- Chimera-users - RBVI Mailing Lists

starting chimera
by Bala subramanian 26 May '09

26 May '09

Friends, I downloaded the latest chimera build and installed it successfully without any error. When i give chimera in command line, i get the following error. But when i start the chimera 1.3 version, it works without any problem. I am using the latest build in Fedora 10. Traceback (most recent call last): File "/usr/local/chimera_new/share/__main__.py", line 65, in <module> value = chimeraInit.init(sys.argv) File "/usr/local/chimera_new/share/chimeraInit.py", line 374, in init tkgui.initializeGUI(exitonquit, debug_opengl) File "CHIMERA/share/chimera/tkgui.py", line 2587, in initializeGUI File "/usr/local/chimera_new/lib/python2.5/site-packages/PIL/__init__.py", line 309, in checkConfig File "/usr/local/chimera_new/lib/python2.5/site-packages/Togl.py", line 27, in __init__ Tkinter.Widget.__init__(self, master, "togl", cnf, kw) File "/usr/local/chimera_new/lib/python2.5/lib-tk/Tkinter.py", line 1930, in __init__ (widgetName, self._w) + extra + self._options(cnf)) _tkinter.TclError: couldn't choose pixel format Couldn't configure togl widget Thanks, Bala

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Chimera API
by christopher lau 26 May '09

26 May '09

Hi, Does anyone have any documentation on the chimera API? I want to familiarize myself more with the commands that can be used in the Chimera IDLE and python scripts. I have looked at the Example tutorials ( http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Examples/) but aside from the commands used in the tutorial I do not know how to perform other actions on the molecule. One of the commands I would like to run is to rotate the molecule ("roll", in the command line) using IDLE commands. Thanks for your help, Chris

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nmrclust additional request
by Austin B. Yongye 22 May '09

22 May '09

Hi chimera-users/developers, Is there a way to save all the structures (not only the representative structures) of all the clusters identified from an ensemble cluster analysis into their respective clusters? The g_cluster tool of gromacs does these, but I don't think it uses Kelley values to determine the optimal number of clusters. Any help will be greatly appreciated. I would like to perform further analyses on each cluster. Thanks, Austin-

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define attribute error
by Roberto Kopke Salinas 22 May '09

22 May '09

Dear All, I am trying to color code a structure according to HetNOE. When I load the attribute list using "Define Attribute" via the "Structure Analysis" menu the program does not automatically open the "Render by Attribute" menu. If I click and open the "Render by Attribute" menu, the program does not show my file in the attributes list for residues. Does anyone have an idea of why this happen? I have pasted my attribute's list below. Thank you, Roberto attribute: teste recipient: residues :377.000000 0.842818 :378.000000 1.273292 :379.000000 0.763398 :384.000000 0.852818 :387.000000 0.999787 :388.000000 0.572572 :389.000000 1.016109 :393.000000 0.950908 :397.000000 0.761818 :399.000000 0.712411 :402.000000 0.388721 :403.000000 0.495060 :408.000000 0.460664 :411.000000 0.973597 :412.000000 1.036187

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Aspect ratio
by hsosa＠aecom.yu.edu 21 May '09

21 May '09

Is there a way to specify the aspect ratio of the display window. Let say that I want to make sure that it is 4 by 3 or 16 by 9. I want to make chimera movies that are easy to merge with still images using some video editing programs (e.g. Windows MovieMaker) and these programs assume some standard video formats (with a given aspect ratio). The results when using movie clips and images created with arbitrary and different aspect ratios is not very good (jumpy transitions) so I would like to create all images and movie clips with the same (standard) aspect ratio. Thanks Hernando -- ----------------------------------- Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 FAX (718) 430-8819 email hsosa(a)aecom.yu.edu -----------------------------------

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povray error using surfrepr mesh
by Sebastian Kruggel 20 May '09

