- Chimera-dev - RBVI Mailing Lists

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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