- Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] Chimera Shutting Down
by Tom Goddard 31 Mar '14

31 Mar '14

Hi Joshua, Glad to hear that the new graphics driver fixed the Chimera side view crash on your Ubuntu 12.04 system. Maybe this will help some other Chimera users. Tom On Mar 31, 2014, at 12:33 PM, Joshua Broyde wrote: > Dear Tom, > I installed a new graphics driver, so now it works. In case anybody else has this same problem, I installed the Gallium Radeon driver and it worked fine. I followed step 2 from this link: > http://arstechnica.com/civis/viewtopic.php?f=16&t=1137372 > > Thanks for the tip. > Sincerely, > Joshua Broyde > ----- Original Message ----- > From: "Tom Goddard" <goddard(a)sonic.net> > To: "Joshua Broyde" <jb3401(a)c2b2.columbia.edu> > Cc: chimera-users(a)cgl.ucsf.edu > Sent: Thursday, March 27, 2014 12:58:50 AM > Subject: Re: [Chimera-users] Chimera Shutting Down > > The crash is due to a buggy graphics driver and the only fix is likely to be installing a working graphics driver. Sometimes some trick like starting the side view before opening models as described in the post you referenced avoids the problem, but usually there is no way to avoid a graphics driver crash other than replace the driver with one that doesn’t have the bug. > > Tom > > > On Mar 26, 2014, at 6:05 AM, Joshua Broyde wrote: > >> Hi, >> I am using the Chimera Linux 64-bit (chimera-alpha-linux_x86_64.bin), and Chimera shuts down when I try to open the Side View option. I tried the workaround mentioned here: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2013-April/008765.html but it is not working for me. >> >> OS: Ubuntu 12.04 >> Version of Chimera: Linux 64-bit Daily Build (Mar 24, 2014) >> >> >> For what it's worth, on another computer where I am running Ubuntu 12.10, with Chimera Linux 64-bit Daily Build (July 10, 2013), I did not have this problem. >> Is there another workaround that I could do to open the side view? >> >> Thanks! >> >> Sincerely, >> Joshua Broyde >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> >

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Binding pocket surface command script not working
by Markus Heller 28 Mar '14

28 Mar '14

Hello, I'm trying to reproduce the Binding Pocket Surface image from the Gallery with a different pdb file. I can successfully reproduce with the pdb used in the example (2zcp), but not with 2v5z. Running latest Chimera. Steps to reproduce: open 2v5z delete :.b split atoms :sag surface measure contactArea #0.2 #0.1 3 slab -.1,0 color tan gives an error: error: Array must be 2-dimensional, got 1-dimensional File "C:\Program Files\Chimera 1.8.1\share\MeasureVolume\__init__.py", line 60, in surface_area area = surface_area(varray, tarray) See reply log for Python traceback. Why, and would it be helpful to file a bug report? Thanks and Cheers Markus -- Markus Heller, Ph.D. NMR Scientist CDRD - The Centre for Drug Research and Development 2405 Wesbrook Mall, Fourth Floor | Vancouver, BC V6T 1Z3 | Main: (604) 827-1147 Direct: (604) 827-1122 | F: (604) 827-1299 | E: mheller(a)cdrd.ca<mailto:mheller@cdrd.ca> | www.cdrd.ca [cid:image007.png@01CF49BD.0097D1F0] Follow us: [Description: cid:image003.jpg@01CD86A6.39B41A10] <https://twitter.com/C_D_R_D> [Description: cid:image005.jpg@01CD86AE.B197F5D0] <http://www.linkedin.com/groups/CDRD-3186016/about?report%2Esuccess=3NcE4iZo…> [Description: cid:image009.png@01CD86AE.B197F5D0] <https://www.facebook.com/pages/The-Centre-for-Drug-Research-and-Development…> [Description: cid:image010.png@01CD86AE.B197F5D0] <http://www.youtube.com/user/CDRDCVI?view_as=public> This email and any files transmitted with it are confidential and intended solely for the addressee. If you are not the named addressee you should not disseminate, distribute, copy, or alter this email.

