June 2012 - Chimera-dev - RBVI Mailing Lists

Re: [chimera-dev] Chimera/Python sparse matrices
by Greg Couch 06 Dec '13

06 Dec '13

On 8/13/2010 12:06 PM, Forbes J. Burkowski wrote: > What are the steps that need to be taken if the Python used in Chimera is > to have the ability to import functions from SciPy or PySparse? > > Thanks for any advice that you can provide. > > Cheers, > Forbes Burkowski If you want to use prebuilt SciPy binaries with chimera, you need one that is compatible with the version of chimera that chimera is using. Chimera 1.4.x uses Python 2.5, and the daily builds use Python 2.7. You would add those packages to chimera by either (1) given the '--pypath dir' command line option, (2) setting your CHIMERAPTH environment variable (instead of PYTHONPATH, PYTHONPATH is ignored so chimera won't be accidentally broken by other installed Pythons), or (3) add the installation directory to sys.path in Python. If you're not using a daily build on Linux, then you should edit CHIMERA/share/chimeraInit.py and comment out or remove the part that sets the RTLD_GLOBAL flag -- it appears to be no longer needed and its presence breaks SciPy. If you're going to compile from source, which you'll need to do if you're using a daily build, I'd recommend trying PySparse first, since it is a smaller package. Python packages that incorporate C (or C++ or Fortran) code are more difficult than prebuilt binaries because (a) you need a compiler, and (b) if the code calls the Python C API, you need a compatible compiler, ideally the same one as what the rest of Chimera was build with. PySparse needs BLAS and LAPACK libraries and optionally wants UMFPACK and/or SuperLU. On on Redhat and Fedora Linux, you can get the first three libraries by installing the blas-devel, lapack-devel, and suitesparse-devel packages. Chances are you'll be able to install PySparse into chimera's python by running "CHIMERA/bin/pythonXXX setup.py install" in the pysparse source tree (where CHIMERA is the path to where chimera was installed). On Linux, you might have to set the LD_LIBRARY_PATH environment variable to CHIMERA/lib. On Mac OS X, the path to the chimera binary is CHIMERA/Contents/Resources/bin/pythonXXX and the environment variable is DYLD_LIBRARY_PATH. Or you could install PySparse into another Python and use the --pypath/CHIMERAPATH/sys.path approach as given above. Hope this helps, Greg

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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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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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Chimera-dev June 2012