- 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 12 Jun '06

12 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 23 May '06

23 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 22 May '06

22 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 22 May '06

22 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 17 May '06

17 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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Stereo angle value
by Prof. Fabrizio Briganti 02 May '06

02 May '06

Hi, I have not been able to find any reference to the value for the angle difference between Right and Left views in Stereo Images made with Chimera. Can you help me find it? Is there any way to change such angle value? Thanks Fabrizio

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Paper virus models
by Thomas Goddard 02 May '06

02 May '06

I made a Chimera tool that flattens icosahedral virus models. Printing, cutting, folding, and taping produces a paper model. http://www.cgl.ucsf.edu/chimera/experimental/flatten_icosahedron/flaticos.h… The flatten icosahedron tool can be downloaded from the Chimera experimental features web page: http://www.cgl.ucsf.edu/chimera/experimental/experimental.html Tom

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writing mrc files
by Eran Shacham 21 Apr '06

21 Apr '06

Hey there, I am trying to write an mrc file using the write_mrc2000_grid_data module. My function is below. My array of data is a <scitbx_array_family_flex_ext.double object at 0x58b9502c>. Which is a basically a matrix with dimensions: (243, 243, 243). When trying to write an mrc file using this array I get the following error: ************************* File "/home/eshacham/cctbx/mrc_functions.py", line 20, in write_mrc write_mrc2000_grid_data(g, path) File "CHIMERA/share/VolumeData/mrc/writemrc.py", line 44, in write_mrc2000_grid_data File "CHIMERA/share/VolumeData/arraygrid.py", line 48, in submatrix ValueError: need more than 1 value to unpack Code used *********************** def write_mrc(data): print data origin = (1.54, 2.45, 3.45) # XYZ coordinates of array index (0,0,0) step = (.25, .25, .25) # Spacing between grid points import Numeric a = Numeric.array(data, Numeric.Float32) arrays = [a] import VolumeData g = VolumeData.Array_Grid_Data(arrays, origin, step) path = '/home/eshacham/structures/result.mrc' from VolumeData.mrc import write_mrc2000_grid_data write_mrc2000_grid_data(g, path) I am assuming that it has to do with my array dimensions. Any help would be greatly appreciated. Cheers, Eran.

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Re: [Chimera-users] Rotation about an axis
by Thomas Goddard 21 Apr '06

21 Apr '06

Hi Jordan, Aha! It turns out I wrote code that does exactly what you want last year. It is called the symmetric molecule copies command at the bottom of the Chimera experimental features web page: http://www.cgl.ucsf.edu/chimera/experimental/experimental.html It is not distributed with Chimera yet but you can download it on that page and install it with your existing Chimera. I hate to discourage you from Python programming in Chimera but I think this is just what you need. You open one copy of your molecule and then use this "sym" command to make the hexamer. Then when you move the original copy of the molecule relative to your map, the other 5 copies automatically reposition to maintain the 6-fold symmetry. To get a more detailed description look at the "details" link on the experimental features page. The hexamer symmetry comes from the BIOMT matrices in the PDB file. This sym command treats those matrices in the coordinate system of the density map (yes, a bit weird). The key here is to make sure the symmetry axis of the density map matches the symmetry axis of the BIOMT matrices. The easiest approach is probably to make the BIOMT matrices produce a hexamer about the z-axis through (0,0,0). When you open your density map in Chimera it may not have the hexamer density centered at (0,0,0). You will need to adjust its origin so the density hexamer is centered at (0,0,0). Use the volume dialog menu entry Features / Origin and Scale to adjust the position of the lower left front corner of the map. Assuming the hexamer is centered in a 128 x 128 x 100 grid with voxel size 0.8 angstroms you would set the origin to (-50.8, -50.8, -39.6) = (-63.5 * 0.8, -63.5 * 0.8, -49.5 * 0.8). The weird 63.5 = 128/2 - .5 instead of 64 = 128/2 is easiest to understand if you think of a map that is only 2 by 2 by 2 in size. Remember to press the Enter key in one of the origin fields in the volume dialog to have the new position take effect. In any case that may still be a half voxel off depending on your map, or it may be way off. Of course you have to know the position of the center of the hexamer in your density to make this work. A way to verify that you have set the correct origin is to open 2 copies of the map -- set the map origins, then use constrained move to rotate just one copy keeping the other one fixed. It is easy then to visually see if the two copies are concentric. For convenience you can save your map as an MRC file with the new origin with the volume dialog File / Save As... menu entry. Saving a Chimera session also saves the origin in the Chimera session file (the map is not modified). I can see various troubles with using the Multiscale tool. First Multiscale low resolution surfaces are not reliably synchronized to the individual PDB models. If you change a PDB model position Multiscale won't realize it and the low resolution surface will not move to the new location. If you are using the latest Chimera snapshot (1.2224, April 10, 2006) then the problems will be even more severe because I changed the way Multiscale positions PDB models. Instead of setting the pdb_model.openState.xform it changes the atom coordinates of the model (setting atom.coord = x,y,z). All the xforms of the 6 models in a hexamer would be the same in Chimera 1.2224. This change was made to allow correctly moving individual chains of multiscale models, possible with the "movement mouse mode" feature on the experimental features web page. Lastly some clarification about Chimera's coordinate systems. First there is a global Chimera coordinates system with the x axis always horizontal relative to your graphics window, the y axis always vertical, and the z axis always pointing out of the screen at you. When you rotate models with the mouse, this coordinate system does not change -- the individual matrices positioning the models are changed. The origin of this global coordinate system is not necessarily in the center of the screen. It can be anywhere including off-screen. The global coordinates for the center of the screen are set to match the center of the bounding box of the first model you open in Chimera. Besides the global coordinate system each model has a local coordinate system. With a PDB file, the atom coordinate positions are in the local coordinate system. If you open a PDB model in Chimera and rotate it, the atom.coord x,y,z values do not change -- they are expressed in the local coordinate system which is fixed to the atoms and rotates with the model. (You can however change the atom.coord positions using Python code.) The pdb_model.openState.xform 3 row by 4 column matrix gives the rotation and translation that maps the local coordinates (e.g. a PDB atom position) into Chimera global coordinates. Other types of Chimera models like density maps are just like PDB models having a local coordinate system -- the density map grid points have unchanging coordinates in the local coordinate system. More than you wanted to know. Tom > Date: Thu, 20 Apr 2006 19:51:40 -0700 > From: "Jordan Benjamin" <jordan.benjamin(a)gmail.com> > To: "Thomas Goddard" <goddard(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Rotation about an axis > > Ah, it looks like it still works for normal models. The weird behavior > was with a model that had been generated with the Multiscale Models > tool from crystal contacts. I still wish I understood the > global-vs-local issue better though. > > > On 4/20/06, Jordan Benjamin <jordan.benjamin(a)gmail.com> wrote: > > Thank you for your help on this. I have a further question. Basically, > I'm trying to dock into electron density the crystal structure of a > protein that forms a hexamer. I would like to be able to have six > copies of the monomer structure loaded at once, and when I move or > rotate one copy, I'd like to be able to transform the other five to > match. So, I thought the ConstrainedMove code would be a good starting > point, since what I'm trying to do is the same thing it does, just > with the rotation specified by degrees instead of by dragging the > mouse. > > After you sent the email below, I modifed the function I was writing > accordingly, and it worked. However, I'm trying to use it now, and > it's not working. I'm a little lost on debugging it, because I don't > even know what Chimera's concept of a global coordinate system is, nor > do I have any way to visually display the local origin and axis for > each object. Is there a way to do these things that you know of? Do > you know of a simple way to rotate an object X degrees around a > specified axis (relative to another object if needed)? > > If these are really hard questions and the answer is just that I > should read the source code until I figure it out, that's totally > fine. I just thought I'd ask. > > At least with Chimera the code IS available, unlike the situation with > Amira where things would be undocumented and broken, and there'd be no > way to fix them... > > Thanks so much, > Jordan > > The function I was using is as follows (yes, it's brittle and ugly, > but it's all I had time for): > def update_hexamer(ref_model,model,*rest): > origin = (0,0,0) > axis = (0,0,1) > angle_deg = 60 > > mvo = chimera.Point(*origin) > vo = ref_model.openState.xform.apply(mvo) > mva = apply(chimera.Vector, axis) > va = ref_model.openState.xform.apply(mva) > > xf_original = model.openState.xform > > for i in range(5): > xf = chimera.Xform() > xf.translate(*vo) > xf.rotate(va, angle_deg+60*i) > xf.translate(-vo.x, -vo.y, -vo.z) > model.openState.globalXform(xf) > rest[i].openState.xform = model.openState.xform > model.openState.xform = xf_original >

