- Chimera-users - RBVI Mailing Lists

ligand comformation clustering
by Maurice Ho 06 May '10

06 May '10

Hi there, How to cluster the different conformations of a ligand after a docking experiment according to their relative orientations in the binding pocket? Any software can help to do so? I've tried the Ensemble Cluster function in Chimera but it seems clustering the different conformations according to the relative positions of the atoms of the ligand itself. I know that the command rmsd #0.1:UNK #0.2:UNK (UNK is the ligand) could be a way to illustrate how distant in average between different conformations. How could I make use of this command in script so that I could have all the possible comparisons and cluster them in a sensible way? Best regards, Maurice Ho

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Re: [Chimera-users] Sequential stereo
by Greg Couch 05 May '10

05 May '10

(Forgot to cc the list.) Chimera already works with NVidia's 3D Vision, in Windows XP/Vista/7 and Linux, as long as you have a 3D Vision supported Quadro FX card, see <http://www.nvidia.com/object/quadro_pro_graphics_boards.html> for details. Since chimera does stereo within a window, the GeForce cards are not supported. FYI, the latest NVidia drivers, version 197.59, have a bug that affects chimera stereo, so you'll need to use an earlier version of the driver (or presumably a latter version which has the bug fixed). When working with chimera in stereo, you really want a display that shows full resolution left and right eye images, and that generally means that the display refreshes at 120 Hz for 60Hz per-eye (100Hz would work too). If they don't support 120Hz, then the left and right eye images are interlaced when transmitted to the display and adjacent pixels can end up being shown in opposite eyes. And that makes 2D text, like the text in labels or dialogs, very fuzzy until you take the glasses off, but that makes the 3D fuzzy. That is annoying, but if the display is cheap enough, you might be able to live with it :-). For large groups of people, the cost of the active glasses becomes significant (and maintaining the batteries is a chore). So for a large display, I'd recommend considering a technology with passive glasses, like the RealD LP, <http://www.reald.com/Content/proProducts.aspx?pageID=122>, and the DepthQ Polarization Modulator, <http://www.depthq.com/modulator.html>. They are setups for a projector that polarizes the light onto a silver screen (that reflects polarized light coherently) and you use cheap polarized glasses to view the content (same glasses as a movie theater with RealD 3D). And if you use this technology, then you have the option of using a NVidia Quadro FX graphics card or an ATI FirePro graphics card (only the V8700, V8800, and V8750 have stereo DIN connectors). Hope this helps, Greg On 05/05/2010 08:47 AM, Daniel Hitchcock wrote: > Howdy, > > My advisor was interested in setting up a large display (52" screen) > with a computer controlling it for viewing and presentation of > structures in chimera. I have been commissioned to purchase the > hardware, and naturally I want to take it a step further. > > With new "3D Ready" LG and Samsung displays (as opposed to regular > >120Hz displays) they supposedly have an extra chip to properly sync > with an incoming 3D signal from a device, be it a bluray player or > whatever. Nvidia has begun to work on their system and promises a > software update to their 3Dvision line which would allow for the > native signal to be sent to the screen as opposed to just sending a > sequential 2D signal. My questions (if that all made sense), > > 1. Is there or will there be support for nvidia's 3d Vision line? We > will be running windows 7 and the program itself will be run in > windowed mode probably, not always full screen. > > 2. If that does not work, what would be the best recommendation for > some sort of stereoview (prefereably sequential) on a large LCD or > plasma display? > > > Thanks for the help! > -Daniel Hitchcock

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Sequential stereo
by Daniel Hitchcock 05 May '10

05 May '10

Howdy, My advisor was interested in setting up a large display (52" screen) with a computer controlling it for viewing and presentation of structures in chimera. I have been commissioned to purchase the hardware, and naturally I want to take it a step further. With new "3D Ready" LG and Samsung displays (as opposed to regular >120Hz displays) they supposedly have an extra chip to properly sync with an incoming 3D signal from a device, be it a bluray player or whatever. Nvidia has begun to work on their system and promises a software update to their 3Dvision line which would allow for the native signal to be sent to the screen as opposed to just sending a sequential 2D signal. My questions (if that all made sense), 1. Is there or will there be support for nvidia's 3d Vision line? We will be running windows 7 and the program itself will be run in windowed mode probably, not always full screen. 2. If that does not work, what would be the best recommendation for some sort of stereoview (prefereably sequential) on a large LCD or plasma display? Thanks for the help! -Daniel Hitchcock

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Adjust torsion and bump checking
by Kim, Sunghoon 04 May '10

04 May '10

Hi all, I would like to do the bump checking for the various rotameric states of a specific side chain generated by the rotation about dihedral angles. Bumps were detected by chimera command 'rotation' and 'findclash' and at first the script seemed working OK, but I'm not sure if the chi angles were correctly defined. When we look at the 'clashes/contacts' panel in Chimera, there are atom options for "Near" and "Far" positions in the rotating bonds. How can I specifying the 'Near' and 'Far' atoms in my 'rotation' command line in my python script to define my chi angles ? Thanks in advance for any info that you can provide. Thanks, Sunghoon Kim

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place fragment (again)
by Elisabeth Ortega 04 May '10

04 May '10

Dear all, We are trying to place a fragment in an exact position. We created a fragment with tetrahedral symmetry and we are trying to link an atom of other molecule at 2.00 A of the central atom of the new fragment and making a certain angle (120 degrees for example) with one of the substituents to get the correct orientation of the new fragment. Has anybody an idea that how can we do that? Thanks.