20 May '09

Dear Chimera-users and team, I tried to generate a POV-Ray image making use of mesh style surface by > surfrepr mesh When I go to 'save image' with activated POV-Ray option, I get the attached error message. I tried several versions ('stable' and daily build, linux and windows) and different molecules but it doesn't work out. Isn't it possible to get raytraced mesh-surface pictures in chimera or do I miss anything? Thanks in advance and best regards Sebastian Kruggel -- Sebastian Kruggel Institut für Pharmazie Bundesstr. 45 | Raum 112 (406) D 20146 Hamburg Tel +49 (0)40 42838-3626 (-3484) kruggel(a)chemie.uni-hamburg.de Surface ANP_in_1j1bB, category main, probe radius 1.4, vertex density 2 1 connected surface components Total solvent excluded surface area = 345.475 Total solvent accessible surface area = 606.13 running "/usr/local/chimera/bin/povray" "/home/kruggel/chimera/4wiebke/image.ini" "+I/home/kruggel/chimera/4wiebke/image.pov" "+O/home/kruggel/chimera/4wiebke/image.png" "+V" povray: cannot open the user configuration file /home/kruggel/.povray/3.6/povray.conf: No such file or directory Persistence of Vision(tm) Ray Tracer Version 3.6.1 (g++ -pipe -ansi -pthread -fPIC -I/home/chimera/chimeraBuild_X11/build/build/include 3.3.4 @ i686-pc-linux-gnu) This is an unofficial version compiled by: UCSF Chimera <chimera(a)cgl.ucsf.edu> The POV-Ray Team(tm) is not responsible for supporting this version. POV-Ray is based on DKBTrace 2.12 by David K. Buck & Aaron A. Collins Copyright 1991-2003 Persistence of Vision Team Copyright 2003-2004 Persistence of Vision Raytracer Pty. Ltd. Primary POV-Ray 3.5/3.6 Developers: (Alphabetically) Chris Cason Thorsten Froehlich Nathan Kopp Ron Parker Contributing Authors: (Alphabetically) Steve Anger Eric Barish Dieter Bayer Steve A. Bennett David K. Buck Nicolas Calimet Aaron A. Collins Chris Dailey Steve Demlow Andreas Dilger Alexander Enzmann Dan Farmer Mark Gordon Christoph Hormann Mike Hough Chris Huff Kari Kivisalo Lutz Kretzschmar Jochen Lippert Pascal Massimino Jim McElhiney Douglas Muir Juha Nieminen Bill Pulver Eduard Schwan Wlodzimierz Skiba Robert Skinner Yvo Smellenbergh Zsolt Szalavari Scott Taylor Massimo Valentini Timothy Wegner Drew Wells Chris Young Other contributors are listed in the documentation. Support libraries used by POV-Ray: ZLib 1.2.3, Copyright 1995-1998 Jean-loup Gailly and Mark Adler LibPNG 1.2.16, Copyright 1998-2002 Glenn Randers-Pehrson LibJPEG 6b, Copyright 1998 Thomas G. Lane LibTIFF 3.8.0, Copyright 1988-1997 Sam Leffler, 1991-1997 SGI Redirecting Options All Streams to console..........On Debug Stream to console.........On Fatal Stream to console.........On Render Stream to console........On Statistics Stream to console....On Warning Stream to console.......On Parsing Options Input file: /home/kruggel/chimera/4wiebke/image.pov (compatible to version 3.61) Remove bounds........On Split unions.........On Library paths: /usr/local/chimera/share/povray-3.6 /usr/local/chimera/share/povray-3.6/ini /usr/local/chimera/share/povray-3.6/include /usr/local/chimera/share/fonts Output Options Image resolution 1730 by 1280 (rows 1 to 1280, columns 1 to 1730). Output file: /home/kruggel/chimera/4wiebke/image.png, 24 bpp PNG Graphic display......Off Mosaic preview.......Off CPU usage histogram..Off Continued trace......Off Tracing Options Quality: 9 Bounding boxes.......On Bounding threshold: 1 Light Buffer.........On Vista Buffer.........On Draw Vista Buffer....Off Antialiasing.........On (Method 1, Threshold 0.300, Depth 3, Jitter 1.00) Clock value: 0.000 (Animation off) 0:00:00 Parsing File: /home/kruggel/chimera/4wiebke/image.pov Line: 92 Parse Warning: Should have at least 2 objects in csg.

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POV-RAY tracing in Mac OSX (a workaround)
by Miguel Ortiz Lombardia 20 May '09