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Re: [Chimera-users] Sum of volume data values
by Thomas Goddard 13 Apr '06

13 Apr '06

Hi Eran, Ok, here is code to read an MRC file and print the sum of map values without using Chimera. You need Python, the Numeric Python module which handles multidimensional arrays and the VolumeData module from Chimera. Numeric is obtained from sourceforge: http://sourceforge.net/project/showfiles.php?group_id=1369&package_id=1351 The VolumeData module is in your Chimera distribution. chimera/share/VolumeData Here's an example running the script where I've set PYTHONPATH to have access to the VolumeData module: % env PYTHONPATH=/usr/local/chimera/share python2.4 volumesum2.py Sum of values of groel.mrc = 21720.8984375 Send future questions to chimera-users(a)cgl.ucsf.edu so others who have similar problems can benefit. I get that email just as fast. Tom ------- file volumesum2.py follows: # Script to print the sum of volume data values. # Does not need Chimera, just the VolumeData module and Numeric and Python. path = 'groel.mrc' # Read the MRC volume data and get the 3-D Numeric array. from VolumeData.mrc.mrc_format import MRC_Data data = MRC_Data(path) m = data.matrix() # Compute the sum of the elements of the volume matrix. import Numeric sum = Numeric.sum(m.flat) # Print the sum print 'Sum of values of', path, ' = ', sum ------- > Date: Wed, 12 Apr 2006 14:46:14 -0700 > From: Eran Shacham <eshacham(a)burnham.org> > To: Thomas Goddard <goddard(a)cgl.ucsf.edu> > Subject: Re: Sum of volume data values > > Hey Tom, > > Thanks for your reply. However, I would like to do that from within a > script I already wrote. i.e I would like to integrate a read_in method > for an MRC file, access it values and then calculate the sum. I would > like to avoid doing that by opening my file in Chimera at this stage of > the program. Can it be done by importing some of your code? > > Thanks, > Eran.

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Sum of volume data values
by Thomas Goddard 12 Apr '06

12 Apr '06

Hi Eran, You can open your MRC file in Chimera, then open the following script "volumesum.py" which contains Python code to have the sum of all the volume values printed. Use menu entry File / Open to open both files. If you want to do this many times I can give you a modified version that creates a Chimera menu entry (under the Tools menu) that runs the script. Tom ------------ File volumesum.py follows: # Script to print the sum of volume data values. # Get the volume dialog object import VolumeViewer d = VolumeViewer.volume_dialog() # Get the volume data currently shown by the volume dialog dr = d.focus_region m = dr.full_matrix() # Compute the sum of the elements of the volume matrix. import Numeric sum = Numeric.sum(m.flat) # Print the sum to the reply log dialog. message = 'Sum of values of %s = %.6g' % (dr.full_name(), sum) print message # Display the reply log dialog. from chimera import dialogs dialogs.display('reply') ------------- > Date: Wed, 12 Apr 2006 13:52:26 -0700 > From: Eran Shacham <eshacham(a)burnham.org> > To: Thomas Goddard <goddard(a)cgl.ucsf.edu> > Subject: Reading mrc files > > Hi Tom, > > Can I use Chimera's code for reading in mrc files? Essentially, I would > like to read in an mrc file and access its values. It is a mask file, > and I simply need to add up it values. Any suggestions on how to do that > easily with a Chimera module? > > Cheers, > Eran

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Volume series tool
by Thomas Goddard 12 Apr '06

12 Apr '06

I wrote a Chimera tool to display sequences of volume data sets. They are displayed one at a time like a movie and a slider lets you choose any particular volume. It is intended for looking at 3-D optical microscopy time series, or a sequence of single particle density map reconstructions. Available on the Chimera experimental features web page: http://www.cgl.ucsf.edu/chimera/experimental/experimental.html Tom

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Rotation about an axis
by Jordan Benjamin 12 Apr '06

12 Apr '06

I'm trying to rotate a model about a specified axis and origin (preferably in global coordinates). I would like the rotation to be applied on top of whatever transformations have been applied already. I've looked at the documentation, including the programmer's FAQ and the source code for ConstrainedMove. I couldn't figure out how to do this, so I wrote the following function based on the ConstrainedMove code to do the rotation relative to another model: def rotate_around_model_axis(ref_model, model, origin, axis, angle_deg): mvo = apply(chimera.Vector, origin) vo = ref_model.openState.xform.apply(mvo) mva = apply(chimera.Vector, axis) va = ref_model.openState.xform.apply(mva) xf = chimera.Xform() xf.translate(vo) xf.rotate(va, angle_deg) xf.translate(-vo) model.openState.globalXform(xf) But, this doesn't seem to work as I'd intended. Is there a way to do this? Also, I'm a little confused about the coordinate system. It seems like the concept of a global coordinate system may not apply in Chimera the way I'm used to (like in Amira for example) since the camera is fixed. Is this true, or am I totally lost? Thanks in advance for any help you can provide. Jordan

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Newbie Questions
by Shafrir, Yinon (NIH/NCI) [F] 11 Apr '06

11 Apr '06

Hi there! I have two questions regarding using Chimera. How do you break a molecule to different models using the command line? I have a protein composed of 4 chains. It loads as one piece and designated model 0 I then select a single chain and I want to designate it as a new model. How do I do that using the command line (so I can write a script)? Also, when I select the chain and use the write command in this manner "write selected su1.pdb" the save dialog box pops up (even though I designated a filename) When I try "write selected 0 su1.pdb" nothing happens. My other question is: How can you force chimera to assign secondary type display to residues without editing the PDB file first? Say I want to show 30 residues that are not detected by ksdssp as beta sheets. Still, I want to represent them as beta sheets. Do I need to edit the pdb file? Best regards Yinon Shafrir

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Axis display
by Jordan Benjamin 10 Apr '06

10 Apr '06

Is there a convenient way to display the axes of the coordinate system (and preferably the origin)? Forgive me if this is addressed in the documentation, but I wasn't able to find it. Thanks, Jordan

2 1

Collaboratory session
by Eduardo Sanz Garcia 10 Apr '06

10 Apr '06

I have been trying to set up a collaboratory session, but I could not see the model. I was able to chat and to see the pointer of the other person, anything else. Any idea? How can I know if it is a problem caused by the firewall?

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Move atoms with mouse
by Thomas Goddard 07 Apr '06

07 Apr '06

I put a tool on the Chimera experimental features web page that enhances the standard rotation and translation mouse modes (left and middle mouse buttons) to enable moving helices, strands, turns, PDB chains, any selected set of atoms, or multiscale model chains. http://www.cgl.ucsf.edu/chimera/experimental/experimental.html The molecular pieces are translated or rotated by dragging them with the mouse. It requires Chimera version 1.2206 or newer, and that is only available for Macintosh computers right now. Tom

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Newbie Questions
by Shafrir, Yinon (NIH/NCI) [F] 07 Apr '06

07 Apr '06

Hi there! I have two questions regarding using Chimera. How do you break a molecule to different models using the command line? I have a protein composed of 4 chains. It loads as one piece and designated model 0 I then select a single chain and I want to designate it as a new model. How do I do that using the command line (so I can write a script)? Also, when I select the chain and use the write command in this manner "write selected su1.pdb" the save dialog box pops up (even though I designated a filename) When I try "write selected 0 su1.pdb" nothing happens. My other question is: How can you force chimera to assign secondary type display to residues without editing the PDB file first? Say I want to show 30 residues that are not detected by ksdssp as beta sheets. Still, I want to represent them as beta sheets. Do I need to edit the pdb file? Best regards Yinon Shafrir

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Re: [Chimera-users] Read PDB file
by Elaine Meng 07 Apr '06

