
by Eric Pettersen 02 Apr '09

02 Apr '09

Hi Matt, You can find out about the (C++) attributes/methods of a class by using help() in the IDLE interpreter, e.g.: help(chimera.Residue) There is also declaration of the Python-visible attributes of Atom/ Residue/etc. in the source distribution in libs/_chimera/pyinterface. The more convenient way nowadays to get pyinterface is by browsing our SVN repository, i.e. from: /trunk/libs/_chimera/pyinterface – Chimera The other thing you might want to know that seems germane to your specific query is that the PDB headers are stored in the pdbHeaders dictionary in Molecule (key: header type [e.g. REMARK], value: list of strings). --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Apr 2, 2009, at 1:23 PM, Matthew Dougherty wrote: > I was writing some python code involving PDB data. > > looking at pre-existing code involving PDB: > > > m = om.open(pdb_path, 'PDB')[0] > rlist = m.residues > > for r in rlist: > > lc = 'monomer residue %d' % (r.id.position) > if r.isHelix: > lc += ' HELIX' > elif r.isSheet: > lc += ' SHEET' > > > > > > I was trying to track down the data structure for r/rlist, to see if > there are any other parameters I could use besides isHelix, isSheet, > and id.position. > where would that be located in the Chimera package? > > thanks, Matt > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

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Re: [chimera-dev] [Chimera-users] reset/savepos
by Eric Pettersen 02 Apr '09

02 Apr '09

import Midas Midas.positions.keys() FYI, most command-line commands are implemented in the Midas module, usually in a function of the same name as the command. So the implementation of "reset" is in "def reset" in Midas/__init__.py. The implementation for commands that do the same things as tools (e.g. findhbonds, volume) are usually found in that tool's module though. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Apr 2, 2009, at 2:06 PM, Matthew Dougherty wrote: > thanks, > > > how would I get the same list in python? > > > On Apr 2, 2009, at 4:01 PM, Elaine Meng wrote: > >> Hi Matt, >> The command "reset list" will list the names of saved positions in >> the status line and Reply Log. >> Best, >> Elaine >> >> On Apr 2, 2009, at 1:37 PM, Matthew Dougherty wrote: >> >>> I have a chimera session file that is being passed around. >>> Different users are using savepos with no common nomenclature for >>> the >>> view_name. >>> >>> How can I get a list of all view_names? >>> >>> thanks, Matt >> >> >> >> > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

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Re: [chimera-dev] [Chimera] #7111: problem with "toolbar buttons" programmer's example (was: Chimera bug report submission)
by Eric Pettersen 01 Apr '09

01 Apr '09

Hi Richard, The issue here is that Chimera executes Python scripts in temporary modules so that they don't interact with Chimera's own global namespace (they don't accidentally pick up names from the global namespace nor do they leave definitions there). After the script is executed, the temporary module is deleted from sys.modules. When that happens Python clears references in the module's globals dictionary by setting the values to None in an attempt to break circular references for garbage-collection and destructor-invocation purposes. So... the script's attempt to use those names later (when the toolbar button is pressed) produces the "'NoneType' object has no attribute 'compile'" error since when Python looks up "re" in the module's globals dictionary it gets 'None' back. The fix is to put "import re" inside the function definition (as well as an additional "import chimera" [an import is still required at the global level for code after the button-callback function]). I will need to update the example to account for this behavior. The example was written back when scripts were executed in Chimera's own namespace. --Eric On Apr 1, 2009, at 11:36 AM, Chimera wrote: > #7111: problem with "toolbar buttons" programmer's example > ----------------------------------------------- > +---------------------------- > Reporter: richard.marhoefer@… | Owner: pett > Type: defect | Status: accepted > Priority: normal | Milestone: > Release 1.4 > Component: Core | Version: 1.0 > (build 2540) > Severity: normal | Keywords: > Blockedby: | Project: chimera > Platform: all | Blocking: > ----------------------------------------------- > +---------------------------- > Changes (by pett): > > * status: new => accepted > * reporter: chimera-bug-report@… => richard.marhoefer@… > * component: => Core > * project: => chimera > * platform: => all > * version: => 1.0 (build 2540) > * milestone: => Release 1.4 > * owner: => pett > > > -- > Ticket URL: <http://socrates2.cgl.ucsf.edu/trac/chimera/ticket/7111#comment:2 > > > Chimera <http://socrates2.cgl.ucsf.edu/trac/chimera> > Chimera Issue Tracker

