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Re: [chimera-dev] [Chimera-users] Amber Force Field
by Tom Goddard 17 Oct '12

17 Oct '12

Hi Forbes, I think Eric and Conrad may no more about your problem than I do. But I can tell you my best guess why your calculation is abysmally slow. I think the basic trouble is that useRotamer() decides to replace the existing residue rather than simply update its coordinates. In other words it deletes the old side chain atoms and bonds and makes new ones. Then the new ones don't have charges assigned for energy calculation. So the minimize "prep" option adds hydrogens and computes charges. It does this for the entire molecule because it doesn't know how to prep just one atom. So for each residue and each rotamer tried you end up adding hydrogens and recomputing charges for the whole molecule. Turning prep off in the minimize() call will just cause an error because the charges are missing. The "cache" option in the minimize() call also won't work because the molecule has changed. In fact the minimize code is not smart enough to realize the molecule has new atoms and will try to use the cached MMTK copy of the former molecule and this will probably lead to errors (as you describe). So my 30 minute look at the various parts of the Chimera code without any testing suggests the slowness is because hydrogens/charges are recomputed for every rotamer. The new MMTK molecule object is just the one residue you are calculating the energy of. You realize your code does not take account of any interactions of that residue with any other residues. The other residues are completely ignored. That is what exclres means. So you may as well be asking for the energy of a one residue molecule starting in the rotamer configuration with the actual residue backbone atom positions. I bet this would be very much faster if using a rotamer simply changed existing atom coordinates, then you add hydrogens and charges just one time for all the calculations, and you can cache the MMTK molecule object for each single residue energy calculation which will speed up calculating the different rotamer energies for that residue. Eric is the one who would know why the useRotamer() code deletes atoms and adds new ones instead of just changing the coordinates. It would probably be pretty easy to make a new routine to use instead of useRotamer() that simply copied atom coordinates from the rotamer molecules returned by getRotamer() to the original molecule. Or what about just calculating the energy of the rotamer molecules directly without trying to put them into the protein (with all its other residues ignored)? I see when I use the Rotamer dialog and hide the original molecule that the returned rotamers include CA and N backbone atoms but not C, O. Tom > Hi Tom: > > Thanks for your email of May 4. After some experimenting I got the code > to work but the execution times are deplorable! As I indicated earlier I > want to use the Amber energy calculations to compare various confirmations > involving different rotamers. My problem seems to be that I cannot get a > fast execution because I am unable to cache the results of various > computations and I believe the calculations are starting from scratch for > each rotamer combination. Here is a simplified version of the code that I > am using (in this case working with only one rotamer and essentaily > computing its intrinsic energy (I hope)): > > import chimera > import Rotamers > from Rotamers import getRotamers, useRotamer, NoResidueRotamersError > from MMMD import base > > > def evaluateAmberEnergy(res_L, prot): > > fixedAtoms = set() > molecules = list([prot]) > usingResidues = set(res_L) > > exclres = set(sum((m.residues for m in molecules), [])) > exclres.difference_update(usingResidues) > > def run(minimizer): > minimizer.run() > > minimizer = base.Minimizer(molecules, nsteps=0, stepsize=0.02, > cgsteps=0, cgstepsize=0.02, interval = 10, > fixedAtoms=fixedAtoms, nogui=True, > addhyd=True, callback=run, > exclres=exclres, cache=False, prep=True) > > energy = minimizer._mi.universe.energy() > print "energy value: ", energy > return energy > > #========================================================================== > > # Global variable: > prot = chimera.openModels.open("1CRN", type="PDB")[0] > > for rc in prot.residues: > rotCur_L = getRotamers(rc)[1] > for rotC in rotCur_L: > useRotamer(rc, [rotC]) > energyAmber = evaluateAmberEnergy([rc], prot) > print rc.type, rc.id.position, energyAmber > > > > This is producing a lot of text in the Python Shell and when the program > is run with a large protein it will go for hours... > > Any suggestions for speeding this up would be greatly appreciated. I > tried different settings of cache and prep but got Chimera errors such as > missing C++ atom objects. > > Depressing.... > > Best regards, > Forbes > > > > > > On Fri, 4 May 2012, Tom Goddard wrote: > >> Hi Forbes, >> >> If you want to get the minimized energy within your Python script >> then you need to run the minimization using a Python function call >> rather than a Chimera text command. To figure out how to do that I look >> at the Python code that is called by the Chimera text command in your >> Chimera distribution >> >> chimera/share/MMMD/cmdline.py >> >> or also available online >> >> >> http://plato.cgl.ucsf.edu/trac/chimera/browser/trunk/libs/MMMD/cmdline.py >> >> The minimize() Python function is called using the text command >> arguments. I see it basically does >> >> from MMMD import base >> minimizer = base.Minimizer(molecules, nsteps, stepsize, cgsteps, >> cgstepsize, interval, >> fixedAtoms, memorize, nogui, addhyd, lambda m: >> m.run(), exclres, cache, prep) >> >> Looking at base.py in the same directory and tracking back from where >> "Initial energy..." is printed in file MMTKinter.py I see the energy is >> obtained using >> >> minimizer._mi.universe.energy() >> >> I have not tested this out but perhaps it will move you in the direction >> you want to go. >> >> Tom >> >> >>> Hi: >>> >>> Thanks for the response. The code that you suggested seems to work. I am >>> getting the initial energy reported in the Python Shell along with other >>> lines that are reporting on the activities of the command. >>> >>> Since I am embedding this command in a runCommand statement, I would like >>> to get the initial energy value put into a variable within the Python >>> script instead of the Python Shell window. Is there any way to accomplish >>> this? >>> >>> Cheers, >>> Forbes >>> >>> >>> On Fri, 13 Apr 2012, Elaine Meng wrote: >>> >>>> Hi Forbes, >>>> The minimization tool reports the total energy, not any breakdown into components (electrostatic, VDW, strain) or interactions between sets of atoms. However, the "minimize" command has a "fragment" option for ignoring all but the specified residues, so you could at least limit what is considered the total system. That also makes the calculation faster, although single-point energy calculation (0 steps minimization) should already be pretty fast. >>>> Best, >>>> Elaine >>>> >>>> Example (and see also "nogui true"): >>>> >>>> minimize spec :13.a,17.a fragment true cgsteps 0 nsteps 0 >>>> >>>> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/minimize.html> >>>> >>>> On Apr 13, 2012, at 10:38 AM, Conrad Huang wrote: >>>> >>>>> Chimera's "Structure Editing -> Minimize Structure" tool (or the "minimize" command) may be used to do this. The tool reports the initial energy of the system in the Reply Log. If you give zero as the number of steps for both steepest descent and conjugate gradient minimization, then Chimera should return immediately. >>>>> >>>>> Conrad >>>>> >>>>> On 4/13/12 7:09 AM, Forbes J. Burkowski wrote: >>>>>> Hi: >>>>>> >>>>>> I have noticed that scripts can start with: >>>>>> >>>>>> import MMTK >>>>>> import MMTK.ForceFields >>>>>> from MMTK.ForceFields import Amber94ForceField >>>>>> >>>>>> We are doing some side chain packing studies that would benefit from the >>>>>> availablity of "easy" force field calculations. Currently, the algorithm >>>>>> works with useRotamers() to set two neighbouring rotamers and this is >>>>>> followed by a simple energy calculation to evaluate the interaction energy >>>>>> between the two rotamers. Right now, the energy calculation is only a bit >>>>>> more sophisticated than a steric collision detector. >>>>>> >>>>>> Question: Can we use some functions in the MMTK.ForceFields module to get >>>>>> an improved energy calculation? >>>>>> >>>>>> Any suggestions would be appreciated. >>>>>> >>>>>> Cheers, >>>>>> Forbes >>>>>> _______________________________________________ >>>>>> 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 >>> _______________________________________________ >>> Chimera-users mailing list >>> Chimera-users(a)cgl.ucsf.edu >>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >>> >>