07 Apr '06

Hi Eduardo, Aha! You can see all the header information from the PDB file (the lines that come before the coordinates). How to do that: open the Model Panel (Favorites... Model Panel) and for the model you are interested in, click "attributes..." Click the "PDB Headers..." button at the bottom of the resulting attributes panel. Currently the header lines are shown in a different order than in the original PDB file (they are sorted alphabetically by type, but wthin each type such as REMARK the order is not changed), so you will have to scroll down to the SOURCE record to see the organism. Best, Elaine On Apr 7, 2006, at 11:29 AM, Eduardo Sanz Garcia wrote: > My real situation: > 1. I have File... Fletch by ID using 2ypi > 2. I didn't know what source organism they are using to get the > structure. > > Option a: go to www.pdb.org and obtain the information. > Option from chimera?: display the text file 2ypi.pdb to get the > necessary information? > > I was wondering if there is a command or function to display (the > text) of a PDB file. > ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

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Read PDB file
by Eduardo Sanz Garcia 07 Apr '06

07 Apr '06

Hi, Is it possible to read the PDB file of the molecule directly from chimera? Thank you Eduardo Sanz

2 1

Name selection
by Eduardo Sanz Garcia 06 Apr '06

06 Apr '06

Hi everybody, Is there any way to give a name to a selection from the command line? Same as: *Select... Name Selection...* <cid:part1.01070107.06060601@terra.es> but from the command line. Thank you.

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further levels of detail in low-res surface of a single chain Multiscale model
by Klinkhardt＠em.uni-frankfurt.de 05 Apr '06

05 Apr '06

Hello, I would like to divide/define the low-res structure of a multiscale model which contains only one chain. I need further levels of detail in this single chain (preferentially all single nucleotide bases as small podgy shapes and the backbone of phosphate-sugars as an irregular rope) so I can can animate the resulating smaller units later. In your online hept (documentation) there is written that a python script like #bluetongue.py# can create a multiscale model with further levels of (individual?) structure. I have opend the python script but unfortunately I am no programmer so I am not able to modify this script to my requirements. Is there a #more general# script which I can use for my chain or any other workaround?? Thanks a lot in advance, best regards Ute Klinkhardt

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question about CHIMERA
by Guy Nimrod 04 Apr '06

04 Apr '06

Hello, I am a PhD student in the department of Biochemistry of the Tel-Aviv University and often use your great application, CHIMERA. Is it possible to view on chimera the selected part only? Regarding this, is it possible to split a model to its units (so each chain/ligand) will be considered as a model? Thanks Guy Nimrod http://ashtoret.tau.ac.il/~nimrodg

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Please consider adding PyTables to Chimera
by David E. Konerding 04 Apr '06

04 Apr '06

Hello, Recently I have been converting most of my scientific data to the HDF5 format. HDF5 is a powerful, high performance data format library. I found an absolutely wonderful open source code, PyTables, which provides an HDF5 interface. It adds enormous value to HDF5 by making it much easier to use, and exposing a lot of the complex functionality that HDF5 supports (such as variable-length records). http://www.pytables.org/moin I would really appreciate it if you guys would consider adding PyTables. I would definitely convert a lot of my existing extensions and processing tools to use PyTables- for example, when I analyze trajectories to find hydrogen bond data and use that to render long movies, PyTables makes it a lot easier (I already used the Chimera headers to build my own copy of PyTables on Linux, but it would be a lot more painful to do on Windows). PyTables depends on numarray (although it also provides Numeric Python support). I'd like to see numarray in Chimera as well (although I could live with just Numeric support) Dave

3 5

trigonometry
by jean-francois menetret 03 Apr '06

03 Apr '06

What is Chimera's trigonometry convention ? How can get angles out of the rotation matrix (saved with "matrixget") ? Jean-Fran�ois M�n�tret, PhD Boston University School of Medicine Physiology and Biophysics Department 700 Albany Street W315 Boston, MA 02118 Email: menetret(a)bu.edu Mailing address: 715 Albany Street

3 4

Different colors for individual chains within a model
by Karpen, Saul J. 31 Mar '06

31 Mar '06

Dear Chimera group, Simple question from a new user--How do I distinctly color ribbon representations of different chains within the same model? Thanks, Saul J. Karpen, M.D., Ph.D. Baylor College of Medicine

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Re: [Chimera-users] Question about background transparency
by Weldon, Scott 28 Mar '06

28 Mar '06

Thanks to all for the help. I have transparent images now. Thanks, Scott Weldon, M.A. Supervisor, Medical Illustrator Division of Cardiothoracic Surgery Michael E. DeBakey Department of Surgery Baylor College of Medicine One Baylor Plaza, BCM 390 Houston, TX 77030 TEL: (832) 355-9941 FAX: (832) 355-9948 E-mail: sweldon(a)bcm.edu -----Original Message----- From: Thomas Goddard [mailto:goddard@cgl.ucsf.edu] Sent: Tuesday, March 28, 2006 11:43 AM To: Weldon, Scott Cc: chimera-users(a)cgl.ucsf.edu Subject: Re: [Chimera-users] Question about background transparency Hi Scott, You need 2 dashes in the background opacity option --bgopacity According to the Chimera manual that option should occur before input PDB files in the Chimera startup command. Here are the relevant pages of the Chimera User's Guide: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/startup.html http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/options.html Tom

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Question about background transparency
by Weldon, Scott 28 Mar '06

28 Mar '06

Hello, I'm not having any luck using command line to change the background to transparent. I've tried "-bgopacity" and "bgopacity" and both say it is not a valid command. Would you please provide the exact syntax that should be entered to achieve this? Does this need to be entered before the PDB file is opened? Thank you for your help, Scott Weldon, M.A. Supervisor, Medical Illustrator Division of Cardiothoracic Surgery Michael E. DeBakey Department of Surgery Baylor College of Medicine One Baylor Plaza, BCM 390 Houston, TX 77030 TEL: (832) 355-9941 FAX: (832) 355-9948 E-mail: sweldon(a)bcm.edu

3 2

ses volume
by Charles Spink 21 Mar '06

21 Mar '06

Is it possible to get a calculated volume for the solvent excluded area for a protein or dna? I know the volume for a solvent accessible surface is possible through "measure volume" command. What about SES volumes? Thanks, Charlie Spink

3 2

superimposing proteins on co-factor
by Boaz Shaanan 09 Mar '06

09 Mar '06

Hi Chimera prople, If I want to superimpose proteins on their co-factors (or part of them), is ensembleMatch the way to go or are there other ways to do this ? I'd appreciate your advice. Regards, Boaz -- ************************************************************* Boaz Shaanan, Ph.D. Associate Prof. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel Phone: 972-8-647-2220 e-mail:bshaanan@bgu.ac.il Fax: 972-8-647-2992 or 972-8-646-1710 *************************************************************

3 2

Re: [Chimera-users] (no subject)
by Eric Pettersen 09 Mar '06

09 Mar '06

On Mar 8, 2006, at 2:22 PM, Todd T Talley wrote: > Hay, > Sorry to bother you, but you were so helpful last week > I thought that I would try again. Is there a way to show the > carbonyl of the backbone of a specific residue? I would like to > show the H bond between my ligand and a specific Trp. Well, the vanilla answer is (if we're talking about residue 12.A for example) "disp :12.a@c,o". However, I'm guessing that the reason you've undisplayed the carbonyl in the first place is because you're showing a ribbon -- in which case there are a few more useful things to know. By default the ribbon depiction replaces the backbone atoms (including the carbonyl oxygen) so even if you turn the display of specific backbone atoms back on (e.g. with the above "disp" command), no atoms will be shown. However, Chimera will know that these atoms are now "displayed" and will begin to show things such as H-bonds that involve those atoms (drawing the end of the H-bond to the interpolated ribbon position of the backbone atom). You can force backbone atoms to be explicitly depicted even in the presence of a ribbon with the "ribbackbone" command (e.g. "ribbackbone :12.a") -- they will be shown at their normal non-interpolated positions. --Eric

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Question on Chimera
by Seiha Thorng 06 Mar '06

06 Mar '06

To whom it may concern, My name is Seiha Thorng and I work for BioMarin Pharmaceuticals, Inc. I'm looking into UCSF Chimera as a promising software for our research purposes. I would like to ask you what equipment you would recommend for optimal performance of this software. The answer I'm looking for is in terms of ram, platform, processor, disc space ....etc. We would like very much to be able to run this program at the best possible performance. Thank you. Seiha This message is intended only for the confidential use of the intended recipient(s). If you have received this communication in error, please notify the sender by reply e-mail, and delete the original message and any attachments. Any unauthorized disclosure, copying, or distribution of this message (including the attachments), or the taking of any action based on it, is strictly prohibited.