20 May '09

Hi, I'm almost sure that this problem has been reported here... but couldn't find anything about it. When I try to ray-trace [Chimera 1.3 build 2572 (Darwin/aqua)] I consistently get this error: File Context (5 lines): } object { text { ttf "verdana.ttf" "$" 0.01, 0 texture Parse Error: Cannot open font file. It appears even if I have no labels on the image. I managed to solve the problem but only when I asked for the povray intermediate files not to be deleted and then manually edit them: A) image.ini file: I changed the line: Library_Path="/Applications/Chimera.app/Contents/Resources/share/fonts/" to Library_Path="/Applications/Chimera.app/Contents/Resources/share/fonts/ freefont/" B) image.pov file: All calls to verdana.ttf were changed to FreeSans.ttf It would be great if you point me to an easier solution or if you could make such changes in the code. Thanks! Miguel -- Miguel Ortiz Lombardía Architecture et Fonction des Macromolécules Biologiques UMR6098 ( CNRS, U. de Provence, U. de la Méditerranée ) Case 932 163 Avenue de Luminy 13288 Marseille cedex 9 France Tel : +33(0) 491 82 55 93 Fax: +33(0) 491 26 67 20 e-mail: miguel.ortiz-lombardia(a)afmb.univ-mrs.fr Web: http://www.pangea.org/mol/spip.php?rubrique2

2 1

residue order for match/rmsd
by Klaus Kopec 19 May '09

19 May '09

Hi everybody, at first I would like to thank you for Chimera, it's the best structure viewer I am aware of! Now to my question: I would like to match residues in two structures, but not in the numerical order. My expectation was that if I run "match #0:1,2,3@CA #1:3,2,1@CA" I would end up with least squares fitted coordinate pairs (#0:1, #1:3), (#0:2, #1:2) and (#0:3, #1:1). What I get, however, is a least-squares fit of pairs (#0:1, #1:1), (#0:2, #1:2) and (#0:1, #1:3). Is it possible to use the order of coordinate pairs given in the command line (e.g. pair first specified coordinate of protein 1 with first specified coordinate of protein 2, second with second, etc.) instead of the numerical order of the residue numbers? I would be really glad if someone could help me out on this! Klaus PS: I use Chimera 1.3.2577 under a 64-Bit Kubuntu. I also tried some older (1.2.something) version which gave the same results.

2 2

2d labels and pov-ray option
by Bala subramanian 19 May '09

19 May '09

Friends, I opened a molecule, made some 2d labels and saved the image in jpeg format. But the 2d labels are not apperaing in the final picture. What could be the reason for the same ? When i try to set POV-RAY as True and save the image, the POV-RAY progress till 98% and stays for longtime but dosent save the image. Has anyone come across such problems before ? Thanks, Bala

2 1

residue order for match/rmsd
by Klaus Kopec 19 May '09

19 May '09

Hi everybody, at first I would like to thank you for Chimera, it's the best structure viewer I am aware of! Now to my question: I would like to match residues in two structures, but not in the numerical order. My expectation was that if I run "match #0:1,2,3@CA #1:3,2,1@CA" I would end up with least squares fitted coordinate pairs (#0:1, #1:3), (#0:2, #1:2) and (#0:3, #1:1). What I get, however, is a least-squares fit of pairs (#0:1, #1:1), (#0:2, #1:2) and (#0:1, #1:3). Is it possible to use the order of coordinate pairs given in the command line (e.g. pair first specified coordinate of protein 1 with first specified coordinate of protein 2, second with second, etc.) instead of the numerical order of the residue numbers? I would be really glad if someone could help me out on this! Klaus PS: I use Chimera 1.3.2577 under a 64-Bit Kubuntu. I also tried some older (1.2.something) version which gave the same results.

1 0

Principal axis of inertia
by A. Di Fenza 18 May '09

18 May '09

Hi Tom, I saw your message on the web and I tried to use your script on Chimera 1.3. Unfortunately it does not work, it give me the following message: 0 models opened Do you think it is because of the Chimera version? Do you have suggestion? Thank you very much, Armida Oops. That script I posted for calculating the inertia of a molecule had some problems. The printed matrix of axes was transposed though the correct axes were used for the displayed ellipsoid. Also I was using inertia matrix I_ij = sum_over_k(m_k*r_ki*r_kj) omitting the diagonal term. Should have been I_ij = sum_over_k(m_k*(|r_k| - r_ki*r_kj)). And finally I incorrectly computed the ellipsoid size along each axis. Everything was a little bit wrong. Here's the fixed version. Tested in Chimera version 1.2500 but should work with earlier versions. Tom

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multiple morphs
by Charles Midgett 18 May '09

18 May '09

Dear Chimera developers, I am trying to make a movie of how we think domains of our complex interact. Essentially, there will be three morphs, made from different pdb files, that need to be displayed simultaneously. How can I get the three trajectories to happen at the same time? Sincerely, Charles Midgett

