- Chimera-users - RBVI Mailing Lists

1.2251 snapshot release
by Eric Pettersen 06 Jun '06

06 Jun '06

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

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Stereographics support
by Eduardo Sanz Garcia 01 Jun '06

01 Jun '06

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

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

01 Jun '06

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

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

26 May '06

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

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editing Python saved sessions
by Jonathan Hilmer 22 May '06

22 May '06

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

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Question
by szklars2＠tcnj.edu 21 May '06

21 May '06

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

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

21 May '06

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

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Chimera crash on SGI
by Thomas Goddard 19 May '06

19 May '06

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

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

17 May '06

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

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Chimera movie commands
by Thomas Goddard 16 May '06

16 May '06

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

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

15 May '06

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

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

09 May '06

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

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manual
by Oscar Moran 08 May '06

08 May '06

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

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

07 May '06

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

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B-factors
by Narender Singh Maan 05 May '06

05 May '06

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

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

05 May '06

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

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

05 May '06

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

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absolute scale?
by Cathy Lawson 02 May '06

02 May '06

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

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Broken labels!
by Changhoon Kim 02 May '06

02 May '06

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

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libGL.so
by Isaac Amela Abellan 02 May '06

02 May '06

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

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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 11 Apr '06

11 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 08 Mar '06

08 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 *************************************************************

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Re: [Chimera-users] (no subject)
by Eric Pettersen 08 Mar '06

08 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

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delphi in chimera
by Thomas Goddard 02 Mar '06

02 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

2 2

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

2 1

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

2 1

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.

2 1

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 27 Feb '06

27 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 10 Feb '06

10 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 09 Feb '06

09 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 07 Feb '06

07 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.

3 5

Re: [Chimera-users] Dockprep and WriteMol2
by Eric Pettersen 04 Feb '06

04 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 04 Feb '06

04 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 03 Feb '06

03 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

2 1

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 >

1 0

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

1 0

Background transparency
by Alon Ben-David 26 Jan '06

26 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

2 1

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 24 Jan '06

24 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 >>> >> > >

2 1

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!

2 1

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

2 1

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 -------------------------------------------------

3 2

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

2 1

distance not shown
by Mingfeng Yang 10 Jan '06

10 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

2 1

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

2 7

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

2 1

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

2 1

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

2 1

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

2 1

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

7 20

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

2 2

Concerns regarding secondary structure
by rquiroga＠immf.uncor.edu 08 Dec '05

08 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

1 0

Re: [Chimera-users] Moving selected atoms
by Thomas Goddard 08 Dec '05

08 Dec '05

I improved the mouse mode for moving selected atoms so if no atoms are selected it moves everything like the normal rotation and translation mouse modes -- all active models are moved. The new code is http://www.cgl.ucsf.edu/home/goddard/temp/moveselection.tar For installation instructions see my previous chimera-users message. http://www.cgl.ucsf.edu/pipermail/chimera-users/2005-December/000609.html The new behaviour makes it easy to move some atoms, then rotate the view, then move the atoms again. After moving the atoms you can clear the selection using ctrl-click on the background of the graphics window, then rotate everything to the new view point, then press the left arrow key (undo selection) to revert to the previous selection, and continue moving the atoms. Tom

1 0

Moving selected atoms
by Thomas Goddard 07 Dec '05

07 Dec '05

I wrote a Chimera extension that allows moving just selected atoms with the mouse. This is for modifying molecular structures. Here is the code http://www.cgl.ucsf.edu/home/goddard/temp/moveselection.tar that adds mouse modes to move selected atoms. The archive contains a directory called MoveSelection. Put it in your Chimera distribution in chimera/share or on Mac in Chimera.app/Contents/Resources/share Then when you start Chimera use menu entry Favorites / Preferences, and choose category "Mouse" from the preferences dialog. This shows the mouse modes table with the available modes along the top line. The last two are for shifting and rotating selected atoms. Reassign mouse buttons (say buttons 1 and 2) to these modes and you can move selected atoms. There is no undo. I'll have to make this easier to use and put it into Chimera. Tom

1 0

Re: [Chimera-users] chimera for linux ppc
by Geoffrey H Wathen 07 Dec '05

07 Dec '05

I've used YellowDog in the past, and I think it is a good dist. I wouldn't mind seeing a PPC Linux version of Chimera, either. Geoff. On Dec 7, 2005, at 10:50 AM, A. Zelter wrote: >> I think Conrad is saying that on the x86 architecture they can >> compile for RedHat and it will run on most distributions of x86 >> Linux. He's asking if there's a similar situation on PPC Linux, >> and which distribution of PPC Linux would provide the best >> prospects for such coverage. It seems to me that this is to >> minimize the occurrence of someone saying "I see you have the >> binaries for XYZ PPC Linux, but they don't run on my distribution >> of ABC PPC Linux. Could you please compile it for ABC PPC Linux?" > > Ahhh thanks. I knew I didn't get something. Well, I'm no expert on > that kind of thing, but Fedora Core 4 has a ppc version. I think > this is a little more modern than Red Hat Linux 7.1 - it runs > kernel 2.6.11. However, RedHat did make a PPC version of their 7.1 > distro (Red Hat Linux 7.1 for pSeries). I suppose that would be > equivalent. Another good bet might be yellowdog linux. The latest > version is 4.0.1, and it uses kernel 2.6.10. Yellowdog is based on > redhat but built specifically for Macs. This is probably what I > would try using. > Alex > >

3 3

Missing tools
by Luke Kontogiannis 07 Dec '05

07 Dec '05

I had installed the current production release chimera-1.2184-linux.exe. Just now I downloaded and installed the latest snapshot release chimera-1.2186-linux.exe and this version has the multiscale tool under Tools -> Higher-order structure Luke

2 1

chimera for linux ppc
by Alex Zelter 07 Dec '05

07 Dec '05

Hi, I was wondering if it would be possible for the developers to compile a binary version of chimer for use on linux ppc architecture seeing as it is not possible for a user to compile for themselves due to the proprietary solvent-accessible molecular surfacing library. I know this is not a common architecture, but some people do use it. Thanks in advance, Alex Zelter

3 2

Missing tools
by Luke Kontogiannis 07 Dec '05

07 Dec '05

Hi all, I installed chimera on windows and everything works fine. However, I installed it on ubuntu linux 5.10 yesterday and there are some tools that are missing such as multiscale. Is the windows version of chimera simply more capable or have I done something wrong? I simply ran the chimeral.exe file as root and it seemed to install fine. I even tried replacing the share directory on the linux box at work with the one from the windows version but that gave errors upon launching. Any ideas? Thanks Luke