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Re: [Chimera-users] Show me the disulfides!
by Eric Pettersen 03 Mar '06

03 Mar '06

Todd Talley writes: > Hay, > > I am sure that this is a dumb problem BUT I am unable > to “turn on” the disulfide bonds in my structures. They are a > crucial part of the structures that I am publishing and I really > would like to use Chimera to render the images for our publication > but I am not a code guy and none of the combos I have tried > worked. If anyone is out there with the answer please let me know! > > Thanks! Deposited PDB structures specify disulfide linkages using CONECT records, which Chimera honors. So one way to go is to add such CONECT records to your structures. CONECT records are documented here: http://www.rcsb.org/pdb/file_formats/pdb/pdbguide2.2/part_69.html You can also add the linkages directly in Chimera. If you select a pair of sulfurs that should have the linkage, then the command "bond sel" (Favorites->Command Line) will add the linkage. Sessions and PDB files that you save thereafter will have the linkage information (i.e. a saved PDB file will have the appropriate CONECT record). If you have a lot of disulfide bonds or a lot of structures, I could send you a short Python script to add the linkages automatically. --Eric Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

1 0

delphi in chimera
by Thomas Goddard 03 Mar '06

03 Mar '06

Hi Damien, Chimera Delphi Controller tries to execute the command-line program "delphi" so it must be in your shell executable search path. On Linux you need it in the directory containing the delphi executable in the PATH environment variable. On the Mac I'm not sure how to set the search path when you start Chimera by double clicking on it. You can still set the shell PATH variable and start Chimera from a terminal like: % path-to-chimera/Chimera.app/Contents/MacOS/chimera The Chimera User's Guide (under Tools / Delphi Controller) says that Delphi Controller does not work on Windows. Maybe it is easier to just edit the line in Delphi Controller code that starts delphi. Just edit line 97 in chimera/share/DelphiViewer/DelphiExecutor.py changing from cmd = "delphi %s > %s" % (self.prmFileName, self.outputFileName) to for example cmd = "/usr/local/bin/delphi %s > %s" % (self.prmFileName, self.outputFileName) giving an explicit path to the Delphi executable. On the Mac this file would be Chimera.app/Contents/Resources/share/DelphiViewer/DelphiExecutor.py Keep the indentation of the Python line the same as this is important. All that said, I would suggest just running Delphi yourself then opening the resulting *.phi file in Chimera. The Delphi Controller Chimera tool was written by a summer intern 5 years ago and has not been worked on much since then. The electrostatic potential file produced by MolMol is not in Delphi format. It uses a MolMol specific format (described at the end of this email) that Chimera does not read. You could hand convert it to another text file format by changing the header, to say the one used by APBS (called OpenDX). But I'd suggest calculating the electrostatic potential with APBS instead. Tom ------- Manual page for MolMol potential file format. NAME ReadPot - read potentials for surface coloring SYNOPSIS ReadPot fileName DESCRIPTION Read a file with potentials, these are used for coloring surfaces. The file must contain values on a grid, the format is: x0 xSize xInc y0 ySize yInc z0 zSize zInc val val val .... where x0, y0, z0 (float) are the coordinates of the grid origin, xSize, ySize and zSize (int) are the sizes of the grid in each dimension, and xInc, yInc and zInc (float) the spacing between two grid points in each dimention. This must be followed by xSize * ySize * zSize values (float), where the x-coordinate is the one that is running the fastest. The potentials will be set for all selected surfaces, but the PaintSurface command has to be given to update the colors. EXAMPLE ReadPot /home/joe/struct/my_pot.dat SEE ALSO CalcPot, AddSurface, SelectPrim, PaintSurface DATE 960509 > From: Damien Devos <damien(a)salilab.org> > Date: March 2, 2006 4:04:02 PM PST > To: "Eric Pettersen (chimera)" <pett(a)cgl.ucsf.edu> > Subject: delphi in chimera > > hi Eric, > i'm trying to use delphi in chimera, but couldn't get the delphi > controller to help me. > alternatively, i used molmol to generate the .phi file and tried to > open > it in chimera, but i got this message on the reply log: > > > Done opening /viol1/damien/fgf/molmol/1nuna.pdb > Opening /viol1/damien/fgf/molmol/1nuna.phi > /viol1/damien/fgf/molmol/1nuna.phi: Record size 539833144 > file size > 2725332 > Done opening /viol1/damien/fgf/molmol/1nuna.phi > > it seems that my .phi file is too big? does this make sense? > on the other side, if i could get the delphi controller to work on > chimera, that would solve all problems. we have delphi installed > localy, > but i don't know where to put the path of it and how so that chimera > could locate it. > > thanks > d > > -- > Damien Devos > Andrej Sali Lab > California Institute for Quantitative Biomedical Research > University of California at San Francisco > QB3, Box 2552 > 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 > Email: damien(a)salilab.org > URL: http://www.salilab.org >

1 0

plotting RMSD vs Residue number
by Isherwood, James 02 Mar '06

02 Mar '06

Hi, I was wondering if there was a way to use chimera to calculate Root Mean Squared Deviations for individual residues or backbone atoms. In order to produce a graph showing the relative freedom of different areas of a protein. James Isherwood

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3D Graph
by Jake Chrzanowski 02 Mar '06

02 Mar '06

Hi, I've been reading about the program your working on,Chimera, and was wondering if it had the functions I need for a project I'm working on: I'm trying to create a 3D graph to represent an image and the distance that image is away from a source. I was looking at your Chimera program to do this. I was wondering if your Chimeraprogram had the necessary functions I needed to do this? If so, can you point me in the right direction on what the functions I need would be? Below I described a little more in depth of what I'm trying to do. First, I'll give you a little detail on our overall project so you have a better idea of what I'm dealing with. We're trying to measure the distance of an object using two cameras. Two identical cameras are positioned near each other with a separation distance and focusing angle. The Image-Processing Computer applies filters to conform the images so that meaningful features stand out in contrast to non-meaningful features (i.e. shadows, textures, glare, and reflections). The computer uses a vast array of image-processing algorithms to find key features in the images. Cross-correlation is performed between the features in both images to determine the line-of-site angle and separation distance. With that found, triangulation is performed to determine the distance that an object(s) is away from the cameras. ------------------------------------- Now, once we have determined the distance, we want to have a 3D graph display the object's distance away from the camera (part where I'd like to use Chimera), as they come into focus. (i.e. The graph will be continually updating at 10 frames/sec along with the cameras) I have attached a general 3D graph .bmp file to show you kinda what I'm looking for. (Obviously, the graph won''t portrude negative as the .bmp file since the camera only look in one direction) What I'm thinking is I will basically take in two parameters. 1) The coordinates of the edge detected (horizontal and vertical pixel location). Edges won't be detected in the entire area ( i.e. a wall focused in too closely will ideally show no edges). The graph will only be concerned with areas that edges were detected. 2) The other parameter that needs to be taken in is the computed distance from the cameras of the detected edge. This is the parameter that will determine how far the graph protrudes out in the z direction. Ideally, I would like for portions of the graph to change colors corresponding to a certain distance detected (i.e. 0-1 feet red, 1-2 feet orange, etc...). Also, something that isn't needed (but would make the graph look a lot better), is if I could use some interpolation functions so areas that were encompassed by edges would protrude out, too, instead of just the edges. Sorry about the length of this email. I just wanted to give you a good idea of what I'm looking for. I also attached a picture (" picture2.bmp") that had gone through an edge detection program. The white lines are detected edges. Everywhere else in the image now has a pixel intensity of 0. I'm looking for a library to help me accomplish all or most of these things listed with the 3D graph. I am an amateur at computer programming , so the simpler the better (I'm an electrical engineering major, we don't get a chance to learn too much about how to program). Anything you can help me with I would really appreciate. Thanks a lot for your time and I'll look forward to your response. -- Sincerely, Jacob Chrzanowski Electrical Engineering Student, NDSU jmchrz(a)gmail.com (701) 866-3120

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movies of gromos files
by John Robinson 01 Mar '06

01 Mar '06

Trying to visualize gromos trajectories. The Tk popup is asking for three files: Topology, Coordinates, and PROMD. I don't seem to be giving it the files it needs. What are the file extensions corresponding to these file types? (.top, .trr, .tpr)? Thx, -------------------------------------------- John M. Robinson, M.D., Ph.D. mailto:johnmrobinson@mac.com

2 1

selection of atoms on the surface of a molecule
by kovzany＠go.com 28 Feb '06

28 Feb '06

Dear All, Is there an easy way to select and save set of atoms (with their names and coordinates) representing VdW or solvent accessible surface of the given molecule? thanks, PK

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MTZ files
by Eran Shacham 28 Feb '06

28 Feb '06

Hey there, I am not sure if this question should go into users or developers but I will first try here. Accept my apologies if this does not concern you and maybe you could fwd this email to someone who could help me out. I am looking to convert MTZ files into ccp4 map files (using Python). Is there an extension of Chimera that allows that? Can you please point out some documentations about the issue? Thanks in advance for your help and time, Eran.

