- Chimera-users - RBVI Mailing Lists

Colored Rays
by Mark Cunningham 12 Jun '06

12 Jun '06

Elaine, thanks for your response to my question on the coordinate system problem. My problem, as you suggested, was not related to coordinate systems, rather there was a problem with GOLD writing extra coodinates (electron pair coordinates) to its output file, which caused the structures to have enormously large rmsd, so much until the GOLD ligand appeared to be in a different coordinate system relative to the reference ligand. After going in and deleting the extra coordinates, everything worked fine. But now I have another question. Occassionally, while visualizing and manipulating a protein structure (1XAP) with Chimera, I get colored rays (30-40) stretching across the screen. Is this a bug in the program? How can I stop this from happening? If I close Chimera, and open it again, it works for a while, and then sporadically the rays reappear. Thanks. Mark A. Cunningham, Ph.D. Assistant Professor of Chemistry CPO 2191 Berea College Berea, KY 40404 (859)985-3029 Office (859)985-3303 Fax

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Sporadic Colored Rays Across Screen
by Mark Cunningham 11 Jun '06

11 Jun '06

Elaine and Eric, thanks for your responses to my question on the coordinate system problem. My problem, as you suggested, was not related to coordinate systems, rather there was a problem with GOLD writing extra coodinates (electron pair coordinates) to its output file, which caused the structures to have enormously large rmsd, so much until the GOLD ligand appeared to be in a different coordinate system relative to the reference ligand. After going in and deleting the extra coordinates, everything worked fine. But now I have another question. Occassionally, while visualizing and manipulating a protein structure (1XAP) with Chimera, I get colored rays (30-40) stretching across the screen. Is this a bug in the program? How can I stop this from happening? If I close Chimera, and open it again, it works for a while, and then sporadically the rays reappear. Thanks. Mark A. Cunningham, Ph.D. Assistant Professor of Chemistry CPO 2191 Berea College Berea, KY 40404 (859)985-3029 Office (859)985-3303 Fax

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Reading Frame Problem
by markcunningham 10 Jun '06

10 Jun '06

Could someone please help with this. . Using Chimera, I am trying to calculate rmsd between an observed ligand versus GOLD docked ligand, however the problem is the ligands load into different reading frames. The format for both ligands is .mol2. How can I correct this problem, in other words load both ligands into the same reading frame so that I can then calculate their rmsd. Thanks. Mark

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Reading Frames
by Mark Cunningham 09 Jun '06

09 Jun '06

Hopefully someone can please respond to this before the weekend. I have Windows version of Chimera. I am using Chimera to run rmsd between observed ligands and GOLD calculated ligands. When I open both ligands ( with .mol2 format) with Chimera, they load in different reading frames, thus I can't make the rmds calculation. Please address this issue. The rmsd works fine otherwise, its just with the GOLD ligand files that I am getting the reading frame problems. Thanks very much. Mark Mark A. Cunningham, Ph.D. Assistant Professor of Chemistry CPO 2191 Berea College Berea, KY 40404 (859)985-3029 Office (859)985-3303 Fax

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Writing a .x3d file that other programs can read
by Esther Bullitt 07 Jun '06

07 Jun '06

Hi, I am having trouble exporting a .x3d file in a format which programs that convert .x3d data to VRML data can read. The error message for one of them is: Xj3D Version: 1_0 Device found: Mouse-0 Device found: Keyboard-0 Error: Unexpected Exception: Unknown field name: chimera:hither for node: org.web3d.vrml.renderer.ogl.nodes.navigation.OGLViewpoint@1080876 Error: Failed to load file -- The ultimate goal is to have a VRML file that includes both the EM surface map and the pdb subunit structure together in a file that can be read by one of the companies that laser etches the structure into a glass cube. Some companies can read the pdb, some the VRML, but none can read both. Chimera says the .x3d can be converted into .vrml if there are no clipping planes or perspective, which there are not. But I still get this error. Any suggestions, pls? thanks, Esther --- Esther Bullitt, Ph.D. Dept. of Physiology & Biophysics, Room W302 Boston University School of Medicine 715 Albany Street (mail only; couriers use 700 Albany Street) Boston, MA 02118-2526 Email: bullitt(a)bu.edu Telephone: 617-638-5037 Facsimile: 617-638-4041