2 1

Saving Render by Attribute Values
by Kevin Wu 18 May '09

18 May '09

Hi all, I'm having trouble saving some data to the session. I've rendered a figure using the "render/select by attribute" by either the occupancy or beta field in a pdb file. However, when I save session and restore it, the colors that I've chosen seem to be erased, and need to be reset again. Is there a way to save this data? Thanks in advance! Kevin Wu

4 4

fit map --nogui
by sean connell 18 May '09

18 May '09

Hello, I am having some problems using/adapting a script I found by searching the mailing list. The script is pasted below but to summarize it should print out the transformation matrix used to fit one map to another. In principle I would like to do the same but in addition to writing out the matrix I would also like to apply it and save the resulting map. I am currently using chimera 1.4 build 27496 (Aqua on OSX 10.5.7) the first problem I have is just invoking the python interpreter..... if I use: Chimera.app/Contents/MacOS/chimera --nogui fittomap.py Executing fittomap.py... Traceback (most recent call last): File "/Users/src/Downloads/Chimera.app/Contents/Resources/share/ __main__.py", line 65, in <module> value = chimeraInit.init(sys.argv) File "/Users/src/Downloads/Chimera.app/Contents/Resources/share/ chimeraInit.py", line 407, in init chimera.openModels.open(a, prefixableType=1) File "/Users/src/Downloads/Chimera.app/Contents/Resources/share/ chimera/__init__.py", line 1357, in open models = func(filename, *args, **kw) File "/Users/src/Downloads/Chimera.app/Contents/Resources/share/ chimera/__init__.py", line 794, in _openPython loadFunc(sandboxName, fileName, f) File "fittomap.py", line 70, in <module> fit_map_in_map(p1, p2) File "fittomap.py", line 24, in fit_map_in_map from VolumeViewer import Data_Region, full_region, Rendering_Options ImportError: cannot import name Data_Region Error while processing fittomap.py: ImportError: cannot import name Data_Region (see reply log for Python traceback info) # ----------------------------------------------------------------------------- # Example script for fitting one map in another without the graphical user # interface. # # chimera --nogui fitnogui.py # # It can also be run using the graphical Chimera interface using File/ Open. # def fit_map_in_map(map1_path, map2_path, initial_map1_transform = None, map1_threshold = None, ijk_step_size_min = 0.01, # Grid index units ijk_step_size_max = 0.5, # Grid index units max_steps = 100, optimize_translation = True, optimize_rotation = True): # Files have to have file suffix indicating volume format. from VolumeData import open_file data1 = open_file(map1_path) data2 = open_file(map2_path) from VolumeViewer import Data_Region, full_region, Rendering_Options ro = Rendering_Options() map1 = Data_Region(data1, full_region(data1.size), '', ro) map2 = Data_Region(data2, full_region(data2.size), '', ro) if initial_map1_transform: from PDBmatrices.matrices import chimera_xform xf = chimera_xform(initial_map1_transform) map1.surface_model().openState.globalXform(xf) use_threshold = (map1_threshold != None) from FitMap import map_points_and_weights, motion_to_maximum points, point_weights = map_points_and_weights(map1, use_threshold) if len(points) == 0: if use_threshold: print 'No grid points above map threshold.' else: print 'Map has no non-zero values.' return move_tf, stats = motion_to_maximum(points, point_weights, map2, max_steps, ijk_step_size_min, ijk_step_size_max, optimize_translation, optimize_rotation) if initial_map1_transform: from PDBmatrices.matrices import multiply_matrices move_tf = multiply_matrices(move_tf, initial_map1_transform) header = ('\nFit map %s in map %s using %d points\n' % (map1.full_name(), map2.full_name(), stats['points']) + ' correlation = %.4g, overlap = %.4g\n' % (stats['correlation'], stats['overlap']) + ' steps = %d, shift = %.3g, angle = %.3g degrees\n' % (stats['steps'], stats['shift'], stats['angle'])) print header from FitMap.gui import transformation_description tfs = transformation_description(move_tf) print tfs # ----------------------------------------------------------------------------- # Example call fitting map into itself. # p1 = p2 = '/usr/local/src/chimera-demos/volume/examples/groel.mrc' fit_map_in_map(p1, p2)

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Solvent Occupancy Calculation
by Saikumar Ramadagu 18 May '09