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Ribbon path smoothing
by Jakob Toudahl Nielsen 28 Feb '06

28 Feb '06

Dear Chimera users, I trying to create a ribbon model drawing of a DNA structure containting several abrupt chain-reversals in the DNA-backbone. By default the ribbon path is smoothed over five successive residues. This resuls in the ribbon path supressing the chain-reversals by oversmoothing the path. Is there any way to overide the default value of the FIVE succesive residues to a smaller number (e.g. TWO). Regards, Jakob Jakob Toudahl Nielsen Dep. of Chemistry University of Southern Denmark

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Making a new covalent bond
by Goel, Manisha 28 Feb '06

28 Feb '06

Hi, I have often come across detailed answers from chimera group for a variety of modelling problems on pdb-l or bioinformatics mailing lists. My problem should relatively easy to solve except that I havn't been able to figure it out myslef on chimera. I just need to make a covalent bond between a sugar molecule and an aminoacid (aa-COOH + sugar-OH --> H2O + aa-sugar). Is there an easy way of doing this manipulation in Chimera ? Please advice ? Thanks a lot for your time and effort. -Manisha Goel Post-doc associate Bioinformatics Lab Stowers Institute for Medical Research Kansas city-66210

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chimera vrml issues...
by Thomas Goddard 27 Feb '06

27 Feb '06

------- Start of forwarded message ------- Date: Thu, 16 Feb 2006 23:47:38 -0800 From: Janet Iwasa <jiwasa(a)gmail.com> To: Thomas Goddard <goddard(a)cgl.ucsf.edu> Subject: chimera vrml issues... Hi Tom, I was trying out some of those new scene export functions in Chimera that you showed me a while back, and I've been running into some issues. I've got a large ribbon structure that I wanted to export as VRML, but Chimera only wrote a small file that couldn't be opened. Using notepad, all the file included was the following: #VRML V2.0 utf8 Transform { children [ ] } Saving as a X3d file seemed to work (seemed like a reasonable size at 10 MB) but I couldn't use the translator (X3dToVrml97.xslt) to change to VRML since it appeared to run into memory issues. Trying to save as POV or Renderman either failed or crashed Chimera. Any suggestions? Janet ------- End of forwarded message -------

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question
by Stefano Ciurli 23 Feb '06

23 Feb '06

Hello, I am a new user of Chimera and I need to ask a question: let's say that I am loading several PDB files from the RCSB, all of them belonging to the same protein, the latter having 3 subunits A, B, and C. I need a way to operate on single PDB files (select and manipulate features of each PDB file at once). How do I do it? I can easily find the select->chain option, but it would operate on all chains of that type in all PDB files. Regards, Stefano

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Re: [Chimera-users] chimera vrml issues...
by Greg Couch 23 Feb '06

23 Feb '06

Forgot to cc the list. So to summarize: There some major bugs fixed with the X3D ribbon output in chimera version 1.2180 that affected the Renderman and POV-ray output as well. So please upgrade your chimera. I think I have fixed all of the problems, so if it still fails, please submit a bug report (ideally with enough data to reproduce the problem). As for vrml output, the xslt technology is slow, but works. In the X3dToVrml97.xslt file, it suggests using saxon.sourceforge.net's java-based converter, and I second that recommendation (it was the fastest of the alternatives I tested). Even when the X3dToVrml97.xslt method works, it has problems -- it outputs VRML 3.0 and most VRML importers expect VRML97 aka VRML 2.0. This is especially problematic for ribbons because ribbons use triangle strips for their geometry and 3.0 supports triangle strips while 2.0 doesn't. VRML97 doesn't support translucent colors either. Consequently, I have put improving the VRML output on my list of things to do. And if you have the option of using the Renderman output, use it, because it reproduces what you see in the chimera window the best of the various export formats. Greg Couch UCSF Computer Graphics Lab

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chimera vrml issues...
by Thomas Goddard 23 Feb '06

23 Feb '06

Janet Iwasa reports problems exporting ribbons and nucleotide renderings as x3d, problems converting x3d to vrml, and problems with POV and Renderman output. Tom ------- Start of forwarded message ------- Date: Wed, 22 Feb 2006 17:49:33 -0800 From: "Janet Iwasa" <jiwasa(a)gmail.com> To: "Thomas Goddard" <goddard(a)cgl.ucsf.edu> Subject: Re: chimera vrml issues... Hi Tom, Unfortunately, I still ran into a bunch of problems. The structure I had was a bunch of ribbons with some colored sphere residues. When I exported the scene as x3d and used the vrml converter (which did work but took forever on my home computer) it only appeared to export the sphere surfaces, not the ribbon. I ended up using a different program (called 'ribbons' - I think I talked to you about it before) to make a vrml of the ribbon structure. Then I took the colored spheres and superimposed it over the ribbon in Maya. It was pretty time consuming, but worked in the end. The structure (which was a nucleosome) also had some nice DNA representations using the depiction > nucleotide option, and those didn't seem to get exported to x3d either (could have been a problem with the x3d -> vrml conversion -- hard for me to tell where things went wrong). So I used multiscale models and exported the DNA as VRML that way, which worked perfectly, as always. I haven't tested it to see whether the x3d export only works with spheres or what. It took the better part of an hour to convert from x3d to vrml (and this for only 20 or so residues!), so I would love to find a better solution... Ideas? I think I'm pretty much done with that project for the time being, but it would be really nice to have the scene export stuff working. Any clue about what's up with the pov and renderman formats? Those may be easier to find converters for. thanks! Hope you're doing well, Janet ------- End of forwarded message -------

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Re: [Chimera-users] Chimera on Intel macs
by Eric Pettersen 19 Feb '06

19 Feb '06

Having received no major bug reports for the 1.2199 release candidate, we are promoting it to production release status. We have figured out how to make a combined release for Mac Intel and PPC, 10.3 and 10.4, so the download page is a little shorter. :-) --Eric

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Re: [Chimera-users] chimera vrml issues...
by Thomas Goddard 17 Feb '06

17 Feb '06

Hi Janet, The Chimera VRML export only exports surfaces (molecular surfaces, volume data surfaces, multiscale model surfaces). It does not export ribbons or atomic models. Some text in the Export Scene dialog describes this limitation when you select VRML as the File Type. The X3D export is probably the best option. It is a pain to convert but I would try the X3dToVrml97.xslt translator on a machine with more memory if you think that is the reason it is not working. If you don't have a machine available, we can try on one of our machines. Greg Couch here will need to look at the POV and Renderman failures. Tom

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Chimera 1.2176: surfaces fail for some structures?
by Anna Feldman-Salit 13 Feb '06

13 Feb '06

Hello, I have noticed that for 1.2199 version there is a "know bug" of surface failure. We have been working with 1.2176 version (which is probably even not release version). Apparently, I have the same problem with some of molecules (working with 1.2176). Is it occasionally or there is a "known bug" for 1.2176 too? Can you maybe recommend some version that has not such a problem? Thank you in advance! Sincerely, Anna.