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1.2251 snapshot release
by Eric Pettersen 06 Jun '06

06 Jun '06

Hi all, There is a new snapshot release (1.2251) available, with a potpourri of new features, listed below. The release is for all platforms, but on Mac we had a little difficulty getting things to work for OS X 10.3, so this release is 10.4 only, but the next production release will include 10.3 support. --Eric Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu --- 1.2251 release (changes since 1.2199 release) GENERAL: Session files are smaller, use less memory, and start faster. CIF/mmCIF files can be read (or fetched by ID from RCSB) Electron density maps can be fetched by PDB ID from Electron Density Server Virus Particle Explorer (VIPER) files can be fetched by ID VIPER input automatically starts Multiscale Models and constructs viral capsid Thinner default ribbons Files opened by scripts (either Python or Chimera commands) are now searched for relative to the script location, not Chimera's startup location. Can switch to sequential stereo mid-session without having used --stereo at startup (except on certain Windows systems) New stereo mode: anaglyph (offset red/cyan-tinged views, like 3D movies) NEW TOOLS: Add Charge (Structure Editing) - assigns partial charges to atoms; Amber (Cornell et al. 1995) charges used for standard residues, Amber's Antechamber module (now included with Chimera) used to calculate charges for nonstandard residues Build Structure (Structure Editing) - under construction but basic functions work; not much documentation ReadStdin (Utilities) - allows communication with Chimera through standard input/output TOOL CHANGES: AddH (Structure Editing) - new options including how to treat histidines Adjust Torsions (Structure Editing) - interface reorganized to show atoms defining a torsion in order 1-2-3-4 - options added to control decimal places and show degree symbol in angle labels Dock Prep (moved to Structure Editing) - option added to delete alternate locations of atoms - hydrogen addition and charge addition details split off into separate tools called from Dock Prep (AddH and Add Charge, respectively) - terminal carboxylates/amines completed as appropriate Effects (Viewing Controls) - background transparency option added (previously only available as --bgopacity startup option) Minrms Plot (Structure Comparison) - Show Alignment option added MPOSE extension removed (Structure Comparison) Multalign Viewer (Structure Comparison) - .ali extension interpreted as PIR format - .pfam extension no longer indicates Stockholm format, instead indicates Pfam format ("Plain Pfam format" at the Sanger Institute Pfam site) - changed default residue letter/region colors for improved readability - improved editing response time - editing no longer pushes residues that are not in the active region - added control over whether a region depiction spans gaps - option to associate a structure chain with the best-matching sequence in the alignment (when criteria for automatic association are not met) - new Edit menu allowing sequence reordering and deletion, gap column addition and deletion COMMAND CHANGES: ribbonjr removed NEW COMMANDS: addcharge - assign partial charges to atoms (command-line implementation of new Add Charge tool) intersurf - generate and display interface surfaces (command-line implementation of Intersurf) setattr - set a new or existing attribute to a specified value surftransparency - adjust molecular surface transparency COMMAND CHANGES: longbond - now takes an atom or model specification to restrict the calculation to certain models TUTORIALS: figures added to Getting Started tutorials

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Stereographics support
by Eduardo Sanz Garcia 01 Jun '06

01 Jun '06

Hi, We've recently purchased a Stereographics E-2 Emitter to go with our Mac G5 equipped with an NVIDIA Quaddro FX 4500 Graphics Card. As far as we know, the hardware is hooked up correctly, but when we try to run Chimera using command "./chimera --stereo", the following error appears: 'Unable to find hardware stereo support TOGL Couldn't get visual' We called the Stereographics company regarding this error and they mentioned that our software should have "blue line code" enabled. They couldn't give me more details because they said they were unfamiliar with Chimera. Could someone enlighten us with how we can get Chimera to run with stereo enabled? Thanks.