18 May '09

Hi Elaine, I know people in the past have asked a question about the solvent Occupancy Calculation, but please help me. I have an oligosaccharide simulaiton trajectory from AMBER9. I used a 100ps trajectory for solvent occupancy calculation using Chimera. Everything looks absolutely fine. The questions I have are as follows: I have 0-220 in my levels section of volume viewer. If I fix the level of 80, what does that mean? When I'm sliding the bar of levels from left-right what information about solvent density am I obtaining? For example does a value of 80 mean low density when compared with a value of 70? or is it the other way? When I have two different oligosaccharide simulations and I want to say that oligosaccharide 1 has more water density around it, what value of levels should I choose? What I mean by this statement is do I select same value of levels? or do I calculate the percentage i.e., 80/220 for first model gives me 36% and for second sugar if the levels are 0-300 the i should choose a level of 109 which gives 36%? Also is there any reference paper by which Chimera calculates the solvent occupancy? Thanks very much for your time Sai

2 1

Formation of coordination bond
by Enrico Morelli 18 May '09

18 May '09

Dear all, We would like to know if is it possible, when we have two molecules docked together, to form a coordination bond between a metal ion present in one of the two molecules and a donor atom of the other molecule, in such way forming a covalent bond between the two proteins. Thanks -- ------------------------------------------------------------------- (o_ (o_ //\ Coltivate Linux che tanto Windows si pianta da solo. (/)_ V_/_ +------------------------------------------------------------------+ | ENRICO MORELLI | email: morelli(a)CERM.UNIFI.IT | | * * * * | phone: +39 055 4574269 | | University of Florence | fax : +39 055 4574253 | | CERM - via Sacconi, 6 - 50019 Sesto Fiorentino (FI) - ITALY | +------------------------------------------------------------------+

3 2

A request
by Soumya Ghosh (Systembiologie) 18 May '09

18 May '09

Dear Chimera, Thanks for giving such a wonderful software for molecular modelling. I am a PhD student in Germany and using the CHIMERA programme for my molecule. I want to increase the font and the font size of the highlighted amino acid in my protein and thats why I was trying in the Command: Tools - Utilities - Colour key where there is a option for font size but so far remain unsuccessful. Can you kindly advise me how I should proceed. Waiting eagerly for your kind reply, Soumya Ghosh, TUM, Freising, Germany

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Verify integer/non-integer charges in mol2
by Francesco Pietra 18 May '09

18 May '09

Hi: I assigned Amber ff99SB charges to a proven pdb file of standard amino acids and capping groups (ACE NME), saving as mol2. Conversion to a pdbqt file with ATD (autodock tool) resulted in non-integer charge (-5...). Unless something occurred that escaped my attention, the protein has -5.00000 charge. My question: how to verify a posteriory the total charge in the Chimera-written mol2 file, in order to trace back were I have blurred things? I don't see the total in the mol2 file. Thanks francesco pietra

2 2

Morphing with two models
by Enrico Morelli 18 May '09

18 May '09

Dear all, I'm a new chimera user and I'm asking about morphing. I've two models and I'm able to move one to contacts the other. But what if I need to move both to converge on a specific center? There is some shortcut? Thanks to all -- ------------------------------------------------------------------- (o_ (o_ //\ Coltivate Linux che tanto Windows si pianta da solo. (/)_ V_/_ +------------------------------------------------------------------+ | ENRICO MORELLI | email: morelli(a)CERM.UNIFI.IT | | * * * * | phone: +39 055 4574269 | | University of Florence | fax : +39 055 4574253 | | CERM - via Sacconi, 6 - 50019 Sesto Fiorentino (FI) - ITALY | +------------------------------------------------------------------+

2 4

apple ui
by Nils Becker 15 May '09

15 May '09

hi, just a quick user interface suggestion: it would be great if mouse-over over all directory listings (when choosing files to load etc) could activate the mouse wheel for both x and y scrolling. right now, only placing the cursor directly over the scroll bars allows scrolling by mouse wheel, and there is only one mouse wheel axis to scroll with. i am on mac is x 10.5.6 and using a recent native snapshot cheers, nils

3 3

Floating exception
by hsosa＠aecom.yu.edu 14 May '09

14 May '09

Hi, I am having the following problem with the latest production version of Chimera (1.3) on a linux computer. Chimera crash and exit after doing some actions like rotating a molecule several times or simply trying to open the side-view window. After the program ends there is a Floating exception message in the console. The problem occur with the latest production release (1.3) and daily build versions but not with an older production version of chimera (1). I installed the latest nvidia driver but this didn't solve the problem. I am running the old linux 2.4 kernel (Suse 9.0) and I am not sure if this has anything to do with the problem . I am hesitant to upgrade the OS and break all the other programs that now work in this machine (you got to love linux :-)) Thanks Hernando Computer: Dual Xeon processor. Graphic card: NVIDIA Quadro4 XGL 9800 OS: Linux Suse 9.0 UCSF Chimera 1.3 Thanks Hernando -- ----------------------------------- Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 FAX (718) 430-8819 email hsosa(a)aecom.yu.edu -----------------------------------