2 1

Chimera on Intel macs
by Eric Pettersen 11 Feb '06

11 Feb '06

The 1.2199 release candidate was compiled for PPC macs and fails on Intel macs despite Apple's emulation software. We are working on compiling natively for Intel macs and will send another mail when an Intel version is available. --Eric Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

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labels in Chimera
by Sergey Ryazantsev 10 Feb '06

10 Feb '06

Dear Chimera users I am new in this area, so my question may sound stupid, but anyway. I am using Chimera for 3D model visualization (nothing to do with PDB etc). It's 3D models of biological macromolecules obtained using EMAN 3D reconstruction software. Often I need to compare a bunch of the models at the same time and I need them to be labelled (like 1,2,3,4 etc). I did not find easy way to label multiple objects, so labels would sort of stick to particular object and be independent from the other labels. How also, I could place labels in 3D space, so labels would be at different depth? Any ideas? Many thanks, Sergey. _____________________________________ Sergey Ryazantsev Ph. D. Electron Microscopy Lab UCLA School of Medicine Department of Biological Chemistry 10833 Le Conte Ave, Room 33-080 Los Angeles, CA 90095 Phone: (310) 825-1144 (office) (310) 206-1029 (Lab) FAX (departmental): (310) 206-5272 mailto:sryazant@ucla.edu

2 1

chimera: gnuplot.py
by John Robinson 09 Feb '06

09 Feb '06

Dear chimera power-users: I can use the gnuplot.py library from the python command line without issue. However, when I try to do the same in IDLE under chimera, I get a broken pipe error. Any suggestions? --John -------------------------------------------- John M. Robinson, M.D., Ph.D. mailto:johnmrobinson@mac.com

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Chimera for 64-bit Linux machines
by jbrown 09 Feb '06

09 Feb '06

I'm curious - which production/snapshot release runs best on a 64-bit Linux machine? Also, if the current production releases don't run on such a machine, will there b onee in the near future? Thanks a lot. - Jesse Brown

2 1

Stereo on Mac OS X, 10.4
by David Belnap 08 Feb '06

08 Feb '06

Almost a year ago, I asked if there were plans to support stereo on Mac OS X. Greg replied that Chimera could only when Mac OS X supported stereo-in-a-window (see my question and Greg Couch's answer below). There seems to have been some progress on this by Apple. Their "scientific visualization" page (http://www.apple.com/science/ researchsolutions/visualization.html) says: Thanks to its PCI Express architecture, the Power Mac G5 with the optional NVIDIA Quadro FX 4500 graphics card gives researchers 3D stereo-in-a-window capabilities using a CRT display and Stereographics CrystalEyes liquid crystal shutter eyewear and E2Mac emitter. See also http://www.stereographics.com/apple.html. If I buy the NVIDIA Quadro FX 4500 graphics card, will I now be able to run Chimera in stereo on a Mac? Thanks. David On Wed, 16 Mar 2005, David Belnap wrote: > As a follow-up to the discussion about stereo by Virginia and > Sabuj, will > Chimera currently, or in the future, work in stereo on a Mac > running OS X? > Only if Mac OS X supports stereo-in-a-window. That appears to be unlikely because stereo-in-a-window is a feature that is only supported on workstation-class graphics cards (NVidia Quadro, ATI FireGL, 3DLabs Wildcat), and Apple only sells consumer-class graphics cards (NVidia GeForce, ATI Radeon). chimera needs stereo-in-a-window, instead of full-screen stereo, so the scientist can still use the dialogs to control chimera. If we figure out a reasonable way to keep the (mono) dialogs working in full-screen stereo, then we will support stereo on the Mac. (This also presupposes that most of the Tcl/Tk on Aqua bugs are fixed.) For some other thoughts about stereo hardware, see: <http://www.cgl.ucsf.edu/pipermail/chimera-users/2004-September/ 000197.html> Greg Couch UCSF Computer Graphics Lab gregc(a)cgl.ucsf.edu ============================================ David M. Belnap Department of Chemistry and Biochemistry Brigham Young University Provo, Utah 84602 USA Phone: 801-422-9163 FAX: 801-422-0153 David_Belnap(a)byu.edu ============================================

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release candidate
by Eric Pettersen 08 Feb '06

08 Feb '06

Hi all, We've put a release candidate (1.2199) on the web. Here's a list of changes and new features: http://www.cgl.ucsf.edu/chimera/docs/ relnotes/1.2199.html . If any of them appeal to you, please download the candidate and give it a whirl and let us know if you find any problems. The main motivation for getting this release out is so that web-fetching PDB files doesn't break in a few months (the previous release is using a legacy URL to the RCSB web site that will likely go away). --Eric Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

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DMS installation
by Steven Finckbeiner 06 Feb '06

06 Feb '06

The Dockprep and WriteMol2 files worked like a charm. Could anyone give me any pointers on installing DMS? I have spent the better part of a day following the instructions on the web site and I can't get the damn thing to work. I've gotten this far: 2187 atoms usr/local/lib/dms/radii: no such file or directory Thanks again! "Sometimes, life hits you in the head with a brick." Steve Jobs ---------------------------------------------------------------- Steve Finckbeiner 132 Grace Cancer Drug Center Roswell Park Cancer Institute Elm and Carlton Streets Buffalo, NY 14263-0001 (716)845-5818 --------------------------------- Brings words and photos together (easily) with PhotoMail - it's free and works with Yahoo! Mail.

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Re: [Chimera-users] Dockprep and WriteMol2
by Eric Pettersen 05 Feb '06

05 Feb '06

Hi Steve, Your Googling hit our development documentation, which includes features not in the latest production release and in some cases features that aren't in any release yet. Dock Prep is one of those. We are preparing a release candidate that we anticipate being on the web early next week that will include Dock Prep -- though I can't absolutely guarantee that there won't be an unforeseen hangup that delays it a few days. If you want to use Dock Prep ASAP, I could send you the relevant Python files to drop into your 1.2186 distribution -- let me know. As you noticed, the WriteMol2 module got mistakenly left out of the 1.2186 snapshot, so I would be sending you the files for that as well. The files I'd send you would include one small feature that won't be making it into the release candidate: structures with alternate atom locations will have them pruned to the locations with highest occupancy. --Eric Eric Pettersen UCSF Computer Graphics Lab On Feb 4, 2006, at 4:13 PM, Steven Finckbeiner wrote: > I have Chimera beta version 1 build 2186. I think it's the latest > beta available. I'm trying to clean up some structures to run in > Dock. When I do a google search, the following page comes up: > > http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/dockprep/ > dockprep.html > > I can't find Dockprep under the Surface/Binding Analysis menu. Is > this something that will come out in future versions but the web page > is already built? Or is it in later versions? If so which? My > particular situation makes it hard to get to SYBYL to assign charges > and define rigid and anchor sets. I was thrilled to see that > something like Dockprep has at least been concieved of. > > Also, when I try to save as mol2, I ! get the following error: > > "Import Error: No module named WriteMol2." > > I apologize ahead of time if this marks me as a hopeless novice. Any > help would be much appreciated. > > Steve > > > "Sometimes, life hits you in the head with a brick." > Steve Jobs > > ---------------------------------------------------------------- > Steve Finckbeiner > 132 Grace Cancer Drug Center > Roswell Park Cancer Institute > Elm and Carlton Streets > Buffalo, NY 14263-0001 > (716)845-5818 > > Yahoo! Mail - Helps protect you from nasty > viruses._______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

1 0

Dockprep and WriteMol2
by Steven Finckbeiner 05 Feb '06

05 Feb '06

I have Chimera beta version 1 build 2186. I think it's the latest beta available. I'm trying to clean up some structures to run in Dock. When I do a google search, the following page comes up: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/dockprep/dockprep.… I can't find Dockprep under the Surface/Binding Analysis menu. Is this something that will come out in future versions but the web page is already built? Or is it in later versions? If so which? My particular situation makes it hard to get to SYBYL to assign charges and define rigid and anchor sets. I was thrilled to see that something like Dockprep has at least been concieved of. Also, when I try to save as mol2, I get the following error: "Import Error: No module named WriteMol2." I apologize ahead of time if this marks me as a hopeless novice. Any help would be much appreciated. Steve "Sometimes, life hits you in the head with a brick." Steve Jobs ---------------------------------------------------------------- Steve Finckbeiner 132 Grace Cancer Drug Center Roswell Park Cancer Institute Elm and Carlton Streets Buffalo, NY 14263-0001 (716)845-5818 --------------------------------- Yahoo! Mail - Helps protect you from nasty viruses.