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set bond to wire and specific width
by Jean Didier Pie Marechal 11 Oct '12

11 Oct '12

Sorry to bug again, I'd like to change the aspect of the bonds I selected using a python code. I'd like a wide wire representation. I am not sure how to handle the Wire attribute. With the drawMode I can switch the representation from ball and stick to wire. However, I do not manage to change the width. I thought that radius would work out but it sounds that is does not work for this mode. Any help? Cheers JD for b in chimera.selection.currentBonds(): b.drawMode=0 b.radius=1 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 2:19 pm Assumpte: Re: attribute for selection? > 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 > somethingelse: 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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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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Patch to center_of_points()
by Nader Morshed 10 Jul '12

10 Jul '12

It seems that the code in the Segger module for calculating the center of a region breaks when the region contain a large number of points. I don't have the error message on hand, but it complains about calling _contour.affine_transform_vertices with a double, rather than a float. It seems that in regions.py the summed coordinate is cast to a float32, then divided by the number of points, which can cause an implicit cast up to float64's when point_count is large! Here's a simple patch to share/Segger/regions.py that re-orders the calls to cast after division, rather than before: --- old/share/Segger/regions.py 2012-03-19 13:45:34.000000000 -0700 +++ new/share/Segger/regions.py 2012-07-09 14:55:26.241372503 -0700 @@ -873,7 +873,7 @@ plists = [r.points() for r in self.childless_regions()] s = numpy.sum([numpy.sum(plist, axis=0) for plist in plists], axis=0) - com = s.astype(numpy.float32) / self.point_count() + com = (s / self.point_count()).astype(numpy.float32) if transform: tf = self.segmentation.point_transform() import _contour -- Nader Morshed <morshed.nader(a)berkeley.edu>

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Motion of an atom
by Raju Purohit 10 Jul '12

10 Jul '12

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

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Fwd: Question about coloring the points on a Ramachandran plot
by Eric Pettersen 20 Jun '12

20 Jun '12

Hi Trina, I'm forwarding this to the chimera-dev list to give the "Ramachandran plot guy" (Conrad Huang) a chance to answer. I think he's recently done many of the same things for a custom script so he's better suited for answering... --Eric Begin forwarded message: > From: Trina Manalo <trinamanalo_2014(a)depauw.edu> > Date: June 19, 2012 7:56:53 AM PDT > To: pett(a)cgl.ucsf.edu > Subject: Question about coloring the points on a Ramachandran plot > > Hi Eric, > > I had emailed you about the animated Ramachandran plots, which I have gotten to work. I have a new question to ask you concerning the points of the plot. > > I've tried coloring the plots by opening Chimera as an administrator and going to IDLE. Then I tried editing the file labeled "_init_" under the "Ramachandran" folder that comes with the program when it is installed. In the file, under "def _displayData(self)" I tried to do 2 things: > > 1. Change the non-selected residue points to be transparent, so that only the outlines of the non-selected residue points are visible. I want to do this so that the selected residue point is visible when it is behind a lot of points. I got it to be somewhat successful, however, only half of the points turn out this way. The other half turned out to be blacked out and I'm not sure why. > > 2. Get rid of the non-selected residue points all together so that the only point I see is the residue point that I am interested in following. I tried adding the phrase "marker='None' " in the "ax.scatter" line, but that didn't work. > > I'd greatly appreciate your help. > > Thanks, > Trina > > >

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Re: [chimera-dev] Chimera-dev Digest, Vol 98, Issue 1
by ladam 07 Jun '12

07 Jun '12

Le 04/06/12 21:00, chimera-dev-request(a)cgl.ucsf.edu a écrit : > Message: 2 Date: Mon, 04 Jun 2012 15:28:27 +0200 From: ladam > <ladam(a)smbh.univ-paris13.fr> To: chimera-dev(a)cgl.ucsf.edu Subject: > [chimera-dev] Rotating about an axis with mouse Message-ID: > <4FCCB7FB.5060709(a)smbh.univ-paris13.fr> Content-Type: text/plain; > charset=ISO-8859-1; format=flowed Hi all, I have a python script that > allows me to rotate a residue in a molecule of a desired angle around > a predefined vector. Now I'd like to be able to do this graphically > with the mouse on a selected residue. I have almost found what I want > if I use the 'Move selection' option in the 'Movement Mouse mode' but > this does rotate around the center of Mass or geometric center, not > around a vector. What I plan to do is derive the code from the > corresponding /share/MoveSelection/move.py module and try to insert a > vector instead of the center_of_rotation(self.movable_groups) but > there is maybe a better, simpler idea. Any suggestion? Thanks a lot > -- -------------------------------- Patrick Ladam Ma?tre de Conf?rence > Universit? Paris 13 - UFR SMBH CSPBAT - Service RMN 74, rue Marcel > Cachin 93017 Bobigny Cedex Tel: 01 48 38 73 25 Fax: 01 48 38 77 77 > mail: ladam(a)smbh.univ-paris13.fr ------------------------------- > ------------------------------ Message: 4 Date: Mon, 4 Jun 2012 > 09:04:03 -0700 From: Elaine Meng <meng(a)cgl.ucsf.edu> To: ladam > <ladam(a)smbh.univ-paris13.fr> Cc: chimera-dev(a)cgl.ucsf.edu, > "chimera-users(a)cgl.ucsf.edu BB" <chimera-users(a)cgl.ucsf.edu> Subject: > Re: [chimera-dev] Rotating about an axis with mouse Message-ID: > <1A06A067-7C81-49D0-B154-D1CC50737764(a)cgl.ucsf.edu> Content-Type: > text/plain; charset=iso-8859-1 Hi Patrick, If I understand correctly, > you can do what you want with "Constrained Move" (in menu under > Tools... Movement): > <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/constrained/constr…> > (The purpose of "Movement Mouse Mode" is different, mainly to allow > moving subparts of a model. By default, mouse manipulation moves whole > models.) You can also specify center and axis of rotation if using > commands (turn, roll). > <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/turn.html> > <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/roll.html> I > hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer > Graphics Lab (Chimera team) and Babbitt Lab Department of > Pharmaceutical Chemistry University of California, San Francisco On > Jun 4, 2012, at 6:28 AM, ladam wrote: Thank you for the answer Elaine, Well the "constrained move" allows me to rotate the whole model, not a selected residue in the model (which is actually what i want to do). What I would need is to use the constrained mouse rotation on a subpart of the model (a previously selected residue or set of atoms for instance). So my guess is I should start from this Constrained Move module and modify it to apply the movements to the currently selected residue or atoms. At the moment I am going throught the code to see how to do it, I'll probably need some advice later on. Thanks again Patrick