2 1

DMS citation
by Ben Keshet 14 May '09

14 May '09

Hi, I have used DMS to calculate accessible surface prior to the usage of Dock6. Is there any specific citation for the DMS application? Thank you, Ben Keshet Chemical Engineering UMBC

1 0

surface spanning multiple models
by Nils Becker 14 May '09

14 May '09

Hi, is it possible to define surfaces that seamlessly span multiple models? when i define a surface category spanning multiple models, i always get distinct surfaces around each model. saving as a single pdb and re-importing does not help, since then i have the same problem with multiple submodels... thanks for any help! cheers, nils

2 1

Multiple sequence alignment
by Avner Schlessinger 13 May '09

13 May '09

Dear Chimera experts, Once I create multiple structure alignment i was wondering how I can view the corresponding multiple sequence alignment. when I try to view it through the MultiAlignViewer it shows all possible pairwise alignments with the sequence of the first structure rather than all the sequences together. Thanks! Avner -- Avner Schlessinger, Ph.D. Department of Bioengineering and Therapeutic Sciences Mission Bay, Byers Hall 1700 4th Street, Suite 501 University of California, San Francisco San Francisco, CA 94158-2330 Tel +1 (415) 514-4258 Fax +1 (415) 514-4231

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a small suggestion
by Jean Didier Pie Marechal 13 May '09