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question on monitoring hydrogen bonds
by knutsost 04 Feb '06

04 Feb '06

Hi: I am interested in monitoring the hydrogen bonds which form/break between specific residues over the course of a MD simulation in CHARMM. I am wondering if you have any way to record things like bond counts over time for the set of residues, or just to spit out a list of the bonds which form and break over the trajectory time course? I really appreciate any help you could give me with this! Thanks, Stacy Knutson Research Associate Wake Forest University

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Re: [Chimera-users] control the movie play speed
by Mingfeng Yang 31 Jan '06

31 Jan '06

Eric Pettersen wrote: > Hi Mingfeng, > It hadn't occurred to me that one might want more than a 1-second > delay per frame (which is what you get when the slider is all the way > over to the left). Maybe I can do something about that in the future. > You can define a script to avoid all that clicking. Use the Movie > dialog's Per-Frame->Define Script... menu entry to bring up a panel > that allows you to define a script to run at each frame. You can > define a script of Chimera commands or Python commands. For what you > describe, Chimera commands can do the job. In the "Script" field just > enter "copy file <FRAME>.png png". When the command is executed, > "<FRAME>" will be replaced with the current frame number. You might > want to check the "Use leading zeroes..." check button so that the > files sort into the correct order when you 'ls' them. Then just run > your trajectory (probably with the "Loop" button checked off). > Bravo! This command rocks. Thanks! I should forward this to the mailing list; someone else must want to know it. Mingfeng > --Eric > > On Jan 31, 2006, at 11:16 AM, Mingfeng Yang wrote: > >> Hi, Eric, >> >> I did get your email. I am sorry that I didn't get back to you in >> time. The position of the slider does control the playback rate, but >> even the slowest is not slow enough for my case. I want at least a >> second pause after each snapshot, so that people can see the >> conformational change clearly. Finally, I just export every snapshot >> as png image and make a gif movie by connecting all the snapshots. >> Though I have to spend more time on it, this way gave me better >> picture quality. >> >> Can I define a script which automatically export each frame in the MD >> trajectory as png image? It's really a pain to click "save as" again >> and again. >> >> Eric, you are such a nice person. Thank you very much! >> >> Mingfeng >> >> >> >> Eric Pettersen wrote: >>> Hi Mingfeng, >>> Did you get my mail where I attached the two MPEG-4 files? >>> >>> --Eric >>> >>> On Jan 27, 2006, at 2:01 PM, Mingfeng Yang wrote: >>> >>>> Eric Pettersen wrote: >>>>> Hi Mingfeng, >>>>> You can use the main interface's playback slider to change the >>>>> rate that frames are played back. With the slider to the far >>>>> right there is no delay between frames, with it to the far left >>>>> there is a one-second delay between frames. This interacts with >>>>> recording just like you would expect -- extra frames get recorded >>>>> during the delay which produces a movie with the same apparent >>>>> playback speed as with a non-recorded playback. >>>>> >>>> Hi, Eric, >>>> >>>> Thank you for your replay! But actually, the recorded playback is >>>> more faster than the non-recorded playback. I tried the slider at >>>> different position many times. BTW: I save the movie as mpeg >>>> format. As usual, gentoo linux, chimera buld 2186. >>>> >>>> Mingfeng >>>> >>> >>> >> > >

1 0

Chimera memory management
by lutetium＠gmx.net 31 Jan '06

31 Jan '06

Hi, I am currently working on few datasets that exceeds the given memory limit for chimera. The log file indicates: MemoryError: can't allocate memory for array How can I increase the memory for chimera? Any suggestion regarding chimera´s memory management would be appreciated. Thanks a lot, Mike -- Lust, ein paar Euro nebenbei zu verdienen? Ohne Kosten, ohne Risiko! Satte Provisionen für GMX Partner: http://www.gmx.net/de/go/partner

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problem in displaying pdb file
by venkataraman kabaleeswaran 30 Jan '06

30 Jan '06

I am having a problem in displaying the pdb file, chimera didnot display the whole molecule , around 100 residues is missing in the display, but other programs like pymol displaying without any problems. what is wrong? thanks vk Kabaleeswaran Venkataraman Arise, Awake and stop not until goal is Reached - Swami Vivekanand __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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Fwd: control the movie play speed
by Eric Pettersen 27 Jan '06

27 Jan '06

Forgot to cc this to the list for the good of future generations. :-) --Eric Begin forwarded message: > From: Eric Pettersen <pett(a)cgl.ucsf.edu> > Date: January 27, 2006 1:42:37 PM PST > To: Mingfeng Yang <mfyang(a)gmail.com> > Subject: Re: [Chimera-users] control the movie play speed > > Hi Mingfeng, > You can use the main interface's playback slider to change the > rate that frames are played back. With the slider to the far right > there is no delay between frames, with it to the far left there is > a one-second delay between frames. This interacts with recording > just like you would expect -- extra frames get recorded during the > delay which produces a movie with the same apparent playback speed > as with a non-recorded playback. > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > pett(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu > > On Jan 27, 2006, at 12:59 PM, Mingfeng Yang wrote: > >> Hi, >> >> I am using chimera to record the movie of a MD trajectory into a mpeg >> format vedio. How can I set the interval between neighboring >> snapshots? >> It seems the playback option in the MD movie dialog can't do >> that. Thanks! >> >> Mingfeng >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >

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control the movie play speed
by Mingfeng Yang 27 Jan '06

27 Jan '06

Hi, I am using chimera to record the movie of a MD trajectory into a mpeg format vedio. How can I set the interval between neighboring snapshots? It seems the playback option in the MD movie dialog can't do that. Thanks! Mingfeng

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Background transparency
by Alon Ben-David 27 Jan '06

27 Jan '06

Hi My name is Alon and I am a graduate student at the Technion, Israel institute of technology. My question is how can I create a transparent background to pictures I am generating with Chimera. I read at the site that not all hardware's permit a transparent background, but I don't know how can I check if my hardware do. Thank you in advance and best regards Alon

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command line for showing and hiding (same as clicking shown checkbox in model panel?) and volume viewer options in a cmd file?
by sabuj pattanayek 26 Jan '06

26 Jan '06

Hi, I'm trying to make a movie using a cmd file. I want to show and hide (same as clicking the checkbox for shown in the model panel) models from the cmd file since the system becomes too slow to do it manually while the movie is recording and timing frames is even more difficult. I also want to decrease and increase the isosurface threshold level in the volume viewer from the cmd file. Is it possible to do these without using the mouse while a movie is recording? Thanks, Sabuj Pattanayek

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Fwd: command line for showing and hiding (same as clicking shown checkbox in model panel?) and volume viewer options in a cmd file?
by Elaine Meng 25 Jan '06

25 Jan '06

> From: Elaine Meng <meng(a)cgl.ucsf.edu> > Date: January 25, 2006 10:42:40 AM PST > To: sabuj pattanayek <sabuj.pattanayek(a)vanderbilt.edu> > Subject: Re: [Chimera-users] command line for showing and hiding > (same as clicking shown checkbox in model panel?) and volume viewer > options in a cmd file? > > Hi Sabuj, > I failed to read Tom's mail first, oops. Just wanted to mention, > however, that I am pretty sure you want the command "modeldisplay" > and not "display": the latter turns all the atoms on, whereas > "modeldisplay" leaves the atom and ribbon display bits as they are > and is equivalent to the Show/Hide stuff in the Model Panel. > Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

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Re: [Chimera-users] distance not shown
by Mingfeng Yang 25 Jan '06