1 0

Data reporting
by Reiner Villavicencio 04 Dec '05

04 Dec '05

Dear all, I have learned that 3D results/data from molecular dynamics or docking can be compressed to produce informative 2D diagrams for publication. Can anyone recommend such a program? Thank you and good day "Its hard to hold on to something that can never be yours in anyway you want... something that wasnt really yours to begin with... you just have to go on and accept the fact that while good things never last some dont even start...." Send instant messages to your online friends http://uk.messenger.yahoo.com

1 0

Add hydrogens to get -NH2 group
by Daniel Svozil 02 Dec '05

02 Dec '05

Hi all, if I use addH tool on the C-N, I would expect to get C-NH2, but I get C-NH3 instead. How should I proceed to get C-NH2 correctly? Thanks Dan -- Daniel Svozil, PhD Institute of Organic Chemistry and Biochemistry Center for Biomolecules and Complex Molecular Systems http://www.molecular.cz/~svozil Czech Republic phone: +420-220 410 312

2 1

Sequence alignment
by David G. Morgan 01 Dec '05

01 Dec '05

Hi, I'm learning to use the sequence alignment tools in chimera. I know that I can highlight sequences in the alignment window and select residues in the structure, but is it possible to do the opposite? In other words, I'd like to box or otherwise select some residue(s) in the structure and have that region highlighted or otherwise marked in the aligned sequence window. David Gene Morgan Advanced Microscopy & Proteomics Molecular & Cellular Biology University of California at Davis 530 752 2693 (lab) 530 752 3085 (FAX)

2 2

Feature Request: Expose rotation to python
by Charlie Moad 29 Nov '05

29 Nov '05

The repr of an xform shows the opengl rotation matrix. I want to get this efficiently in python, but I don't believe it is exposed. Could a getter please be added returning a 4x4 tuple, so a Numeric array can be trivial/efficiently made from it? If there is a current approach please let me know. Thanks, Charlie

4 7

estimaded standard deviation (sigma levels) for electron densities in volume viewer
by Pattanayek, Sabuj 28 Nov '05

28 Nov '05

Hi, Is it possible to specify the estimated standard deviation (sigma level) for electron densities in the volume viewer? Currently, I have to eyeball the distribution of the volume data and place the bar accordingly. Thanks, Sabuj Pattanayek

2 2

Question about connectivity
by Frederick Gimble 22 Nov '05

22 Nov '05

I have just begun using Chimera on my Mac, and find that it will be able to produce the graphics that I need for publication and display purposes. I recently opened a pdb file of a protein that we study bound to DNA and used the depiction, nucleotides tool to render the DNA backbone as ribbons with the bases shown as slabs. I noticed a discontinuity in one of the DNA strands, which may be caused by the severe distortion of the DNA. I think that this also happened with a previous program that I used called SPOCK that I used to draw the DNA strands as worms. In that case I could repair the break by changing the settings for the connectivity distances. How would I repair the break in Chimera? Thanks for your help. Sincerely, Fred Gimble Frederick S. Gimble, Ph. D. Associate Professor Department of Biochemistry BCHM 315 175 S. University St. Purdue University West Lafayette, IN 47906 Telephone: (765) 494-1653 Fax: (765) 494-7897 Email: fgimble(a)purdue.edu

3 2

Chimera failed abnormally
by Johan Börjesson 22 Nov '05

22 Nov '05

Hi I have downloaded the chimera-1.2184-win32.exe version of Chimera and installed it on my laptop running on an Celeron M 370 processor. The operation system is Windows XP. The problem is that I get an error message when I try to run the program. Chimera failed abnormally; the exit code was: 1. use the --debug command line option for the full error message. Hope that you can tell what the problem is and what I can do about it. Best regards Johan Börjesson Dept. of Biochemistry Lund University, Sweden

2 1

Move atoms (selections) in Chimera
by Daniel Svozil 21 Nov '05

21 Nov '05

Hi, is there any possibility, how to move atoms (selections) in Chimera? If, e,g,, I want to make C-H bond a bit longer? move command seems to work only with model. Thanks Dan -- Daniel Svozil, PhD Institute of Organic Chemistry and Biochemistry Center for Biomolecules and Complex Molecular Systems http://www.molecular.cz/~svozil Czech Republic phone: +420-220 410 312

5 9

Selecting Protein portions
by Reiner Villavicencio 20 Nov '05

20 Nov '05

Dear all, I have read a couple of literature which uses the Chimera program. Before performing a docking run, most of them selects only the relevant residues within a certain region (for example in a 20 angstrom core). May I ask how is this done in Chimera? I mean do the "unrelevant" portions get deleted? Thank you and good day - RV "Its hard to hold on to something that can never be yours in anyway you want... something that wasnt really yours to begin with... you just have to go on and accept the fact that while good things never last some dont even start...." Send instant messages to your online friends http://uk.messenger.yahoo.com

2 1

creating cubes and other 3D shapes
by Stephen A. Smith 18 Nov '05

18 Nov '05

Hi I want to create a cube (box; 1Å^3, 2Å^3, etc.) at specific grid points and color them as needed. Is this possible in Chimera? It is easy to do with spheres by specifying an atom at the desired location and then defining its VDW radius. I would like to create cubes and rectangles of various sizes, related to regions of my protein, to denote specific atomic / residue features. Any help would be greatly appreciated. Thanks Steve __________________________________ Yahoo! Mail - PC Magazine Editors' Choice 2005 http://mail.yahoo.com

3 2

Reference Manual
by Reiner Villavicencio 17 Nov '05

17 Nov '05

Dear all, Is an offline reference manual (*.pdf) available for Chimera? I realized that under the documentation section of the website, that only online references are present. Having an offline user guide would be more convenient because there is no need to go online everytime a problem is encountered. Thank you and good day Reiner Villavicencio BS Biochemistry Dept. of Physical Sciences and Mathematics College of Arts and Sciences University of the Philippines, Manila "Its hard to hold on to something that can never be yours in anyway you want... something that wasnt really yours to begin with... you just have to go on and accept the fact that while good things never last some dont even start...." Send instant messages to your online friends http://uk.messenger.yahoo.com

2 1

Reference Manual
by Reiner Villavicencio 16 Nov '05

16 Nov '05

Dear all, Is an offline reference manual (*.pdf) available for Chimera? It woulb be more convenient, because its hard to go online whenever you have a problem. Thank you and good day Reiner Villavicencio BS Biochemistry Dept. of Physical Science and Mathematics College of Arts and Sciences University of the Philippines, Manila "Its hard to hold on to something that can never be yours in anyway you want... something that wasnt really yours to begin with... you just have to go on and accept the fact that while good things never last some dont even start...." Send instant messages to your online friends http://uk.messenger.yahoo.com