13 May '09

Hello everyone, just a small suggestion to the team. Could it be possible that, when clicking on a given angle/torsion in the Structure measurments panel, the involved atom/bond get selected in the visualizer? cheers JD Dr. Jean-Didier Maréchal Lecturer Computational Biotechnological Chemistry @ Transmet 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 ----- Missatge original ----- De: chimera-users-request(a)cgl.ucsf.edu Data: Dimarts, Maig 12, 2009 9:00 pm Assumpte: Chimera-users Digest, Vol 73, Issue 13 > Send Chimera-users mailing list submissions to > chimera-users(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > or, via email, send a message with subject or body 'help' to > chimera-users-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimera-users-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-users digest..." > > > Today's Topics: > > 1. Re: chimera performance (Greg Couch) > 2. adding pseudo bonds (Jean Didier Pie Marechal) > 3. Re: adding pseudo bonds (Elaine Meng) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Mon, 11 May 2009 14:32:22 -0700 (PDT) > From: Greg Couch <gregc(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] chimera performance > To: Bala subramanian <bala.biophysics(a)gmail.com> > Cc: chimera-users(a)cgl.ucsf.edu > Message-ID: <Pine.OSF.4.63.0905111420070.1959390(a)guanine.cgl.ucsf.edu> > Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed > > I have had bad luck with NVidia drivers packaged as RPMs. Instead > I > recommend that you uninstall the RPM you got from rpmfusion.org and > install the NVidia driver from NVidia at > <http://www.nvidia.com/Download/index.aspx>. The "Nvidia.com > Binary > Installer" option given the webpage you cited. As mentioned there, > the > disadvanatge of NVIdia's driver is that you need to reinstall it > every > time your update your kernel -- otherwise the X server won't start. > After > a successful install (and reboot), glxinfo should tell you which > OpenGL > renderer you have and chimera should work too. > > Good luck, > > Greg > > On Fri, 8 May 2009, Bala subramanian wrote: > > > Dear Greg, > > After installing nvidia graphics drivers, i am not able to open > chimera. I > > have attached the xconfig file and the output of glxinfo as text > files.> > > *[cbala@ramana ~]$ chimera > > Traceback (most recent call last): > > File "/usr/local/chimera/share/__main__.py", line 65, in <module> > > value = chimeraInit.init(sys.argv) > > File "/usr/local/chimera/share/chimeraInit.py", line 361, in init > > tkgui.initializeGUI(exitonquit, debug_opengl) > > File "CHIMERA/share/chimera/tkgui.py", line 2525, in initializeGUI > > File "/usr/local/chimera/lib/python2.5/site- > packages/PIL/__init__.py",> line 309, in checkConfig > > > > File "/usr/local/chimera/lib/python2.5/site-packages/Togl.py", > line 27, in > > __init__ > > Tkinter.Widget.__init__(self, master, "togl", cnf, kw) > > File "/usr/local/chimera/lib/python2.5/lib-tk/Tkinter.py", line > 1930, in > > __init__ > > (widgetName, self._w) + extra + self._options(cnf)) > > _tkinter.TclError: could not create rendering context > > Couldn't configure togl widget* > > > > I installed the nvidia driver as follows. I installed it based on > the> information given in the nvidia install guide in the following > link.> > > http://www.mjmwired.net/resources/mjm-fedora-nvidia.html#pci_id > > > > su -c 'rpm -ivh > > http://download1.rpmfusion.org/free/fedora/rpmfusion-free-release- > stable.noarch.rpm> ' > > su -c 'rpm -ivh > > http://download1.rpmfusion.org/nonfree/fedora/rpmfusion-nonfree- > release-stable.noarch.rpm > > ' > > su -c 'rpm --import /etc/pki/rpm-gpg/RPM-GPG-KEY-rpmfusion-*' > > su -c 'yum install kmod-nvidia' > > > > Then i gave the following command > > > > nvidia-xconfig as root. Then i restarted the system. Now i am > able to see > > nvidia display setting. When i give chimera, it dosent work. > > > > Bala > > > > On Thu, May 7, 2009 at 8:44 PM, Greg Couch <gregc(a)cgl.ucsf.edu> > wrote:> > >> Looking at your chimera benchmark scores and at the scores on > the web page, > >> http://socrates2.cgl.ucsf.edu/trac/chimera/wiki/benchmarks, it > looks like > >> you don't have the NVidia graphics driver installed. And that > would make a > >> *huge* difference. To double-check, run the glxinfo command and > look at the > >> "OpenGL renderer string:" line, it should have NVIDIA in it > instead of Mesa. > >> To get the NVidia drivers, go to < > >> http://www.nvidia.com/Download/index.aspx>. > >> > >> - Greg > >> > >> > >> On Thu, 7 May 2009, Bala subramanian wrote: > >> > >> Dear Greg, > >>> You are right. Previously it was normal but now it is slow. I > havent>>> updated > >>> the kernel. I checked and noticed that i dnt have any memory > intensive>>> background jobs also. > >>> > >>> I did benchmarks with two chimera versions 1.3 (attached file > chim_test)>>> and > >>> chimera 1.4 (attached chim_test1). > >>> My graphics card is nVIDIA GETFORCE 9300MG, VRAM: 256 MB. I dnt > know how > >>> to > >>> compare and judge what is going wrong. I wud appreciate your > help on the > >>> same. > >>> > >>> Thanks, > >>> Bala > >>> > >>> So it was formerly fast on the same computer? This could > happen on a > >>> Linux > >>> > >>>> computer if you updated the kernel and forgot to reinstall the > graphics>>>> driver (from ATI or NVidia, the open source 3D drivers > still need work, > >>>> but > >>>> are improving). Another possibility, on all operatings > sytems, is that > >>>> there is a background process that is using a lot of CPU or > memory, so > >>>> chimera