25 Jan '06

Eric Pettersen wrote: > Hi Mingfeng, > ATI has come out with a new driver version for your card: > 8.21.7. Could you try that version and see if things start working? > Let me know. Thanks! > > --Eric > Hi, Eric, I just updated the driver to 8.21.7, and it can't work out. :( Meanwhile, I tried the radeon driver included in Xorg, and the distance can be displayed. So, yes, it's the driver's fault. Mingfeng > On Jan 11, 2006, at 6:09 AM, Mingfeng Yang wrote: > >> Hi, Eric, >> >> I am using ATI FireGL 8800 graphics card with driver fglrx-8.20.8. >> The 2D label does work. Labeling an atom or residue showed nothing. >> Change font size and style didn't solve the problem. >> I remember this feature works perfectly in the previous versions >> (probably before build 1.6???) on this same machine. >> >> Regards, >> Mingfeng >> >> >> Eric Pettersen wrote: >>> Hi Mingfeng, >>> You are the second person to report this behavior -- the other >>> person was also on Linux. Can you tell me what graphics cards you >>> have and what driver version? Do regular atom labels show up? Do >>> 2D labels work (Tools->Utilities->2D Labels)? Can you check your >>> Background preferences and make sure the default font size is > 0 >>> and try changing the font style to see if that makes any difference? >>> >>> --Eric >>> >>> Eric Pettersen >>> >>> UCSF Computer Graphics Lab >>> >>> pett(a)cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu> >>> >>> http://www.cgl.ucsf.edu >>> >>> >>> >>> On Jan 10, 2006, at 2:56 PM, Mingfeng Yang wrote: >>> >>>> >>>> I am using Chimera build 1.2186 on Gentoo linux. Strangely, when >>>> the distance between two atoms is shown by the command "distance", >>>> the number is no longer displayed along the yellow dashed line. >>>> Did the developers removed this function? Or is it a bug? >>>> >>>> Regards, >>>> Mingfeng >>>> >>>> >>>> _______________________________________________ >>>> Chimera-users mailing list >>>> Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> >>>> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >>> >> > >

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Question
by Jin Chai 23 Jan '06

23 Jan '06

Dear Sr/Ms, I wonder if chimera molecular modeling system can be used beyond molecular level. we try to use chimera to create 3D images on mouse colon crossection images(dataset) we collected from SKYSCAN Micro-CT 1076 . Do you think it will work? Looking forward to your opinion. Thanks in advance, Jin --------------------------------- Yahoo! Photos Showcase holiday pictures in hardcover Photo Books. You design it and well bind it!

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CIF file format?
by Jason Sharpe 17 Jan '06

17 Jan '06

Hi, how do I open mmCIF (.cif) files in Chimera. This is the standard format of structure files supplied by the Cambridge Structural Database. thanks, Jason Sharpe University of Toronto

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Saving a multiscale model in VRML
by R. Andrew Byrd 17 Jan '06

17 Jan '06

Greetings, Our publications group has a new device that they call a 3D printer. It can make solid models from a data file. They have made models from pdb files as ball-and-stick, and I saw one surface rendered model. They tell me that the input is in VRML. So, I am wondering how to make a VRML file from a session in Chimera where Multiscale Model tool is used to make a surface rendering of a complex model...several proteins. My model is not as complex as the virus examples for multiscale models, but the ability to make different resolution surfaces is a powerful aid. I would like to try and 'print' a 3D model of this surface rendered complex. Any help in out to output the VRML file for the printer?> Thanks Andy -- R. Andrew Byrd, Chief Structural Biophysics Laboratory National Cancer Institute V 301-846-1407 F 301-846-6231 -------------------------------------------------

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Slow framerates (on a nice laptop)
by Charlie Moad 17 Jan '06

17 Jan '06

So in general I get really good performance with chimera, but for some reason I get really bad frame rates with more recent releases on windows with my laptop. It has a really nice card, GeForce 6200TC Go. It is even on a pcix16 bus. I am guessing that since it is a newer chipset, chimera is using shaders of some kind? The molecule looks visually smoother/better than when in linux. In any case, it seems something is getting enabled that really bogs it down, and I would like to be able to disable it. Sony Vaio FS500 Chimera 1.2184 Thanks, Charlie

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distance not shown
by Mingfeng Yang 11 Jan '06

11 Jan '06

I am using Chimera build 1.2186 on Gentoo linux. Strangely, when the distance between two atoms is shown by the command "distance", the number is no longer displayed along the yellow dashed line. Did the developers removed this function? Or is it a bug? Regards, Mingfeng

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yet another binary plugin question
by Charlie Moad 06 Jan '06

06 Jan '06

So I have been able to create a working binary plugin for windows/linux 1.2184 and osx.4 1.2186. My problem now is osx.3 1.2184. I can compile the plugin, but it crashes chimera with a TCLfree call to a null pointer. I used the chimera-1.2183-linux-headers.tar.gz download. The 1.2186-osx headers didn't work either. 1.2186 won't launch for 10.3 either. The python module is matplotlib. It uses Numeric, freetype, tcl/tk, and libpng. I provide the only missing dep, libpng, and compile against the rest which are provided in chimera. Any help on what approach I should be using? Thanks, Charlie

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Help or feature request
by Mingfeng Yang 22 Dec '05

22 Dec '05

It's a very common problem to calculate the twist angle between to beta-strands or two alpha-helix. So I am wondering if Chimera can fit a group of atoms into a straight line, and give the angle of two fitted line. If chimera does do this, hopefully somebody can tell me how to do this. If not, it would be worthwhile to add this function in. Thank you very much! Happy holiday! Mingfeng

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Save image from Chimera
by Juhan Kim/CIRES 22 Dec '05

22 Dec '05

Hello, Does anybody know how to save the image from the chimera? I'm using PC version of Chimera and whenever I'm trying to save the image using the menu file>save image, I always fail to save the image and only get the following "reply log" ----reply log----- Opening "file.pdb" Done opening "file.pdb" Unable to save image: (0, 'Error') Unable to save image: encoder error -2 when writing image file Unable to save image: encoder error -2 when writing image file Unable to save image: (0, 'Error') If anybody knows how to solve this please let me know. Thank you. Juhan UCB, Boulder

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how to not include CONECT, RIBBON, HELIX, SHEET keywords in a pdb when saving from the pdb file dialog
by Sabuj Pattanayek 19 Dec '05

19 Dec '05

Hi, I was wondering how it might be possible to not include the CONECT, RIBBON, HELIX, or SHEET keywords in a pdb when saving from the save pdb file dialog? It can be done using "pdbrun nouser cat | grep -v HELIX | grep -v SHEET" ...etc but I can't save the pdb model relative to another model on the screen using that command. Thanks, Sabuj Pattanayek

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Fit Models
by Bernard Heymann 14 Dec '05

14 Dec '05

I'm interested in using the "Fit Models in Maps" feature in Chimera. However, the version I installed (release 1.2184) under Mac OSX 10.4 does not have this in the Tools/Volume Data menu as described in the documentation. Can anyone tell me if this is intentional or can I get this feature? Bernard Heymann, Research Fellow Rm 1515, 50 South Dr., MSC 8025, NIAMS, NIH Bethesda MD 20892 Tel. 301-451-8241, Fax. 301-480-7629

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new version available
by Eric Pettersen 14 Dec '05

14 Dec '05

Hi all, We've put out a new version (1.2180) which we believe fixes the problems that some people were having on XP platforms. We're hoping that those of you that were having problems will try out the new version at your earliest convenience and let us know how it works. Thanks! Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

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Concerns regarding secondary structure
by rquiroga＠immf.uncor.edu 12 Dec '05

12 Dec '05

Greetings, I have some concerns with Chimera's secondary structure detection/depiction. I am using Modeller to predict some 3D structures. I open my predicted structure in pdb file in Chimera along with the original structure I based my prediction on, and find that my predicted structure lacks two beta sheets that the model protein has, though the AA that compose the B-sheet are identical for the two proteins when I compare sequences with Matchmaker. I tried opening my predicted structure in MolMol and it detects the B-sheet, though I hugely prefer Chimera, so if you could solve this problem for me I would be very greatful. Thanks in advance, and regards Rodrigo Quiroga

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Concerns regarding secondary structure
by rquiroga＠immf.uncor.edu 09 Dec '05

09 Dec '05

I have some concerns with Chimera's secondary structure detection/depiction. I am using Modeller to predict some 3D structures. I open my predicted structure in pdb file in Chimera along with the original structure I based my prediction on, and find that my predicted structure lacks two beta sheets that the model protein has, though the AA that compose the B-sheet are identical for the two proteins when I compare sequences with Matchmaker. I tried opening my predicted structure in MolMol and it detects the B-sheet, though I hugely prefer Chimera, so if you could solve this problem for me I would be very greatful. Thanks in advance, and regards Rodrigo Quiroga

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