1 0

export tiff...
by Panizzi, Peter 14 Nov '05

14 Nov '05

To whom it may concern, I have been using the chimera program and I cannot save or export a tiff or jpeg file is there some trick to doing this? Thanks, Pete

4 3

Rotation callback
by Charlie Moad 11 Nov '05

11 Nov '05

Is it possible to register a python callback for when a protein is rotated and get the rotation information? Thanks, Charlie

2 1

v1.2184 - Is it possible to specify the color of the tube object (sugar-backbone) bond in nucleic acid models?
by Sabuj Pattanayek 11 Nov '05

11 Nov '05

Hi, In v1.2184 is it possible to specify the color of the tube object connecting the sugar to the backbone in a nucleic acid model? Currently clicking apply in the nucleic acid depiction dialog changes its color to whatever the color of the base is set to. Thanks

2 1

chimera question
by cjamesgrant＠earthlink.net 09 Nov '05

09 Nov '05

Does chimera have the capability of automatically connecting the elements of a protein to reveal its overall shape. I am trying to determine the amino acid sequence of the attached protein, but I am having a hard time visualizing how the elements are connected to each other. I am new to this program, so any help would be greatly appreciated. Thank you, C Grant

2 1

Mac OS X 10.4.3 update breaks Chimera
by Eric Pettersen 03 Nov '05

03 Nov '05

Hi, The 10.4.3 update to OS X breaks a significant amount of Chimera functionality. Attempts to use that functionality cause Chimera to exit. In particular, for structures that contain residues other than the standard amino/nucleic acids or water, anything that directly or indirectly makes Chimera determine atom types will cause the failure. Such things include adding hydrogens, finding hydrogen bonds, and going into ball-and-stick or sphere representation (the atom sizes are based on atom types) -- though stick-only mode is okay. We are working on a fix. Until we have one, you will have to weigh the improvements offered by 10.4.3 against the loss of Chimera functionality. I'll send mail to the list as soon as there are developments. --Eric Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

1 1

RGB->CMYK color conversion
by James Puckett 02 Nov '05

02 Nov '05

Dear Chimera users, I am writing to see if there are suggested methods for ensuring good color conversion of rendered Chimera images from RGB to CMYK in Photoshop (or other image editing programs). When printing to a Tektronix Phaser 740 color laser, I am getting poor correlation between screen colorings and the printed ones. I have heard that the CMYK color space is basically a subset of the RGB color space. If this is actually the case, is there a recommended way to pick RGB colors that are relatively "safe" for conversion to a CMYK color space? Thanks, Jim Puckett

3 3

2D labels not saved ?
by Boaz Shaanan 02 Nov '05

02 Nov '05

Hi, I used the 2D labels utility to make a few labels but when I save the image as tif I don't see them when I re-open the tif file. Is that possible ? Thanks, Boaz

3 3

chimera and STRAP ?
by Dr. Christoph Gille 01 Nov '05

01 Nov '05

Hi, I contact you because users of the program STRAP for protein structures and sequences asked whether Chimera could be used within STRAP for visualization. Currently Jmol and Pymol are used for visualiziation. For example the results of 3D superpositions and the location of mutations can be viewed. But some users apparently prefere Chimera. My question is whether Chimera could be linked to STRAP as well. The most important point is, what mode of interprocess commmunication exists in Chimera. For example Pymol and STRAP are linked via the stdin/stdout streams. STRAP can send commands to Pymol and is notified when atoms are picked. STRAP uses the scripting language of Pymol to load proteins, create selections and rotate proteins. Could all this be done with Chimera in a similar way ? Best regards Christoph

2 1

how to select multiple residues in multiple chains
by Eric Gillitzer 01 Nov '05

01 Nov '05

I work a lot with symmetrical, multi subunit structures and in order to select say residue 45 in every subunit, I must one at a time go in and in the sequence finder select the residue in each chain and then color it. Is there a way to select all of the same number residues (say number 45, might be an alanine) in the structure displayed and color only those. If you select alanine, it will select every single alanine in the structure. Chimera seems to be a really powerful program, but I am pulling my hair out trying to get it to do something productive in a timely fashion. thanks, eric.

3 2

Display of qpack color output
by Eric Dawson 01 Nov '05

01 Nov '05

In the older UCSF MidasPlus incarnation of your software, there was a feature that allowed an interface with Gregort & Cohen's QPACK software for coloring according to molecular packing density using a sphere growth method. Per residue packing scores were applied with a color range after running qpack with the special option, '-m'. http://www.cmpharm.ucsf.edu/cohen/software/pages/qpack.html In the primary literature report of QPACK, it was suggested by the authors that they would work to make this feature available in UCSF MidasPlus and 'its successors'. Since this is a very fast and convenient way to evaluate the quality of models, I would like to recommend/request that this feature be enabled (or added) to Chimera. In MidasPlus, it was a command line option. The user simply entered qpack; there was a .midasrc file that contained the explicit local path to the qpack binary as well as a command line script to launch the package with the '-m' option. Thanks for your consideration of this suggestion. Best regards, Eric ______________________________________________________________________ Eric S. Dawson, Ph.D. CSB Computation, Education & Outreach Research Instructor, Biochemistry Center for Structural Biology (CSB) 5137 MRBIII Vanderbilt University Nashville, TN 37232-8755 Tel: (615)-936-5579 (MRB III) Tel: (615)-322-3303 (5119 SC) Fax: (615)-936-2211 "All that is gold does not glitter, not all those who wander are lost." J.R.R. Tolkien - Fellowship of the Ring

2 1

installing v1.2183 on XP & preserving preferences from previous version
by Boaz Shaanan 01 Nov '05

01 Nov '05

Hi, For some reason I had problems installin 1.2183 under XP which I haven't had before. Only after un-installing the previous version it finally worked. Maybe something with the un-install script isn't quite working properly this time around ? I thought that by saving the preferences file and copying it back to the proper location (as it says under preferences/preferences) after installation, I would be able to continue with the same prerefences setting I had before. Apparently this didn't work. So what should I do in order to properly move the preference file from one version to the other ? Thanks for your help. Boaz

2 1

Re: [Chimera-users] Chimera and secondary structure annotations
by Thomas Goddard 28 Oct '05