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Chimera surface error
by Elaine Meng 28 Mar '14

28 Mar '14

On Mar 28, 2014, at 4:27 AM, Uzma Saqib wrote: > Hi Elaine, > Chimera is not showing me the surface of my protein file and gives the attached eror. > i tried what it suggested, but no improvement. > plz help. > attashed , is the pdb. This is a common problem in Chimera. Some explanation and all of our ideas for possible solutions are in this page (no use for me just to repeat that information here): <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html> #3 and #4 in that page will always work because they use different methods instead of the standard molecular surface calculation. Sorry for the inconvenience, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco P.S. better to send chimera questions to chimera-users(a)cgl.ucsf.edu, unless including private data

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Measuring surface area of region
by Anindito Sen 28 Mar '14

28 Mar '14

Dear all, I was wondering if there is any way one can measure the surface area with a threshold higher than its neighbouring region in a TEM micrograph ? Thanks Andy Dr. Anindito Sen (Ph.D) >

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Chimera Shutting Down
by Joshua Broyde 27 Mar '14

27 Mar '14

Hi, I am using the Chimera Linux 64-bit (chimera-alpha-linux_x86_64.bin), and Chimera shuts down when I try to open the Side View option. I tried the workaround mentioned here: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2013-April/008765.html but it is not working for me. OS: Ubuntu 12.04 Version of Chimera: Linux 64-bit Daily Build (Mar 24, 2014) For what it's worth, on another computer where I am running Ubuntu 12.10, with Chimera Linux 64-bit Daily Build (July 10, 2013), I did not have this problem. Is there another workaround that I could do to open the side view? Thanks! Sincerely, Joshua Broyde

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Viewing Gromacs 4.6.5 trajectories
by William McDonald 26 Mar '14

26 Mar '14

Hello Chimera users, I recently upgraded my gromacs simulation software from 4.5.5 to 4.6.5; however, when I attempt to load a new simulation trajectory (either a .xtc or .trr file), Chimera allocates ~13GB RAM causing my machine to swap, and Chimera never loads the trajectory. The old trajectories from gromacs 4.5.5 load with out any problems. Has anyone else experienced this? I am using 64 bit Chimera 1.8.1 on a dual quad-core Mac Pro running OS 10.6.8. The simulation has ~50000 atoms of protein, lipid, and water and is 1ns long. -- William J. McDonald Postdoctoral Scholar Department of Chemistry and Biochemistry University of California, Santa Cruz

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selection color
by George Tzotzos 26 Mar '14

26 Mar '14

Hi everybody, I’ve conducted Principal Component Analysis on a trajectory and generated an ensemble of structures (see attachment, pc2.pdb). There should be a way of coloring (occupancy?) the most mobile regions of the protein (e.g. residues 67 - 72). I haven’t found a way to do this. Any help would be much appreciated. Best regards George

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stereo3D
by Dougherty, Matthew T 26 Mar '14

26 Mar '14

I have a toshiba qosmio x875-7390 S3D laptop, which is based on the NVidia NVision 3D. Toshiba structured the device to be user unfriendly, limiting stereo3D for bluray and youtube 3d via adobe flash. coming across a pymol S3D post I see there is a workaround, for a different Toshiba model. http://nanonan.wordpress.com/2012/03/28/pymol-and-coot-3d-stereo-on-qosmio-… http://coxcoppes.nl/3DScreenActivator/index.php?pagina=1 Any comments about chimera using S3D on NVidia NVision 3D? Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine

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(no subject)
by Francesco Pietra 23 Mar '14

23 Mar '14

Hello: About stereo drawings with chimera (GNU Linux), I received from the editorial staff: All stereoview illustrations have been drawn in the cross-eye mode, i.e. the > picture for the right eye is on the left and vice versa. > Has this been chosen deliberately? In our opinion, the parallel-eye mode > seems to be used more often. > Please let us know whether we should switch the figures (you would not need > to send new ones) or not. They did the job of transformation to parallel-eye. Next time, I would like to be able to do that myself, while I don't see the parallel-eye mode in chimera. Which is the equivalent? thanks francesco pietra

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Detection of Internal water along MD trajectory
by James Starlight 20 Mar '14

20 Mar '14

Dear Chimera users! I've performed md simulation of water soluble protein having water-assessable channel in its interior. I'd like to perform analysis of average number of water molecules detected within the protein interior during MD trajectory with the possible visualization of such internal water binding sites. Does SASA calculation which I've seen in vmd could provide me with additional insights? I'd be thankful if you provide me with some Chimera tools suitable for such task. Many thanks for help, James

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