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Zalman 3D
by Amédée des Georges 23 Mar '09

23 Mar '09

Dear Chimera developers, We just bought in the our lab (Frank lab) a new Zalman 3D monitor ( http://www.zalman.co.kr/Eng/product/Product_Read.asp?idx=219) Warren Delano has written an extension to get it to work with his Pymol. In our lab, we mainly use Chimera and it would be great if it became compatible with the Zalman system. The way the Zalman monitor works is by giving a different polarization to each row of the screen. The software just has to send the infos for each eye in alternating rows. Would that be something doable in Chimera? By advance thank you, Amedee

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_surface.SurfaceModel
by Randy Heiland 11 Feb '09

11 Feb '09

Hi gang, In trying to finish up my plugin port to the daily/Aqua version of Chimera, I'm confused over the replacement method for what used to be: _surface.Surface_Model.add_group I see that dir(_surface) now has SurfaceModel (without the underscore), but what's the replacement for add_group? >>> dir(_surface.SurfaceModel) ['__class__', '__delattr__', '__destroyed__', '__dict__', '__doc__', '__getattribute__', '__hash__', '__init__', '__new__', '__reduce__', '__reduce_ex__', '__repr__', '__setattr__', '__str__', 'addAssociatedModel', 'addGeometryChangedCallback', 'addPiece', 'associatedModels', 'bbox', 'bsphere', 'callGeometryChangedCallbacks', 'clipPlane', 'clipThickness', 'computeBounds', 'count', 'destroy', 'display', 'frontPoint', 'id', 'intersects', 'material', 'name', 'newPiece', 'openState', 'oslChildren', 'oslIdent', 'oslLevel', 'oslParents', 'oslTestAbbr', 'piecesAreSelectable', 'removeAssociatedModel', 'removeGeometryChangedCallback', 'removePiece', 'selLevel', 'subid', 'surfacePieces', 'useClipPlane', 'useClipThickness'] -Randy

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Question regarding MMTK
by Jean Didier Pie Marechal 11 Feb '09

11 Feb '09

Hi everyone, I have a question regarding the MMTK interfase. How complicate it is to get the hand on a the MMTK script and input files generated by chimera to perform the minimization ? Is it located in some subfolder? Is there a way to write it down so that I can perform further calculations outside the chimera environment? All the best, JD Dr. Jean-Didier Maréchal Lecturer Computational Bioorganic and Bioionorganic Chemistry @ Transmet 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 ----- Missatge original ----- De: chimera-dev-request(a)cgl.ucsf.edu Data: Dimecres, Febrer 4, 2009 9:00 pm Assumpte: Chimera-dev Digest, Vol 61, 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://www.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. alias menu (Richmond Timothy J.) > 2. Re: alias menu (Elaine Meng) > 3. Re: alias menu (Eric Pettersen) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Wed, 4 Feb 2009 14:09:53 +0100 > From: "Richmond Timothy J." <richmond(a)mol.biol.ethz.ch> > Subject: [chimera-dev] alias menu > To: <chimera-dev(a)cgl.ucsf.edu> > Message-ID: <874055BA140585479966DE1694AB0421F058B5(a)EX6.d.ethz.ch> > Content-Type: text/plain; charset="iso-8859-1" > > Dear Chimera Developers, > > > > Perhaps I have missed it, but I would find a menu for selected > aliases very useful. Having returned to Chimera from PyMol > recently, it would be great to have an option for the alias command > that allowed the particular alias to be listed in a separate window > and ran the alias by clicking on the alias name listed there. > > > > Best regards, > > > > Tim > > > > ------------------------- > > > > ETH Zurich > > Prof. Timothy J. Richmond > > Institute of Molecular Biology and Biophysics > > HPK F 18 > > Schafmattstr. 20 > > 8093 Z?rich > > SWITZERLAND > > > > richmond(a)mol.biol.ethz.ch > > http://www.mol.biol.ethz.ch/groups/richmond > > > > +41 44 633 24 70 phone > > +41 44 633 11 50 fax > > > > > >

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