28 Oct '05

Hi Julio, The secondary structure calculation requires all peptide backbone atoms. In the Chimera docs it notes: "Ksdssp uses the coordinates of the backbone atoms (N, CA, C, O, and optionally H) of a protein to determine which residues are in alpha helices and beta strands." There is no way in Chimera to determine secondary structure from just CA positions. The error message you sent for pdb2mrc is a bug in the AIRS package which is developed and maintained by Matt Baker (mbaker(a)bcm.tmc.edu) at Baylor College of Medicine, not our group. It is a problem in file C:\Programme\EMAN\chimeraext\Airs\airsIO.py It occurs because you have a model open in Chimera which is neither a density map surface nor a PDB model (maybe a molecular surface or a solid volume rendering?). The airsIO.py code does not handle that correctly. You could try running it with only the PDB model open in Chimera to avoid this problem. Alternatively you could edit the airsIO.py file with a text editor changing near line 32 from: if str(model.__class__)=="VolumeViewer.surface.Surface_Model": path=str(volume_data_set(model).data.path) elif str(model.__class__)=="chimera.Molecule": modelfile=model.openedAs path=str(modelfile[0]) if filecheck.strip()==path: path=os.path.abspath(model.name) to if str(model.__class__)=="VolumeViewer.surface.Surface_Model": path=str(volume_data_set(model).data.path) elif str(model.__class__)=="chimera.Molecule": modelfile=model.openedAs path=str(modelfile[0]) else: path = "" if filecheck.strip()==path: path=os.path.abspath(model.name) Just two lines are added the "else:" and the "path = ""'. Make sure to use this indentation if you make the change since that is important in Python code. I'll send the error message to Matt Baker. Tom > Date: Sat, 29 Oct 2005 01:58:48 +0200 > From: "Dr .Julio Ortiz" <ortiz(a)biochem.mpg.de> > To: Thomas Goddard <goddard(a)cgl.ucsf.edu> > Cc: meng(a)cgl.ucsf.edu > Subject: Re: Chimera and secondary structure annotations > > Dear Thomas and Elaine: > Thank you very much for your answers, I checked the ksdssp command and it works > for some pdbs, but not for those that I mentioned with the ribosomes. I think > that the problem is that some pdbs from ribosomes (like 1GIX and 1GIY) do not > have complete residues (just CAs). In the case of your images, you have use > 1PNS and 1PNU, and only those proteins in the 30S are complete. > I guess I need to contact some of the authors of the structures to see if the > complete coordinates are available. > > Another question: I installed the new version of Chimera and when using pdb2mrc > I received an error message: > ------------------------------ > Traceback (most recent call last): > File "C:\Programme\Chimera\share\__main__.py", line 59, in ? > value = chimeraInit.init(sys.argv) > File "C:\Programme\Chimera\share\chimeraInit.py", line 308, in init > tkgui.eventLoop() > File "C:\Programme\Chimera\share\chimera\tkgui.py", line 2725, in eventLoop > app.mainloop() > File "C:\Programme\Chimera\bin\Lib\lib-tk\Tkinter.py", line 965, in mainloop > self.tk.mainloop(n) > File "C:\Programme\Chimera\bin\Lib\site-packages\Pmw\Pmw_1_2\lib\PmwBase.py", > line 1751, in __call__ > _reporterror(self.func, args) > File "C:\Programme\Chimera\bin\Lib\site-packages\Pmw\Pmw_1_2\lib\PmwBase.py", > line 1814, in _reporterror > displayerror(msg) > File "C:\Programme\Chimera\bin\Lib\site-packages\Pmw\Pmw_1_2\lib\PmwBase.py", > line 1377, in displayerror > _errorReportFile.write(text + '\n') > File "C:\Programme\Chimera\bin\Lib\site-packages\Pmw\Pmw_1_2\lib\PmwBase.py", > line 1747, in __call__ > return apply(self.func, args) > File "C:\Programme\Chimera\share\chimera\baseDialog.py", line 229, in <lambda> > self.__buttonFuncName(txt))() > File "C:\Programme\EMAN\chimeraext\Airs\pdb2mrc.py", line 73, in Apply > targetPath=airsIO.getPath(target) > File "C:\Programme\EMAN\chimeraext\Airs\airsIO.py", line 32, in getPath > if filecheck.strip()==path: > UnboundLocalError: local variable 'path' referenced before assignment > > > ------------------------- > > I have already added the path of the EMAN in the tool menu. Could you tell me > what I am missing? > > > Thanks you very much, > Julio > > > > --------------------------------------------------------------------- > This message was sent using https://webmail.biochem.mpg.de > If you encounter any problems please report to rz-linux(a)biochem.mpg.de >

1 0

Re: [Chimera-users] Chimera and secondary structure annotations
by Thomas Goddard 28 Oct '05

28 Oct '05

Hi Julio, The "ksdssp" command in Chimera will compute secondary structure for proteins. This uses the Kabsch and Sander algorithm. As far as I know you do not need any secondary structure info for the ribosomal RNA to make a nice ribbon. To use this command use Chimera menu entry Favorites / Command Line and then type ksdssp in the command entry at the bottom of the Chimera window. More details are in the Chimera manual: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ksdssp.html Here are some ribosome pictures I made with Chimera a few months ago. http://www.cgl.ucsf.edu/chimera/complexes05/bakeoff-talk.html Tom > Date: Fri, 28 Oct 2005 21:21:44 +0200 > From: "Dr .Julio Ortiz" <ortiz(a)biochem.mpg.de> > To: Thomas Goddard <goddard(a)cgl.ucsf.edu> > Subject: Chimera and secondary structure annotations > > Hi Thomas: > It is time for a couple of new questions about Chimera. > I am trying to generate some nice representations of the 70S ribosome showing > its proteins as ribbons, but the PDBs do not have annotations of secondary > structure. In many papers that I have seen the people use the program "Ribbons" > and a collegue suggested me also "DSSP" to generate the annotations and > visualize the results in "PyMOL". I am still fighting with some installation > problems, so I have not succeed yet in my original goal. > > The question for you is if Chimera, or some assotiated tool can generate the > annotations for secondary structure from a PDB file. In particular, do you have > some suggestions for the ribosome structures (large file with also RNA?). > > Thanks, > Julio > > > > -- > Max-Planck Institut für Biochemie > Abteilung Molekulare Strukturbiologie > Am Klopferspitz 18 > D-82152 Martinsried > Germany > Tel: +49 (89) 8578 2032 > fax: +49 (89) 8578 2641 > > --------------------------------------------------------------------- > This message was sent using https://webmail.biochem.mpg.de > If you encounter any problems please report to rz-linux(a)biochem.mpg.de

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list index out of range
by Paula Petrone 25 Oct '05

25 Oct '05

Hi, I am trying to load in an MD-ensemble, using a pdb and an X-plor file .dcd. For some reason, it gives me "IndexError: list index out of range". I generated the .dcd file myself (with Fortran). VMD program seems to have no problem with it. Is it a format problem? Is it a bug? Any suggestion? Thanks a lot! (I attach the files) paula

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Error when making Covalent bonds
by David Chenoweth 25 Oct '05

25 Oct '05

Hi! I am trying to pull up two molecules in chimera and link them by forming a covalent bond between a N and C atom. I am selecting only the N of one molecule and the C of the other. When I go to command line and use the bond sel command I get the following error message. Type error: Cannot form covalent bond joining two molecules. Does anyone know how to get around this. Thanks, David C.

