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Re: [chimera-dev] attribute for selection?
by Jean Didier Pie Marechal 11 Oct '12

11 Oct '12

Sorry, just to clarify my previous request: this is a script that does what I want though a selection attribute would be faster I think. for a in chimera.openModels.list()[0].atoms: if a in chimera.selection.currentAtoms(): print "this atom of the molecule is selected" #to say something else: print "this one isn't" cheers 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: Jean Didier Pie Marechal <JeanDidier.Marechal(a)uab.cat> Data: Dijous, Octubre 11, 2012 12:39 pm Assumpte: attribute for selection? > HI, > > I want to add attributes to atoms that are selected and those that > aren't. I thought that atoms had a selection attribute already > defined in chimera (something like a boolean) but I don't find it. > I am wrong with that? > > best, > 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 >

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attribute for selection?
by Jean Didier Pie Marechal 11 Oct '12

11 Oct '12

HI, I want to add attributes to atoms that are selected and those that aren't. I thought that atoms had a selection attribute already defined in chimera (something like a boolean) but I don't find it. I am wrong with that? best, 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

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Xlib: extension "NV-GLX" missing on display ":0".
by Thomas Evangelidis 07 Oct '12

07 Oct '12

Greetings, I am running Fedora 17 64-bit with bumblebee and akmod-nvidia on my laptop (the original nvidia drivers could not be installed). My GPU (not sure if this is helpful to know) is GeForce GT 650M and after doing that workaround with the open source drivers, in order to use the GPU I launch each program using "optirun" command (i.e. to launch pymol "optirun pymol", otherwise I get a black screen and the laptop automatically logs out). I have chimera production version 1.6.2 (build 36855) 2012-07-06 17:55:00 UTC, and whenever I run ./bin/chimera, with or without optirun, I see the small start up window "UCSF Chimera, an Extensible Molecular Modeling System" but after a couple of seconds chimera terminates with the following message: $ ./bin/chimera Xlib: extension "NV-GLX" missing on display ":0". Xlib: extension "NV-GLX" missing on display ":0". X Error of failed request: GLXBadCurrentWindow Major opcode of failed request: 153 (GLX) Minor opcode of failed request: 5 (X_GLXMakeCurrent) Serial number of failed request: 1376 Current serial number in output stream: 1376 Or with optirun: $ optirun --debug ./bin/chimera [18180.513653] [DEBUG]optirun version 3.0.1 starting... [18180.514638] [DEBUG]Active configuration: [18180.514642] [DEBUG] bumblebeed config file: /etc/bumblebee/bumblebee.conf [18180.514646] [DEBUG] X display: :8 [18180.514650] [DEBUG] LD_LIBRARY_PATH: /usr/lib64/nvidia:/usr/lib64/xorg/nvidia [18180.514653] [DEBUG] Socket path: /var/run/bumblebee.socket [18180.514656] [DEBUG] VGL Compression: proxy [18191.641124] [INFO]Response: Yes. X is active. [18191.641145] [INFO]Running application through vglrun. [18191.641242] [DEBUG]Process vglrun started, PID 3339. Xlib: extension "NV-GLX" missing on display ":0". Xlib: extension "NV-GLX" missing on display ":0". X Error of failed request: GLXBadCurrentWindow Major opcode of failed request: 153 (GLX) Minor opcode of failed request: 5 (X_GLXMakeCurrent) Serial number of failed request: 1376 Current serial number in output stream: 1376 [18199.687495] [DEBUG]SIGCHILD received, but wait failed with No child processes [18199.687528] [DEBUG]Socket closed. [18199.687540] [DEBUG]Killing all remaining processes. It is worth mentioning that the small start-up window disappears after saying "initializing OpenGL". Do you have any idea what I can do to fix it? Thanks in advance, Thomas

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The style of Ribbon in alpha 1.7 version
by Cheng Wang 29 Sep '12

29 Sep '12

Dear Chimera Team, Hi. The ribbon style in 1.6 version is a little round for helix, while it is really flat in 1.7 version. I want to use v1.7 since several commands are really good for movie making eg. format option and transparency. However the ribbon style for helix is not as nice as it in 1.6. I am wondering how could I change the style of ribbon in 1.7 to be the same as in 1.6 since the ribbon style seams the same in the panel for both versions. Many thanks. Best, Cheng

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Re: [chimera-dev] Match->Align command line option?
by Eric Pettersen 13 Sep '12

