October 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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sort a list of residues based on the id.position values
by Jean Didier Pie Marechal 26 Oct '12

26 Oct '12

Hi guys, how could I sort a list of residues based on their id.position value? thanks a lot 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 ----- Missatge original ----- De: chimera-dev-request(a)cgl.ucsf.edu Data: Dijous, Octubre 18, 2012 9:00 pm Assumpte: Chimera-dev Digest, Vol 102, 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://plato.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: Moving a residue and an VRML object (Tom Goddard) > 2. Re: Moving a residue and an VRML object (Greg Couch) > 3. Re: Moving a residue and an VRML object (Eric Pettersen) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Wed, 17 Oct 2012 13:25:18 -0700 > From: Tom Goddard <goddard(a)sonic.net> > To: ladam <ladam(a)smbh.univ-paris13.fr> > Cc: chimera-dev(a)cgl.ucsf.edu > Subject: Re: [chimera-dev] Moving a residue and an VRML object > Message-ID: <507F142E.4080906(a)sonic.net> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > The arrow you drew has no idea that the atoms have moved, so of > course > it doesn't move with them. If you just want to rigidly rotate the > whole > molecule in Python you can change the matrix that places it in space > > mol.openState.xform = xf > > instead of changing the coordinates of atoms. Then you could > rigidly > move the VRML model in the same way so that the arrow stays in the > same > position relative to the molecule. > > vrml.openState.xform = xf > > If you are not moving the molecule rigidly then you really do need > to > move individual atoms and then you will have to delete the old > arrow and > make a new arrow if it is intended to have its ends follow certain > atoms. > Tom > > > -------- Original Message -------- > Subject: [chimera-dev] Moving a residue and an VRML object > From: ladam > To: chimera-dev(a)cgl.ucsf.edu > Date: 10/17/12 4:45 AM > > Hi all, > > I have a problem associating a vrml object an a molecule : > > Let's say I have an arrow created using the bild format to which > I gave > > 0.0 0.0 0.0 coordinates. > > This arrow and the molecule translate/rotate together using the > mouse.> Now if I translate / rotate my molecule using the setcoord > command on > > the atoms in a python script, the arrow won't follow up the > molecule.> I tried the addAssociatedModel command to link the arrow > and the > > molecule but still the same result. > > How can I handle this? > > Thanks for your attention > > > > > > ------------------------------ > > Message: 2 > Date: Wed, 17 Oct 2012 15:21:35 -0700 > From: Greg Couch <gregc(a)cgl.ucsf.edu> > To: Tom Goddard <goddard(a)sonic.net> > Cc: chimera-dev(a)cgl.ucsf.edu, ladam <ladam(a)smbh.univ-paris13.fr> > Subject: Re: [chimera-dev] Moving a residue and an VRML object > Message-ID: <507F2F6F.30800(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Salut, > > The other trick is to give the VRML model the same model id and > submodel > id as its associated model. Then the openState is identical, so > there > would be no need to copy the transformation matrix. Again, this > only > works for rigid rotations. > > -- Greg > > On 10/17/2012 01:25 PM, Tom Goddard wrote: > > The arrow you drew has no idea that the atoms have moved, so of > course > > it doesn't move with them. If you just want to rigidly rotate > the > > whole molecule in Python you can change the matrix that places it > in > > space > > > > mol.openState.xform = xf > > > > instead of changing the coordinates of atoms. Then you could > rigidly > > move the VRML model in the same way so that the arrow stays in > the > > same position relative to the molecule. > > > > vrml.openState.xform = xf > > > > If you are not moving the molecule rigidly then you really do > need to > > move individual atoms and then you will have to delete the old > arrow > > and make a new arrow if it is intended to have its ends follow > certain > > atoms. > > > > Tom > > > > > > -------- Original Message -------- > > Subject: [chimera-dev] Moving a residue and an VRML object > > From: ladam > > To: chimera-dev(a)cgl.ucsf.edu > > Date: 10/17/12 4:45 AM > >> Hi all, > >> I have a problem associating a vrml object an a molecule : > >> Let's say I have an arrow created using the bild format to which > I gave > >> 0.0 0.0 0.0 coordinates. > >> This arrow and the molecule translate/rotate together using the > mouse.>> Now if I translate / rotate my molecule using the setcoord > command on > >> the atoms in a python script, the arrow won't follow up the > molecule.>> I tried the addAssociatedModel command to link the > arrow and the > >> molecule but still the same result. > >> How can I handle this? > >> Thanks for your attention > >> > > > > _______________________________________________ > > Chimera-dev mailing list > > Chimera-dev(a)cgl.ucsf.edu > > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev > > > > ------------------------------ > > Message: 3 > Date: Wed, 17 Oct 2012 15:26:03 -0700 > From: Eric Pettersen <pett(a)cgl.ucsf.edu> > To: ladam <ladam(a)smbh.univ-paris13.fr> > Cc: chimera-dev BB <chimera-dev(a)cgl.ucsf.edu> > Subject: Re: [chimera-dev] Moving a residue and an VRML object > Message-ID: <C66C5891-76C8-4D20-B82E-572E6F919DF2(a)cgl.ucsf.edu> > Content-Type: text/plain; charset="us-ascii" > > On Oct 17, 2012, at 3:21 PM, Greg Couch wrote: > > > Salut, > > > > The other trick is to give the VRML model the same model id and > submodel id as its associated model. Then the openState is > identical, so there would be no need to copy the transformation > matrix. Again, this only works for rigid rotations. > > ...and the simplest way to do this is to supply the "sameAs" > keyword, with the associated model as the argument, to the > openModels.add() or openModels.open() call that you use. > > --Eric > > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > > >

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Problem with m.openState.xform.getCoordFrame() ?
by ladam 24 Oct '12

24 Oct '12

Hi all, I noticed this : >>> >>> print m.openState.xform 0.23153 -0.972828 0 0 0.972828 0.23153 0 0 0 0 1 0 >>> print m.openState.xform.getCoordFrame()[0] 0.23153 0.972828 0 >>> print m.openState.xform.getCoordFrame()[1] -0.972828 0.23153 0 >>> print m.openState.xform.getCoordFrame()[2] 0 0 1 >>> Looks like there is a problme with signs here between first two elements [0] and [1] with respect to m.openState.xform or am I missing something? Bye -- -------------------------------- 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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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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Chimera-dev October 2012