3 2

Benchmarks
by Mingfeng Yang 24 Oct '05

24 Oct '05

Just realized there must be some benchmarks on chimera's webpages, and I found them. :) Glad to provide the benchmarks from my systems. Benchmark 1: Computer: IBM T41 Graphics Card: ATI Radeon mobility M7 (32M?, not 100% sure) CPU: pentium-m 1.4GHz System Memory: 512M OS: Ubuntu GNU/LINUX 5.10 Driver for video card: the built-in open-source radeon driver from Xorg-x11 6.8.2 Chimera: version 1 build 2176 Benchmark scores: surface 147 mesh 127 contour 133 solid 128 recolor 68 Benchmark 2: Computer: HP XW5500 workstation Graphics Card: ATI FireGL 8800 (128M memory) CPU: pentium-4 2.4GHz System Memory: 512M OS: Gentoo GNU/LINUX Driver for video card: ATI fglrx driver 8.14.30 Chimera: version 1 build 2176 Benchmark score: surface 234 mesh 227 contour 142 solid 256 recolor 107 Something is confusing me. As you see that scores from benchmark 2 are higher than scores from benchmark 1. But in case that I want to save a protein structure as a png file, the rendering in system 1 is nearly two times faster. How can this happen? Best, Mingfeng Yang

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preferences file
by Boaz Shaanan 22 Oct '05

22 Oct '05

Hi, After upgrading to a new version, is it advisable to use a preferences file from the previous version (which is set up to turn on all sorts of things tuned to my liking) with the new one or are there possible issues of versions incompatibility which should rather be avoided ? I'd appreciate your advice. Thanks, Boaz Boaz Shaanan, Ph.D. Associate Professor Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel Phone:972-8-647-2220 Fax: 972-8-647-2992 972-8-646-1710 E-mail:bshaanan@bgu.ac.il

2 1

1.2180 on Windows
by Eric Pettersen 20 Oct '05

20 Oct '05

We are now aware that the 1.2180 release still doesn't work on some people's XP installations -- so don't rush out to try it! Seems fine on non-Windows platforms. I'll post something when I think we have a fixed version. Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

1 1

Bug?
by Mingfeng Yang 19 Oct '05

19 Oct '05

Chimera version 1 build 2176, 1. start chimera, load in a protein 2. from help-->user guide, open firefox webbrowser to read help information 3. chimera main window becomes dead (black screen, not respond to mouse click and keyboard.) 4. close firefox browser, chimera goes back to normal OS: Gentoo linux, kernel-2.6.10 Firefox: version 1.07, build from gcc-3.4.4

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exporting ribbon models to vrml
by Doug Huff 18 Oct '05

18 Oct '05

Hello I work at Arkitek studios. We create rendered 3D for the science and technology crowd. I am a animator and have been charged with creating a rendering of a ribbon model in 3DS max (our software package). Your Chimera program displays the type of geometry I need and I can import vrml into my application. I can't seem to find the method to export ribbon models to vrml. When I use the multiscale models tools I always wind up with a surface model. Please remember I am not a scientist :) Thanks in advance for your help. Doug Huff 206 286 0337 http://www.arkitek.com

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ATI-Driver & Chimera hangs OS
by Mingfeng Yang 16 Oct '05

16 Oct '05

I am using Chimera build version 1 build 2176 on my Gentoo Linux platform, with ati firegl 8700 graphic card. After I upgraded the ati-drivers from 8.14.13 to 8.16.20, chimera will hang the whole system, everything dead, including the keyboard. I can only see the chimera window frame (the border), nothing else. What could be the problem? Thanks. Yang

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image use
by Rosalba.O'Brien＠informa.com 12 Oct '05

12 Oct '05

Dear Chimera I work for a small circulation trade publication, Animal Pharm. We are doing a story on small interfering RNAs for animal health and would like to use one of the images in the USCF Chimera image library to illustrate (the bluetongue one). Is this allowed? I'm afraid we don't have a budget to pay a fee but we are happy to credit whoever needs crediting. Thanks Rosalba O'Brien Latin America & Southern Europe Reporter Animal Pharm, World Animal Health & Nutrition News Informa Group 69-77 Paul Street London, UK EC2A 4LQ Tel. +44 (0)20 7017 5040 Email rosalba.obrien(a)informa.com Website www.animalpharmnews.com ******************************************************************************** The information contained in this email message may be confidential. If you are not the intended recipient, any use, interference with, disclosure or copying of this material is unauthorised and prohibited. Although this message and any attachments are believed to be free of viruses, no responsibility is accepted by T&F Informa for any loss or damage arising in any way from receipt or use thereof. Messages to and from the company are monitored for operational reasons and in accordance with lawful business practices. If you have received this message in error, please notify us by return and delete the message and any attachments. Further enquiries/returns can be sent to postmaster(a)tfinforma.com

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Solvent Accessibility
by Vincent Lynch 12 Oct '05

12 Oct '05

To Whom It May Concern, I am new to Chimera (and molecular modeling in general) and cant figure out if I can color by residue accessibility to solvent and see the raw value of solvent accessibility. Thanks Vinny

2 2

matchmaker alignment
by Boaz Shaanan 11 Oct '05

11 Oct '05

Hi, Is it possible to save as a file (or print) the alignment that is produced by matchmaker between two structures that are read in ? Thanks, Boaz

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DBFILTER_2.2.8 released
by Sheng-Hung Wang 10 Oct '05

10 Oct '05

Dear all: DBFILTER_2.2.8 has been released. This version fixed the bug in counting for H-bond donors & acceptors! Please UPDATE your version to v2.2.8. Download site: CADD toos in Drug R&D http://home.pchome.com.tw/team/gentamicin/mol/mol.htm ------------------------------------------------------------------------- DBFILTER can check the mol2 format database, and pick out any problematic structure which results in "segmentation fault" of DOCK during flexible docking. (for example, salt or structure which contains multi-moleculars built in....) And DBFILTER will output a new database which you want. There are also 12 kinds of filters for spotlighting drug-like properties. Including: Allowed_atoms, Molecular_weight, LogP, H_bond_donors, H_bond_acceptors, Sum_of_N+O, Halogens, Rings, Max_ring_members, Rotatable_bonds, CH3(CH2)n- , CF3(CF2)n-. To enable LogP filter, XLOGP should be run first to calculate your database by: xlogp -m database.mol2>logp.in File 'logp.in' is needed for dbfilter. XLOGP can be download from FTP site of Institute of Physical Chemistry, Peking University. ( ftp://ftp2.ipc.pku.edu.cn/pub/software/xlogp ) ___________________________________________________ ��°� Yahoo!��Ħ��rͨӍ 7.0 beta��M�W·�Ԓ�� http://messenger.yahoo.com.tw/beta.html