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-S option in ksdssp command
by kovzany＠go.com 01 Jun '06

01 Jun '06

Dear All, I'm trying to get an output with protein secondary structure assignment into a text file, using ksdssp command, unfortunately everytime I get error like this: Computing secondary structure assignments for model #0 using ksdssp (Kabsch and Sander Define Secondary Structure of Proteins) with the parameters: energy cutoff <default> minimum helix length <default> minimum strand length <default> -S option not yet available My question is: am I doing something wrong, or -S option is not yet implemented, despite it is described in ksdssp.html help file? thanks, PK

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Question regarding an inorganic compound to display with Chimera
by Allen Stock 26 May '06

26 May '06

HI, I'm interested in viewing the 3D structure for the following inorganic component: Tantalum Pentaethoxide ... also known as TAETO The following company gives a 3D representation of the compound. Any idea where I can find a 3D description that can be displayed with Chimera. Thanks for your attention and feedback. Regards, --Allen

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editing Python saved sessions
by Jonathan Hilmer 22 May '06

22 May '06

Notepad++ will do a great job of editing the .py files. I've found that this is an extremely convenient way to accomplish certain tasks, such as precise alignment of multiple clipping planes. However, you definitely have to know what you're looking for when digging through the files. On a related issue, I have a question regarding the saved sessions. In some of the viral capsid models I've created a saved session is enormous (about 60 megabytes) and fails to compile either automatically when loading the .py session or manually using the python.exe included with Chimera. It seems to be a result of excessive explicit attribute assignments that I don't really care about (color etc) since they are easy enough to set once the model has loaded. Does anyone have any suggestions or experience with this issue? Jonathan PS: Check out the most recent issue of Science. Although the editors chose the least visually impressive submission, non of the variations would have been possible without Chimera: great program. > Hello. My name is Anne Szklarski and I am a student at The College of New > Jersey. I was wondering if there was a way that the python files could be > modified in notepad. Does it require the Python software? The reason I ask > is because I have been renaming certain atoms in the .ent files using > notepad so that I may specifically select them in chimera. The only > problem with my current method is that I have to start the rendering > process from the beginning which is quite time consuming. So I was > wondering if there was a way that I could alter the chimera file directly > and not lose any of the colors, etc. that I have chosen. I appreciate any > information on this matter. > > Thank you, > Anne Szklarski

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Question
by szklars2＠tcnj.edu 21 May '06

21 May '06

Hello. My name is Anne Szklarski and I am a student at The College of New Jersey. I was wondering if there was a way that the python files could be modified in notepad. Does it require the Python software? The reason I ask is because I have been renaming certain atoms in the .ent files using notepad so that I may specifically select them in chimera. The only problem with my current method is that I have to start the rendering process from the beginning which is quite time consuming. So I was wondering if there was a way that I could alter the chimera file directly and not lose any of the colors, etc. that I have chosen. I appreciate any information on this matter. Thank you, Anne Szklarski

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Problems installing/running chimera
by Christian Schafmeister 21 May '06

21 May '06

Hi there, I tried installing the latest snapshot of chimera for windows: chimera-1.2224-win32.exe as well as the production release 1.2199 and I get an error when it tries to start up. Dialog box: pythonw.exe - Entry Point Not Found The procedure entry point ?pathSeparator@PathFactory@otf@@SADXZ could not be located in the dynamic link library libotf.dcl When I try chimera --debug I get File "C:\Program Files\Chimera\share\chimera\__init__.py", line 15 in ? from _chimera import * ImportError: DLL load failed: The specified procedure could not be found. Return code: 1 I have python 2.4.2 already installed on my machine, is that causing a problem? Cheers, .Chris. -- Christian E. Schafmeister, Ph.D. Assistant Professor Chemistry Department University of Pittsburgh

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Chimera crash on SGI
by Thomas Goddard 19 May '06

19 May '06

Hi Jean-Fracois, If Chimera is crashing your SGI when using solid volume display this is almost surely a problem with your graphics driver. Are you using the IRIX operating system? Which version? Our documentation claims that IRIX 6.5.10 is needed but it may be that a more recent version is actually necessary to avoid the system crash you observe. If you are using an SGI Octane or similar vintage machine I would recommend you find a Windows, Mac, or Linux alternative since the graphics speed will be much better with a consumer graphics card. Tom > Date: Thu, 18 May 2006 14:25:57 -0400 (EDT) > From: jean-francois menetret <menetret(a)bu.edu> > To: Thomas Goddard <goddard(a)cgl.ucsf.edu> > Subject: Re: Volumes shown in Model Panel > > Hi Tom, > > I tried the version 1.2224 on a PC, it works very nicely > Would it be much trouble to have the snapshot compiled for SGI ? > It has been more convenient for me to work on an SGI except for a small > problem: if I click on solid (in the volume viewer), the whole machine=20 > crashes :-( > > best wishes > > Jean-Fran=E7ois