doesn't have the resources it used to. > >>>> > >>>> If you just want to check the graphics performance, then you > can use the > >>>> Benchmark tool in Tool / Utilities to guage the current > performance. And > >>>> then you can compare to the reported scores to see if your > graphics>>>> performance is reasonable (the Show button in the > Benchmark tool brings > >>>> up > >>>> the web page). > >>>> > >>>> - Greg > >>>> > >>>> > >>> > > > > > ------------------------------ > > Message: 2 > Date: Tue, 12 May 2009 17:19:46 +0200 > From: Jean Didier Pie Marechal <JeanDidier.Marechal(a)uab.cat> > Subject: [Chimera-users] adding pseudo bonds > To: chimera-users(a)cgl.ucsf.edu > Message-ID: <165553c1104b.4a09afb2(a)uab.es> > Content-Type: text/plain; charset=iso-8859-1 > > Dear all, > > what is the way to add pseubond between metal and chelating atoms? > if you could tell me what are the "mouse driven" and "script > driven" manner I'll be very pleased.... > all the best, > JD > > > Dr. Jean-Didier Mar?chal > Lecturer > Computational Biotechnological Chemistry @ Transmet > Unitat de Qu?mica F?sica > Departament de Qu?mica > Universitat Aut?noma de Barcelona > Edifici C.n. > 08193 Cerdanyola (Barcelona) > Tel: +34.935814936 > e-mail: JeanDidier.Marechal(a)uab.es > > ----- Missatge original ----- > De: chimera-users-request(a)cgl.ucsf.edu > Data: Diumenge, Maig 10, 2009 9:00 pm > Assumpte: Chimera-users Digest, Vol 73, Issue 11 > > > Send Chimera-users mailing list submissions to > > chimera-users(a)cgl.ucsf.edu > > > > To subscribe or unsubscribe via the World Wide Web, visit > > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > or, via email, send a message with subject or body 'help' to > > chimera-users-request(a)cgl.ucsf.edu > > > > You can reach the person managing the list at > > chimera-users-owner(a)cgl.ucsf.edu > > > > When replying, please edit your Subject line so it is more specific > > than "Re: Contents of Chimera-users digest..." > > > > > > Today's Topics: > > > > 1. Protonate heteroatoms only (Francesco Pietra) > > 2. Re: Protonate heteroatoms only (Eric Pettersen) > > > > > > ------------------------------------------------------------------ > -- > > -- > > > > Message: 1 > > Date: Sat, 9 May 2009 23:35:37 +0200 > > From: Francesco Pietra <chiendarret(a)gmail.com> > > Subject: [Chimera-users] Protonate heteroatoms only > > To: chimera <chimera-users(a)cgl.ucsf.edu> > > Message-ID: > > <b87c422a0905091435q4a1671e2td61284cf092e7fb6(a)mail.gmail.com> > > Content-Type: text/plain; charset=UTF-8 > > > > Hi: > > Is there a command in Chimera to protonate (Sybyl-type) the > > heteroatoms only (or deprotonate the other elements from a fully > > protonated protein)? > > thanks > > francesco pietra > > > > > > ------------------------------ > > > > Message: 2 > > Date: Sat, 9 May 2009 15:27:55 -0700 > > From: Eric Pettersen <pett(a)cgl.ucsf.edu> > > Subject: Re: [Chimera-users] Protonate heteroatoms only > > To: Francesco Pietra <chiendarret(a)gmail.com> > > Cc: chimera <chimera-users(a)cgl.ucsf.edu> > > Message-ID: <67264749-1F9E-4B02-9B42-FF0A1DD99C30(a)cgl.ucsf.edu> > > Content-Type: text/plain; charset=US-ASCII; format=flowed > > > > del HC > > > > will delete all hydrogens bonded to carbons (their IDATM types > are > > HC). > > --Eric > > > > Eric Pettersen > > USCF Computer Graphics Lab > > > > On May 9, 2009, at 2:35 PM, Francesco Pietra wrote: > > > > > Hi: > > > Is there a command in Chimera to protonate (Sybyl-type) the > > > heteroatoms only (or deprotonate the other elements from a fully > > > protonated protein)? > > > thanks > > > francesco pietra > > > _______________________________________________ > > > Chimera-users mailing list > > > Chimera-users(a)cgl.ucsf.edu > > > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > > > > > > ------------------------------ > > > > _______________________________________________ > > Chimera-users mailing list > > Chimera-users(a)cgl.ucsf.edu > > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > > > > End of Chimera-users Digest, Vol 73, Issue 11 > > ********************************************* > > > > > > ------------------------------ > > Message: 3 > Date: Tue, 12 May 2009 08:39:11 -0700 > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] adding pseudo bonds > To: JeanDidier.Marechal(a)uab.es > Cc: chimera-users(a)cgl.ucsf.edu > Message-ID: <06B51782-B5EB-487A-B770-ACA04AA2D738(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes > > Hi JD, > The "user interface" (i.e. no programming) way is to create a text > file listing the desired pseudobonds and their colors and read it > in > with PseudoBond Reader. The tool and file format are described here: > <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/pbreader/pbreader.… > > > > I don't know the python way, but perhaps looking in the code for > PseudoBond Reader will help ( share/PBReader/ within your Chimera > installation). > Best, > Elaine > ----- > Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > http://www.cgl.ucsf.edu/home/meng/index.html > > > > On May 12, 2009, at 8:19 AM, Jean Didier Pie Marechal wrote: > > > Dear all, > > > > what is the way to add pseubond between metal and chelating atoms? > > if you could tell me what are the "mouse driven" and "script > driven" > > manner I'll be very pleased.... > > all the best, > > JD > > > > ------------------------------ > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > End of Chimera-users Digest, Vol 73, Issue 13 > ********************************************* >

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