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adding chain IDs
by Eric Pettersen 07 Oct '05

07 Oct '05

Hi, Since it's a lot easier to do things in Chimera when a file has chain IDs, Maximilian Andrews wrote a script (below) for adding chain IDs to files that lack them. It does require that TER cards be present at the end of chains, but those are a lot easier to add than chain IDs. Enjoy! Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu #! /usr/bin/env python # Filename: rename_pdb_for_chimera.py ###################################################################### # # # Created: Maximilian N. Andrews, July 18, 2005 # # Ciamician, Bologna University # # # # Function: # # # # This script adds a chain ID to all the subunits (column 22) in # # the PDB file. # # The chains are named 'A','B','C',etc. until all of the subunits # # have been labeled. # # # # For the subunits to be renamed properly the PDB must contain a # # line beginning with TER after each subunit, for example: # # ... # # ATOM 1570 OXT HIE 103 24.590 -9.249 30.054 # # TER # # ATOM 1571 N SER 104 16.936 7.767 30.236 # # ... # # # # Notes: # # # # The original file is first read by the script, then copied to a # # backup file - with the same name, but with "~" added at the end # # of it - and then it is renamed and saved with the original name. # # # # Usage: # # # # rename_pdb.py arg1 arg2 # # arg1 is the the number of chains that have to be renamed; # # arg2 is the name of the input file; # # example: rename_pdb.py 4 MY_PDB.pdb # # # ###################################################################### import sys import os def BAILING_OUT(N_ARG): """ The srcipt needs two arguments: [int] The number of subunits to be renamed; [str] The name of the PDB file to be renamed. The correct use of this script is: rename_pdb.py arg1 arg2 arg1 is the number of chains in the protein; arg2 is the name of the input file; example: rename_pdb.py 4 MY_PDB.pdb """ if N_ARG != 3: print BAILING_OUT.__doc__ sys.exit() else: return BAILING_OUT(len(sys.argv)) NUMBER_CHAINS = sys.argv[1] PDB_IN = sys.argv[2] print 'Number of chains is: ',sys.argv[1] print 'The PDB file to rename is: ',sys.argv[2] PDB_OUT = PDB_IN PDB_BAK = PDB_IN+'~' f = open(PDB_IN,'r') lines = f.readlines() f.close() print 'Making backup file '+PDB_BAK+'...' os.rename(PDB_IN,PDB_BAK) print '...done!' print 'Renaming '+PDB_IN+'...' CHAIN = 65 # this is the integer that corrisponds to the character "A" MAX_CHAIN = int(NUMBER_CHAINS) + CHAIN LETTER = chr(CHAIN) NEW_PDB = [] for i in range(len(lines)): line = lines[i] if line.startswith('TER'): CHAIN = CHAIN + 1 if CHAIN < MAX_CHAIN: LETTER = chr(CHAIN) else: LETTER = ' ' if line.startswith('ATOM'): newline=line[0:21]+LETTER+line[22:] NEW_PDB.append(newline) elif line.startswith('TER') and len(line) > 21: # just in case there's a chain identifier in the "TER" line... (the condition len (line) is added just in case the TER line is a just few characters long... i.e. it would add a blank space at the start of the following line) newline=line[0:21]+' '+line[22:] NEW_PDB.append(newline) else: # if line doesn't start with either ATOM or TER, it will print it as is NEW_PDB.append(line) print '...done!' print 'Writing renamed file '+PDB_OUT+'...' f = open(PDB_OUT,'w') for i in range(len(NEW_PDB)): f.write(NEW_PDB[i]) f.close() print '...done!'

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chimera trouble
by flints16 cvd 07 Oct '05

07 Oct '05

Hi Sorry to say this but chimera does not work on win xp, and every computer on campus uses xp, ah so no luck there. Thanks --------------------------------- Yahoo! for Good Click here to donate to the Hurricane Katrina relief effort.

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movie recorder command file help
by Pullan, Lee 05 Oct '05

05 Oct '05

Hi, I am using the movie recorder in Chimera with the command line file, as suggested in the tutorial. What do I enter into the command file in order to switch objects on and off and also how do I change properties like transparencies/colors? Thanks Lee Pullan, PhD Center for Structural Biology Department of Biochemistry and Molecular Biology University of Texas - Houston Medical School Houston TX 77030 Tel: 713 500 6121

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Invitation: Chimera Workshop Announcement - UCSF November 17&18, 2005
by Scooter Morris 05 Oct '05

05 Oct '05

Dear Chimera User: The Resource on Biocomputing, Visualization, and Informatics (RBVI) is going to be holding our Fall UCSF Chimera Workshop on November 17&18, 2005 at the UCSF Mission Bay Campus in San Francisco, CA. More details about the workshop, and a link to the registration form are available at http://www.cgl.ucsf.edu/Outreach/Workshops/. We have also attached a brochure about the workshop which may be distributed amongst any interested colleagues. There are only 30 slots available, so we would recommend that you sign up as soon as possible. Thanks! -- scooter

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Moving molecules independently in chimera
by David Chenoweth 29 Sep '05

29 Sep '05

Hi! I am a new chimera user and was just wondering if someone could tell me how to move a single molecule in chimera when I have two open. I have two separate small molecule pdb files and I want to open both in the same chimera session. I also want to be able to move one independent of the other so I can overlay the two. Once they are overlayed I would also like the option of adjusting either or moving both together. Thanks in advance for the help. David C.