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Volumes shown in Model Panel
by Thomas Goddard 17 May '06

17 May '06

Hi Jean-Francois, I made a change after Chimera version 1.2199 that keeps the volume data sets in the Model Panel even when you press the Unshow button in the volume dialog. So the Model Panel and volume dialog menu should always list the same data sets. You need Chimera snapshot version 1.2224 which is on the download page below the production releases 1.2199 to get this improvement. In 1.2199 pressing the volume dialog unshow removes the volume from the Model Panel list. Tom > Date: Wed, 17 May 2006 11:03:30 -0400 (EDT) > From: jean-francois menetret <menetret(a)bu.edu> > To: Thomas Goddard <goddard(a)cgl.ucsf.edu> > Subject: question > > Hi Thomas, > > is there a way to keep the model panel list and the data sets list=20 > (from volume viewer) in sync ? > > Best wishes > > Jean-Franncois

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Chimera movie commands
by Thomas Goddard 16 May '06

16 May '06

Hi Frank, There are currently no Chimera commands for volume surfaces, and there are not commands to control per-model clipping. We wish to add these commands and others so that movie making is more powerful. Currently we are writing a renewal of our major 5-year grant due June 1 so it will probably not be possible for me to add these commands before then. Here is what is available now. There is a command for changing isosurface threshold level. It is part of "Animation commands" on the Chimera experimental features page. http://www.cgl.ucsf.edu/chimera/experimental/experimental.html It is not part of any Chimera distribution but can be downloaded separately and use with your current Chimera. The most practical way to gradually change from a surface to mesh would be to open the model twice, then gradually change the mesh color from completely transparent to opaque, then gradually change the surface from completely opaque to completely transparent. You can't do those two steps simultaneously because Chimera unfortunately does not correctly display two transparent models -- only one at a time. There are no commands to do volume surface color fades. You can do the color fades though using the Chimera animation editor called EMANimator distributed with EMAN. http://ncmi.bcm.tmc.edu/~stevel/EMAN/doc/ Get the latest EMAN distribution (nightly build) because it also is able to move per-model clip planes. To use EMANimator you install EMANimator the use Chimera menu Favorites / Preferences, category tools and add the EMAN chimeraext directory /usr/local/EMAN/chimeraext to the list of locations Chimera looks for extensions in. Here is some documentation I wrote for an older EMANimator version. http://www.cgl.ucsf.edu/chimera/related/emanimator/emanimator.html This is not an entirely trivial tool to use. It lets you create a timeline of transitions and preview them, and record a movie. The drawback is that it only supports a limited set of smooth transitions, mostly related to volume data display. It does not for instance handle 2D labels. Maybe you could add those in an external movie editor. Using EMANimator is a totally separate option from using Movie Recorder and commands. If you want to know all the current Chimera commands with "frame" options that can do transitions it is a short list: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/recorder/moviecomm… Unfortunately our animation tools are quite primitive now and you will need to make compromises if you want to use them. We are proposing to significantly improve animation capabilities in our new grant and will work on it even before then. So feedback about what is important to you is welcome. Tom ------------- > To: Thomas Goddard <goddard(a)cgl.ucsf.edu> > From: Frank Alber <frank(a)salilab.org> > Subject: chimera movie question > Date: Tue, 16 May 2006 17:39:15 -0700 > > Hi Tom, > I have a question about chimera. I need to make some movies with > chimera in which I like to switch on and off different models (using > the volume viewers volume densities) maybe introduce per-model clipping > and add and remove 2d labels during the movie. I figured out how to > rotate scale and move the model around based on command lines commands > that I read in as a file. Also, how to switch the model in the model > panel on and off. > But is it possible to use volume viewer commands on the command line? > So I could use them in a command file? For example switch the > representation of model 1 from surface to mesh. If so, is it possible > to change representations over a number of frames, so that they blur > into each other? Like the 'visibility show frames 100' option in the > 2dlabels command? I couldn't find such options in the manuel but I am > not sure if I looked careful enough. > In case, do you know anybody who I could ask for some cmd files (used > for moviemaking) that actually do similar stuff and which I could look > at as template examples? That would be great starting point to see what > commands could be useful for making movies. > I found an example on the web page, but it didn't have volume viewing > options there. > Thanks a lot! > Frank > > --- > Frank Alber > Andrej Sali Lab > California Institute for Quantitative Biomedical Research > University of California at San Francisco > QB3, Box2552 > 1700 4th Street, Room 501 > San Francisco, CA 94143-2552 (CA 94158 for courier delivery), USA > Phone: +1 (415) 514 4258 > Fax: +1 (415) 514 4231