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about centroid
by Francesco Pietra 03 May '10

03 May '10

On running movie with centroid - as I was instructed by Eric; sorry I lost the email - I noticed that on long runs a shift is introduced between the protein and the centroid thread. To restore the relative positions between protein and centroid thread, I had to bring back (through the movie) the centroid to its initial position. francesco pietra

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rmsd between two ligands
by Miriam Gochin 01 May '10

01 May '10

Is there a way in chimera to obtain an RMSD between two structures without matching them, ie. just to know the difference between them? Miriam Gochin Touro University - CA miriam.gochin(a)tu.edu 707-638-5463

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Volume Subtractions
by Murali Ayaluru 30 Apr '10

30 Apr '10

Dear Chimera users/developers, I have two EM density maps (in mrc format) of a complex with different conformations. I want to subtract one density from another. I am wondering if it is possible in Chimera to subtract the densities? Cheers, Murali

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(no subject)
by Hanzhong Liu 28 Apr '10

28 Apr '10

Dear Chimera Developer: I tried to use Chimera to display MD movie. I tried both CHARMM trajectory and single pdb. They all works. When I put "ksdssp" in the per-frame script, it gave me a warning "name ksdssp is not defined". I used the latest version and the OS is windows 7. But when I ran chimera under windows xp, there is no such problem. I'm wondering if there is a bug of chimera. Thanks!-

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DCD format error 1
by Lilian OLIVIERI 28 Apr '10

28 Apr '10

Hello, I'm having trouble using MD/Ensemble analysis tool. When I try to check a MD trajectory generated by CHARMM (version C33b1), I get a "DCD format error 1" message. Here is the Reply Log: MDTools 1.2 Exp (2005-08-20) by James Phillips. Trajectory.DCD.MDToolsMarch97.md.help() for more info. - HomoCoord 1.3 Exp (2005-08-20) - Constants 1.1 Exp (2004-05-17) - AtomGroup 1.4 Exp (2007-02-07) - local 1.1 Exp (2004-05-17) Unknown OSTYPE ??? set. Viewing and plotting are disabled. - Trans 1.2 Exp (2005-08-20) - DCD 1.10 Exp (2007-02-07) - Data 1.2 Exp (2005-08-20) * THIS FILE IS LANGEVINEEF1.INP. * USAGE, CHARMM <LANGEVINEEF1.INP >LANGEVINEEF1.OUT. * RUNS LANGEVIN DYNAMICS WITH EEF1 IMPLICIT WATER. * DATE: 3/22/10 10:32:48 CREATED BY USER: lolivier /labos/lbgm/lolivier/chimera/share/Trajectory/DCD/MDToolsMarch97/md_DCD.py:121: DeprecationWarning: raising a string exception is deprecated raise "DCD format error 1" Traceback (most recent call last): File "CHIMERA/lib/python2.5/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py", line 1747, in __call__ File "CHIMERA/share/chimera/baseDialog.py", line 328, in command File "CHIMERA/share/chimera/baseDialog.py", line 543, in OK File "CHIMERA/share/Trajectory/EnsembleLoader.py", line 92, in Apply File "CHIMERA/share/Trajectory/DCD/__init__.py", line 61, in loadEnsemble File "CHIMERA/share/Trajectory/DCD/__init__.py", line 71, in loadEnsemble File "CHIMERA/share/Trajectory/DCD/DCD.py", line 35, in __init__ File "CHIMERA/share/Trajectory/DCD/MDToolsMarch97/md_DCD.py", line 121, in __init__ DCD format error 1 DCD format error 1 File "CHIMERA/share/Trajectory/DCD/MDToolsMarch97/md_DCD.py", line 121, in __init__ See reply log for Python traceback. Is there a quick way to fix this problem? Thanks for any reply. -- Lilian Olivieri PhD student INSERM UMR-S 665, DSIMB/LBGM, Faculte des Sciences et Technologies Universite de La Reunion 15 Avenue René Cassin, BP 7151 97715 Saint Denis Messag Cedex 09 La Réunion, France Tel: +33 262 938 227 (office) Fax: +33 262 938 237 http://lbgm.univ-reunion.fr/ http://www.dsimb.inserm.fr/ **************************************************************************** It has long been an axiom of mine that the little things are infinitely the most important. -- Sir Arthur Conan Doyle, "A Case of Identity" ****************************************************************************

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