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Re: [chimera-dev] [Chimera-users] undisplay label in distance monitor
by Eric Pettersen 07 Jun '12

07 Jun '12

On Jun 4, 2012, at 11:54 PM, Bala subramanian wrote: > Friends, > I have written a script to draw lines between atoms (using distance > monitor). I dnt want the distance label to be displayed with the > pseudo bond. Kindly write me the way to remove the label. My script > is below. > > model=chimera.openModels.open('myavg.pdb') > res=model[0].residues > MAT=loadtxt('mymatrix',dtype=float) > chimera.runCommand('focus') > for x in range(len(res)): > for y in range(len(res)): > if x <> y : > value=MAT[x,y] > > if 0.5 < value > 0.75: > b=distanceMonitor.newPseudoBond(res[x].atomsMap['CA'] > [0],res[y].atomsMap['CA'][0]) > b.drawMode=1 > b.radius=0.05 > #b.label=None I tried keeping this value as None and > empty string but it doesnt help. > b.color=getColorByName('red') > > else: pass > > else: continue > Hi Bala, distanceMonitor pseudobonds are designed to do exactly what you find them to be doing: showing an updated distance as the model is moved. What you need to do is make a normal pseudobond group for your own use that doesn't have all the special processing that distanceMonitor provides. Here is some example code: from chimera.misc import getPseudoBondGroup grp = getPseudoBondGroup("matrix bonds", associateWith=[model]) ...then later... b = grp.newPseudoBond(res[x].atomsMap['CA'][0], res[y].atomsMap['CA'] [0]) You will probably want to set some attributes of your group, like color and line type (dashed vs. solid). Here's some code for that: import chimera from chimera.colorTable import getColorByName grp.color = getColorByName("lime green") grp.lineType = chimera.Dash --Eric P.S. BTW, this question is probably better for chimera-dev than chimera-users...

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Rotating about an axis with mouse
by ladam 04 Jun '12

04 Jun '12

Hi all, I have a python script that allows me to rotate a residue in a molecule of a desired angle around a predefined vector. Now I'd like to be able to do this graphically with the mouse on a selected residue. I have almost found what I want if I use the 'Move selection' option in the 'Movement Mouse mode' but this does rotate around the center of Mass or geometric center, not around a vector. What I plan to do is derive the code from the corresponding /share/MoveSelection/move.py module and try to insert a vector instead of the center_of_rotation(self.movable_groups) but there is maybe a better, simpler idea. Any suggestion? Thanks a lot -- -------------------------------- Patrick Ladam Maître de Conférence Université Paris 13 - UFR SMBH CSPBAT - Service RMN 74, rue Marcel Cachin 93017 Bobigny Cedex Tel: 01 48 38 73 25 Fax: 01 48 38 77 77 mail: ladam(a)smbh.univ-paris13.fr -------------------------------

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Chimera-dev mailing list
by Raju Purohit 04 Jun '12

04 Jun '12

Dear sir/madam, I want to be added to Chimera mailing list. Thank you. -- Raju R.N. Third Year, B.Tech Mechanical Engineering National Institute of Technology Karnataka, Surathkal

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Iterating through chains
by Ryan Doherty 29 May '12

29 May '12

Hello, I'm trying to create a chimera script and am stumped. I'm trying to iterate through a series of PDB entries that contain a specific protein-protein interaction (some are NMR ensembles) to create a list of residues that within specific distances of the binding interface. I am able to successfully iterate through pdb files and residues, but am having difficulty iterating through chains of NMR ensembles. Is there a variable like m.chains or is the number of chains accessible through chimera.openModels.list? Also, do you have any example scripts that could help me? Sincerely, Ryan Doherty