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proposed "backbone" change
by Eric Pettersen 15 May '06

15 May '06

Hi all, RIght now, if you do "Actions->Atom/Bonds->backbone only" Chimera shows the minimum number of atoms to produce a connected peptide/ nucleic acid backbone, which therefore does not include peptide carbonyl oxygens nor nucleic sugar rings/charged phosphate oxygens. We are thinking of changing the behavior so that "backbone only" includes everything that isn't in the side chain/base. The question is: does anyone need/want the current behavior? If not, I'd not only change "backbone only" but would also change Select->Structure- >backbone from a menu (has "full" and "minimal" in it) to just a menu item that selects the full backbone. If there are some people who do use the current behavior, then instead I'd change "backbone only" to be a menu too. --Eric Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

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Non-gui chimera in a shell?
by James Vincent 09 May '06

09 May '06

Hello, I've read several threads about nongui use of chimera and that some work was started. This work seemed mainly aimed at getting a web server script to run chimera and return some result back to a browser. I'm interested in running chimera in a stand alone python script. I'd like to do molecular calculations using the various tools but all on a command line, no graphics. It seems the --nogui option would get this, but the OS X version does not seem to implement that. Perhaps I'm missing something. Can anyone help? ideally I'd like to just have a plain python script that imports the chimera package but does not choke on all the graphics stuff, and then lets me use the chimera object model and other programming objects. Thanks for any assistance, Jim ---- James J. Vincent, Ph.D. National Cancer Institute National Institutes of Health Molecular Modeling and Bioinformatics Section Laboratory of Molecular Biology Building 37, Room 5120 37 Convent Drive, MSC 4264 Bethesda, MD 20892 USA 301-451-8755 jjv5(a)nih.gov

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manual
by Oscar Moran 08 May '06

08 May '06

does exists a printable version of the manual? (pdf, ps or even simple ascii) oscar Oscar Moran, PhSc Istituto di Biofisica Consiglio Nazionale delle Ricerche Via DeMarini, 6 I-16149 Genova, Italy Tel. +39-0106475-558 / 522 Fax +39-0106475-500

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transparency at the command line
by Miguel Ortiz-Lombardia 07 May '06

07 May '06

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi chimerics, I'm not very familiar (yet) to python scripting in chimera, so I am trying to prepare a movie using just line commands in a file. I would like to gradually increase the transparency of a model's surface that has been colored in "rainbow by residue" style. My question is then: is there a way to control the overall transparency of a surface from the command line? I could resort to colordef commands at every step, but this would make things very hard with the rainbow coloring... Thanks a lot! Miguel ( trying to learn more python in the meantime ;) ) - -- Miguel Ortiz Lombardía Centro de Investigaciones Oncológicas C/ Melchor Fernández Almagro, 3 28029 Madrid, Spain Tel. +34 912 246 900 Fax. +34 912 246 976 e-mail: molatwork(a)yahoo.es - ---------------------------------------------------------------------- Et ainsi ne pouvant faire que ce qui est juste fût fort, on a fait que ce qui est fort fût juste. Blaise Pascal, Pensées -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.1 (Darwin) iD8DBQFEXaezF6oOrDvhbQIRAnUNAJ9UJOF3RWv7ohXj+pcmQeD6rU4VBwCfb7PK PDzmG1mMWWL6iW9o+a+ooXk= =Flu6 -----END PGP SIGNATURE-----

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B-factors
by Narender Singh Maan 05 May '06