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Re: [Chimera-users] color-by-element in v. 2172
by Elaine Meng 22 Sep '05

22 Sep '05

Hi Boaz, It is the same procedure as before. However, it sounds like the coloring target is set to something that does not include atoms and bonds. Look in the Actions... Color menu; the default is "all of the above" which would include "atoms/bonds." However, if the coloring target is set to "ribbons" or "background" (for example) there is nothing to color by element. This is most likely what is happening, since with the "all of the above" setting, the copy of 1.2172 I'm using does color by element as before. I hope this helps, 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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color-by-element in v. 2172
by Boaz Shaanan 22 Sep '05

22 Sep '05

Hi, On the new v. 2172 release candidate, I tried to 'colour by element' a selection of residues in the color panel and got a reply "Nothing applicable to color by element". This is true for both windows and linux. I did this many times before, so has something gone wrong or is there a different path I have to follow to get this type of coloring with the new release ? Thanks for your help. Boaz

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Symmetric copies of molecules
by Thomas Goddard 21 Sep '05

21 Sep '05

Hi Ed, I wrote a Chimera command to show symmetry related copies of a molecule. As you move the original molecule relative to a density map the positions of all the symmetry copies are automatically updated. I tested this with Chimera version 1.2172 just released yesterday. I don't think it will work with earlier versions of Chimera because of some function name changes we made. http://www.cgl.ucsf.edu/home/goddard/temp/symcopies.tar This archive contains a directory SymmetryCopies that you put in your Chimera distribution in chimera/share (or on a Mac in Chimera.app/Contents/Resources/share). Then when you start Chimera you will have two new Chimera commands "sym" and "~sym". The symmetry matrices are read from the REMARK 350 BIOMT records in the PDB file header. Probably you will need to put those matrices in by hand with a text editor. Below is an example. The matrices represent the symmetry of the density map. It would make more sense to put them in the map file header but that is not as easy since it is a binary format file. Once you open your PDB file with the BIOMT matrices in the header and display your density map type sym to the Chimera command-line (menu Favorites / Command Line). This will create copies of the molecule for each symmetry matrix (that is not the identity). If you freeze the density map by turning off the checkbutton in the Active column in Model Panel (menu Favorites / Model Panel) and then move the original molecule with the mouse, all symmetry copies will be moved using the BIOMT positioning matrices in the coordinate frame of the density map. To remove the symmetry copies issue the command: ~sym This is a Chimera convention that tilde in front of a command undoes the command. Here are some more details. If you have multiple molecules opened in Chimera you can specify which one to use in the sym command using the model's id number listed in the Model Panel dialog. For example sym #0 The density map shown in the volume viewer dialog will be used as the reference coordinate system for applying the symmetries. If you want to specify which map to use as the reference coordinate system give a second model id number: sym #0 #1 If you are showing symmetry for multiple models you can remove the symmetry copies for just one molecule by giving its model id number with the ~sym command: ~sym #2 Here is an annoying little problem. If you use the Unshow button on the volume dialog it removes the density map surface model and forgets its orientation. The symmetry copies of the molecule will no longer have their positions updated. Even if you redisplay the map by pressing the Show button, the symmetry repositioning will no longer work. You'll have to use ~sym followed by sym to get it working again. If you want to hide the map you can use the checkbutton in the Model Panel dialog to hide it without actually deleting the surface, so the symmetry copies will continue to have their positions updated. Another problem to look for. Chimera can only handle about 100,000 atoms before it gets slow. Also it uses a few Kbytes of memory per atom. If you specify alot of symmetry matrices you can quickly create a large number of atoms. You may need to limit the symmetry matrices in the PDB header to keep the total number of atoms down. Let me if this command does what you want. I had fun experimenting with it. It should make it into a future Chimera release. We plan on making a production release in early October but have a feature freeze in effect so it will not be in that release. Tom Example BIOMT matrices in PDB file 1fav (3-fold axis of symmetry) REMARK 350 REMARK 350 GENERATING THE BIOMOLECULE REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -0.500000 -0.866025 0.000000 35.81900 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 17.90950 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 31.02016 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000

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release candidate
by Eric Pettersen 20 Sep '05

20 Sep '05

So we've put a release candidate on the download page (http:// www.cgl.ucsf.edu/chimera/download.html) We're hoping that if you have the time, you'll download it and bang on it and let us know about any bugs you find before it turns into a production release. It's been a _long_ time since the previous production release (December of last year). Here are the major highlights: General ----------- -> selections can be inverted (Select menu, "select" command, arrow keys) -> additional arrow key functions: left: undo selection shift-left: clear selection right: invert selection in models with selections shift-right: invert selection in all models -> PDB file writing can be restricted to displayed and/or selected atoms -> Chimera scene can be exported (formats: X3D, POV-Ray, Renderman, VRML [latter surfaces only]) -> Actions...Set Pivot sets center of rotation w/o zooming -> Help...Search Documentation searches local documentation -> Tools menu reorganized -> balloon help over bonds/pseudobonds includes length -> residue labels now positioned at centroid of displayed atoms -> new residue attribute "isHet" (whether residue is in HETATM PDB records) -> nucleic-acid ambiguity codes can be used in subsequence searching (R=A/G, Y=C/T/U, N=A/C/G/T/U) -> switched to Python 2.4 New Tools --------------- -> Attribute Calculator (Structure Analysis): generate new numerical attributes from existing ones; calculate totals or averages of an attribute -> Color Zone (Volume Data): color surface patches near selected atoms with those atoms' colors [for GRASP surfaces and Volume Viewer/ Multiscale surfaces rather than standard molecular surfaces] -> Demo Editor (Demos): graphical interface for creating demos -> Movie Recorder (Utilities): capture image frames from Chimera and assemble them into a movie file -> Surface Capping (Depiction): cap surfaces where they intersect a clipping plane (giving the illusion of the surface as a solid object rather than a hollow object) -> Surface Color (Volume Data): color surfaces according to volume data or geometry (distance from a point, plane, or axis) -> Electrostatic Surface Coloring (Surface/Binding Analysis): specialization of preceding tool to facilitate coloring with electrostatic volume data; also replaces DelphiViewer -> Surface Zone (Surface/Binding Analysis): restrict GRASP or Multiscale Models surface display to zone around selected atoms -> Values at Atom Positions (Volume Data): map volume data to atom positions; create atom attributes with the values -> 2D Labels (Utilities): create arbitrary text labels and place them in 2D Tool Changes -------------------- -> Benchmark (Utilities): now also benchmarks molecule display performance -> Demos (Demos): new Hormone-Receptor Complex demo -> Lighting (Viewing Controls): new simplified interface available -> MatchMaker (Structure Comparison): can include secondary- structure term in the alignment score and can iterate the fit -> MD Movie (formerly Movie; Utilities): new "md:" prefix for metafiles; add step size option for playback; RMSD map calculation speeded up; can automatically recolor RMSD map for contrast; ability to collect atom occupancy data and display it with Volume Viewer; user-friendly interface to Movie Recorder for generating movie from trajectory -> MultAlign Viewer (Structure Comparison): all-gap positions can be omitted from saved files; all headers available as residue attributes in associated structures; more sophisticated conservation measures available (calculated with AL2CO program); headers can be saved to a file or loaded from a file; structure association info can be saved to a file -> Multiscale Models (Higher-Order Structure): separate surfacing threshold for CA-only chains -> Nucleotides (Depiction): now assigns a pucker value to all sugar atoms (plane/envelope/endo/exo) -> Per-Model Clipping (Depiction): new slab mode to show just a slice of a model -> ViewDock (Surface/Binding Analysis): saves in sessions; H-bond statistics can included in the columns of ligand descriptors (and used for sorting) -> Volume Viewer (Volume Data): major interface reorganization; added support for UHBD electrostatic potential (binary only), gOpenMol, and PROFEC grid formats; support added for non-orthogonal crystal data New Commands ------------------------ -> 2dlabels: command-line version of 2D Labels tool -> movie: command-line version of Movie Recorder tool -> writesel: command-line version of Actions...Write List Command Changes ----------------------------- -> color: can now also color ribbons -> British spellings added for gray, color, and center -> match: added "iterate" keyword to allow pruning bad pairs until worst pair is below a threshold -> matchmaker (mmaker): added keywords corresponding to new MatchMaker tool abilities -> select: new keyword for inverting selections -> write: keywords for restricting to displayed/selected atoms Documentation ---------------------- -> new Attributes tutorial: covers Render by Attribute, Surface Area/ Volume, Attribute Calculator, and advanced command-line usage full release notes are at: http://www.cgl.ucsf.edu/chimera/docs/ relnotes/1.2172.html Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