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Fwd: Dividing a model into seperate models - one for each chain
by Mateusz Dobrychłop 09 May '12

09 May '12

---------- Forwarded message ---------- From: Mateusz Dobrychłop <dobry(a)g.pl> Date: 2012/5/9 Subject: Re: [chimera-dev] Dividing a model into seperate models - one for each chain To: Chimera BB <chimera-users(a)cgl.ucsf.edu> Hi Tom, Thank you very much for your response. My exact problem is that I'm trying to find a way to automatically save all the models (and submodels) that are opened in Chimera at a time. It's easy when models are numbered #0, #1, #2 etc - then, I use: opened=openModels.list() howmany=len(opened) while howmany>=0: command="write "+str(howmany)+" "+o_path+"/"+str(howmany)+".pdb" runCommand(command) howmany-=1 Unfortunately, when I split, let's say, #0 that contains 3 chains, and then use the above code, I get an error: MidasError: 3 model ids match "0" So maybe there's a different way to do it? I'd like to save #0.1, #0.2 and #0.3 to seperate files. I know it's possible from Chimera's interface, but I have no idea how to do it when my script doesn't have any info about the number of submodels etc. Thank you for your time once again, Mateusz 2012/5/9 Tom Goddard <goddard(a)sonic.net> > Hi Mateusz, > > The "split #0" command produces separate models for each chain. They are > numbered #0.1, #0.2, #0.3, ... with the same primary id number (0) and > different secondary id numbers. You can use these two-part id numbers in > any Chimera command (e.g. color blue #0.2), or you can refer to all the > models using #0. There is currently not a way to change the id numbers of > models. > > Tom > > > Hello, >> >> Is there a command / a way to split a model into seperate models (one for >> each chain)? I know there is the "split" command, but it divides the model >> into submodels. >> >> Mateusz >> >> >

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Dividing a model into seperate models - one for each chain
by Mateusz Dobrychłop 08 May '12

08 May '12

Hello, Is there a command / a way to split a model into seperate models (one for each chain)? I know there is the "split" command, but it divides the model into submodels. Mateusz

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Invitation to connect on LinkedIn
by Christopher Lau 16 Apr '12

16 Apr '12

LinkedIn ------------ I'd like to add you to my professional network on LinkedIn. - Christopher Christopher Lau ODP Associate at Baxter Healthcare United States Confirm that you know Christopher Lau: https://www.linkedin.com/e/qmxwak-h14gpxie-1a/isd/6709452220/_Ma-PXTx/?hs=f… -- You are receiving Invitation to Connect emails. Click to unsubscribe: http://www.linkedin.com/e/qmxwak-h14gpxie-1a/q4TF6l0mGNnJlSZF-zGBU1EDXRtE03… (c) 2012 LinkedIn Corporation. 2029 Stierlin Ct, Mountain View, CA 94043, USA.

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Fwd: Chimera (any version) + Nvidia GeForce GT 430 1GB + OpenSuse (11.0 or 12.1)
by Elisabeth Ortega 28 Mar '12

28 Mar '12

Dear Chimera development team, I have a little problem when I use Chimera with my new Video card Nvidia geforce GT 430. Chimera runs well the firsts 2 minutes but, then, it gets stucked and I can't move whatever I had open in these moment (even if I had a little model of less than 50 atoms!). I've been updated the drivers of the video card twice and also I re-installed the operating System but Chimera remains getting stucked. Before change the Video Card (first I had a ATI Radeon (I don't remember the model) of 1GB) Chimera runs perfectly. Anyone has any idea of how can I fix it without change the video card? (the best solution is using back the ATI video card... but I want to use NVidia in my computer) I'm running Chimera over Linux (Opensuse 11.0 32 bits and Opensuse 12.1 64 bits) in a Intel Dual core CPU E8400 @ 3.00 GHz with 2 GB of RAM. Thank you in advance. Elisabeth Ortega-Carrasco Ph.D. Student. Universitat Autònoma de Barcelona (Spain)

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Re: [chimera-dev] IDE
by Eric Pettersen 07 Feb '12

07 Feb '12

On Feb 6, 2012, at 6:33 PM, Elnaz Rezaei wrote: > I need to know what are the functions and properties of "atom > object" do in chemira. > I searched but I could not find! Hi Elnaz, In IDLE you can type "dir(chimera.Atom)" to see the names of all methods/attrs of Atom, or "help(chimera.Atom)" to get a longer but somewhat more readable listing. We do have some information in the Chimera Programmer's Guide: Chimera Programmer's Guide but an encyclopedic listing of Atom attrs/methods isn't part of it. If you said what you were looking to accomplish I could probably offer better advice. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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