05 May '06

Dear Chimera users, i am looking for a way to write down the average B-factors for each residue from a pdb file (which shows atomic bfactors). I tried using chimera attributes which can color the protein and shows a histogram for bfactors, but i am not able to get those average values in reply log or some other written file. Please let me know if i can get any help in this. thanxs ns

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Chimera under KDE (update)
by Mingfeng Yang 05 May '06

05 May '06

Please disregard my previous message. I just tried to kill the KDE system process one by one and found out that skim (an input program) is the one should be blamed. Mingfeng

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Can't input anything under KDE
by Mingfeng Yang 05 May '06

05 May '06

I am using Chimera build 2199 under KDE 3.5.2, and I can't input anything into the command line (and other input dialogs) of chimera. The linux distribution is Kubuntu Dapper Drake. If I get into the KDE environment with failsafe mode, everything is fine. And I remember chimera works fine under KDE 3.5.2 under gentoo. I guess some service(s) of KDE must have confliction with chimera, but I couldn't figure out which one. :( Best, Mingfeng

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absolute scale?
by Cathy Lawson 02 May '06

02 May '06

Hi, Is there a way to set an "absolute scale" for viewing in chimera? I'm trying to make pictures in multiple Chimera sessions with different molecules and would like for the results to be all on the same scale. I naively thought I could do this with the "camera" scale but then I noticed that for two different sessions where this value was set to 1.0, the actual scales are quite different. Chimera help revealed that the camera scale is relative to the original size when the model was first opened. Any suggestions would be appreciated! thanks, Cathy Lawson *********************************************************************** Catherine L. Lawson Laboratory for Structural Biology and Bioinformatics Department of Chemistry and Chemical Biology Rutgers University 610 Taylor Road, Piscataway, NJ 08854 cathy.lawson(a)rutgers.edu tel 732 445 8074 fax 732 445 5312 http://rutchem.rutgers.edu/~lawson http://roma.rutgers.edu/~lsbb *********************************************************************

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Broken labels!
by Changhoon Kim 02 May '06

02 May '06

Hello? I am using Chimera on Windows XP. It's "beta version 1 build 2199 2006/01/24". When I tried to display residue labels, many of the labels were unrecognizable. I've attached the picture showing the broken labels. Sometimes the distance labels are also unrecognizable. I hope it would be fixed soon. Regards Changhoon Kim

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libGL.so
by Isaac Amela Abellan 02 May '06

02 May '06

Hello, I'm using Linux and when I had tried to execute chimera this message appeared: "OpenGL misconfiguration detected. /usr/lib/libGL.so.1 differs from /usr/X11R6/lib/libGL.so.1. Please read installation instructions." I said it several times to my system administrator and he solved it using your instructions (see below): "If Chimera terminates with the error OpenGL misconfiguration detected, that means that you have two different versions of libGL.so installed -- one in /usr/lib (installed by your graphics card drivers) and one in /usr/X11R6/lib (possibly installed by Mesa, which if so would mean no hardware graphics acceleration if this version were used). Reinstalling your graphics card drivers should remove the /usr/X11R6/lib version. Alternatively, you could rename or remove the /usr/X11R6/lib version yourself. With the latter approach you might want to verify that all OpenGL applications that you use continue to work before permanently removing the library. On startup, you may see the warning Xlib: extension "Xfre86-DRI" missing on display "0.0". That means that there was no graphics driver found for your card that uses the DRI, direct rendering interface, technology for fast 3D graphics. The solution is to either ignore the warning or to upgrade your hardware and software (see Mesa/OpenGL issues below)." The problem is that when I reboot my computer the problem still appears and we should do the same procedure explained above. We can't configure the system conservating the libraries of my card drivers (/usr/lib) without removing the Mesa ones (/usr/X11R6/lib). How can we solve the problem? We will be waiting for your response. -- ------------------------------------------------ Isaac Amela Abellan PhD Student Laboratory of Bioinformatics Institute of Biotechnology and Biomedicine (IBB) Autonomous University of Barcelona (UAB) 08193 Bellaterra, Barcelona. Spain. Phone: 34-93-5812807 e-mail: iamela(a)bioinf.uab.es ------------------------------------------------

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