13 Sep '12

On Sep 13, 2012, at 11:55 AM, Chetanya Pandya wrote: > Hi Eric, > > Thanks for your detailed reply...it has been really useful! As instructed, I've installed today's daily build on my machine (running Fedora 15 32 bit). I've written a python script(see attached) which (hopefully) does what I want. > > Unfortunately, the script is unable to save the alignment as a file. It spits out an error which I'm unable to comprehend (see attached log file). > > Any help would be appreciated! Well, Multalign Viewer was designed a decade ago and has no non-GUI version. Therefore, the script cannot be run in nogui mode if it creates an MAV instance. So you have two options. One is simply to run your script in GUI mode. The Chimera window will come up and you will have to remain logged in until it finishes. The other is to get tomorrow's daily build, where I've modified makeAlignment so it is possible to just get the list of aligned Sequences instead of a MAV instance. That list can then be used to write the output file. The changes to your script would be in the makeAlignment call: seqs = makeAlignment(chains, makeMAV=False) and the way you call save: save(f, None, seqs, {}) (and remove the mav.Quit() call, obv.) > > Thanks, > --Chetanya > > P.S. - I would like to read more about the various packages and their functions. I can't seem to find a detailed writeup/manual. Can you direct me to a good source? This is probably our Achilles' heel -- there really isn't a good source. On the Programmer's Guide page there are links to the help() output for the main Chimera molecular data classes (which can also be viewed with the help() command in the IDLE tool). If you know a tool doesn't something similar to what you want, you can find out how it does it by looking in the source for the tool (all in <chimera installation>/share). If you know a command does what you want, use runCommand to run it, or look at the command's source (in share/Midas/__init__.py unless the command is implemented by a tool). Lastly, and probably most importantly, just asking here on the chimera-dev mailing list if you're stumped. And with our spotty programmer documentation, it's easy to get stumped! --Eric

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Question Matchmaker Picture Chimera
by Mickey Barth 16 Aug '12

16 Aug '12

Dear Chimera Team, first of all we want to thank sincerely you for the great program that you guys developed. We (students of Mainz) are really fond of the different functions provided in your program, especially the match maker funktion. Using this function daily we were wondering who is on this picture. Can you tell us who is the couple on this picture ? That would be great. Bye Michael

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help() output
by Eric Pettersen 14 Aug '12

14 Aug '12

I've put the output that you would get from the help() command in IDLE on the Programmer's Guide's main page: Chimera Programmer's Guide It covers the Molecule, Residue, Atom, and Bond classes. Let me know if you want more classes included. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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Want to Convert PDB to VMRL?
by Calem Bendell 13 Aug '12

13 Aug '12

I'd like to convert PDB to VMRL and OBJ (for some reason hydrophobicity exports well as obj and ribbon as wrl, other than those file formats, I usually get file errors from Blender?) using Chimera via command-line call (doing them one by one will be a pain for several thousand pdb files!). How would I do this? Would I need to modify the Chimera source? (if necessary, I can do this, but it seems like it'd be pretty time consuming) Thank you guys!!! -- Calem Bendell Computer Science Dept McGill University Immunology and Microbiology Dept McGill University 438 881 9189

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Re: [chimera-dev] [Chimera-users] Motion of an atom
by Eric Pettersen 11 Jul '12

11 Jul '12

Hi Raju, During the execution of a Python script, Chimera does not redraw the graphics screen until explicitly requested or when the script ends. The simplest way to ask for a redraw is to execute the "wait 1" Chimera command, which you can do from Python with: from chimera import runCommand runCommand("wait 1") So if you embed that in your loop you should be able to see your atom move. Frames are redrawn at a rate of 25 per second (though future versions of Chimera may allow faster redraw rates), so you may want to wait more than 1 frame if the atoms moves too fast. Alternatively, there is also a direct Python call to wait(): from Midas import wait wait(1) FYI, there is another mailing list, chimera-dev, where programming-intensive questions like this one are more appropriate, so that the regular user's eyes don't glaze over. :-) --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Jul 10, 2012, at 9:07 AM, Raju Purohit wrote: > Hello friends, > > I need some help here. > > I created a basic model having just an atom and set its coordinates as (0,0,0). Now I want to make it move along a certain path defined mathematically (say, along x axis) and I need to see it move. So I used a for loop. But I couldn't see and motion and soon realised that the loop is very quick in executing and thus I could see the atom at its last coordinates. So I tried to add delay of 0.5 seconds for each loop by importing time module and useing time.sleep. But still I couldn't see any motion and the coordinates of the atom is set only at the end of the for loop. I could not see the intermediate path. I am sure you people must have tried this earlier and this problem has a solution but I just couldn't figure it out. > > Can you please help me out? > > Thank you in advance. > > -- > Raju R.N. > Third Year, B.Tech > Mechanical Engineering > National Institute of Technology Karnataka, Surathkal > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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Re: [chimera-dev] [Chimera-users] Programming within Chimera
by Eric Pettersen 11 Jul '12

11 Jul '12

Though one nice thing in Idle is that you can look the attributes/methods of a class (those defined in the C++ layer at least) with the help() function, e.g. "help(chimera.Atom)". I am working on making the output of help() for the most commonly used classes available on the Chimera web site (so that you don't have to start Chimera to get it) and will probably have that done in a week or so. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Jul 10, 2012, at 9:11 AM, Conrad Huang wrote: > Well, there is Idle :-) The menu item "Tools -> General Controls -> IDLE" will bring up an Idle window. > > I usually use Idle for testing out snippets of code but prefer to edit scripts outside of Chimera. Keeping the "Open File" dialog up by checking the "Keep dialog up after Open" box (above the Close button) helps a lot. The file you last opened remains selected, so you can repeatedly edit your script and hit the Open button to reload it. All a matter of preference... > > Conrad > > On 7/10/12 7:18 AM, Mario Dejung wrote: >> Hi all, >> is there an easy way to test and develop programs within Chimera? I >> always write python scripts and open these in Chimera… Would be much >> easier to have something like idle or similar to develop scripts and >> test them. >> Or is there a better way I did not found? > >> Looking forward to any suggestions. >> Kind regards >> Mario >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >

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