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OS X Native
by William Sofer 20 Sep '05

20 Sep '05

Hi, We're using Chimera for educational purposes for a university program aimed at high school teachers and students. I love the program, but am a bit frustrated by the lack of an aqua version for OS X. Do you plan on developing a native version for OS X 10.4? Bill Sofer Professor Dept. Genetics Waksman Institute Rutgers University Piscataway, NJ 08854

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creating a symmetric tetramer from a PDB file for a monomer?
by gtseng＠mail2.vcu.edu 14 Sep '05

14 Sep '05

Dear Chimera creators: Could you please let me know whether it is possible to create a tetramer structure with 4-fold symmetry from a PDB file for a monomer? Specifically, I want to create a structure of a voltage-gated K channel which has 4 monomers surrounding a central pore symmetrically, beginning with the PDB file for a monomer. There is no 'transformation matrix' in the PDB file to allow me to create the tetramer easily. Thank you very much for your help! Gea-Ny Tseng

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Re: [Chimera-users] Re: stereo viewing on Windows
by Kishor Kulawade 12 Sep '05

12 Sep '05

Hello, Thank you very much for your reply. We have the required hardware here. We have NVidia Quadro FX 3400/4400 video card. I am trying to figure out how to start stereo mode on Windows XP machine. Documentation states that append the desired options and inputs to the command in the target field. What command should I type in Target field to start stereo mode. If you can provide any kind of help with that, would be wonderful Thanks >>> Greg Couch <gregc(a)cgl.ucsf.edu> 9/9/2005 4:50 PM >>> For the --stereo option to work you need a graphics card that supports "stereo in a window" (consumer/gaming cards only do full screen stereo) and the associated special glasses that alternate which eye can see the screen at any moment. Those graphics cards are the workstation graphics cards -- the 3DLabs Wildcat series, the ATI FireGL series and the NVidia Quadro series. See <http://www.3dlabs.com/>, <http://www.ati.com/products/workstation.html>, or <http://www.nvidia.com/page/workstation.html> -- stay away from the versions designed for 2D applications and make sure the card you buy has a stereo connector. High-quality glasses (and the emittors that control them) can be purchased from StereoGraphics Corporation, <http://www.stereographics.com/>. Cheaper alternatives exist, but we don't have any experience with them (google for "stereo glasses"). Make sure that the emittor that controls the glasses works with the graphics card you get (there are different connectors out there). Hope this helps, Greg Couch UCSF Computer Graphics Lab gregc(a)cgl.ucsf.edu On Fri, 9 Sep 2005, Virginia B. Pett wrote: > Date: Fri, 9 Sep 2005 16:26:16 -0400 > From: Virginia B. Pett <pett(a)wooster.edu> > To: chimera-users(a)cgl.ucsf.edu > Cc: Kishor Kulawade <kkulawade(a)wooster.edu> > Subject: [Chimera-users] Re: stereo viewing on Windows > > We have windows XP machine in one of our labs. The machine is running > chimera. We want to run chimera in stereo mode on this machine. as per the > documentation, create a shortcut of chimera on the desktop and then append > "--stereo" options in target mode. But target mode does not recognize this. > Which file helps start the stereo mode on windows machine, so that i can put > that file path in target? > > > ________________________________________ > Virginia B. Pett > Professor of Chemistry > Department of Chemistry, The College of Wooster > 943 College Mall, Wooster, OH 44691 > Telephone: 330-263-2114 > Fax: 330-263-2386

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Re: [Chimera-users] Re: stereo viewing on Windows
by Eric Pettersen 12 Sep '05

12 Sep '05

Hi Virginia, Another thing to note is that in the target field, the path to the Chimera executable is embedded in double quotes (e.g. it is something like: "C:\....\chimera.exe"). To add the --stereo option, you need to add it outside the ending double quote and separated by a space, like this: "C:\...\chimera.exe" --stereo . Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

1 0

phi psi angles
by Zenon Grabarek 12 Sep '05

12 Sep '05

Hello, I am looking for a script that would allow me to change the phi psi angles in a selected residue (allowing the C-terminal part of the chain to move) and output the coordinates. Chimera has a very nice interactive tool to do that, but I need to do it systematically in small increments over a specified range of angles. I would be grateful for any help in this matter. Zenon Grabarek Ph.D. Boston Biomedical Research Institute 64 Grove St. Watertown MA 02472 tel: 617-658-7805 email: Grabarek(a)BBRI.org

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Re: stereo viewing on Windows
by Virginia B. Pett 09 Sep '05

09 Sep '05

We have windows XP machine in one of our labs. The machine is running chimera. We want to run chimera in stereo mode on this machine. as per the documentation, create a shortcut of chimera on the desktop and then append "--stereo" options in target mode. But target mode does not recognize this. Which file helps start the stereo mode on windows machine, so that i can put that file path in target? ________________________________________ Virginia B. Pett Professor of Chemistry Department of Chemistry, The College of Wooster 943 College Mall, Wooster, OH 44691 Telephone: 330-263-2114 Fax: 330-263-2386 On Sep 7, 2005, at 3:00 PM, chimera-users-request(a)cgl.ucsf.edu wrote: > Send Chimera-users mailing list submissions to > chimera-users(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > or, via email, send a message with subject or body 'help' to > chimera-users-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimera-users-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-users digest..." > > > Today's Topics: > > 1. creating a symmetric tetramer from a PDB file for a monomer? > (gtseng(a)mail2.vcu.edu) > 2. Re: creating a symmetric tetramer from a PDB file for a > monomer? (Elaine Meng) > 3. Visualizing Electrostatic Potential of *.grd format? > (Anna Feldman-Salit) > 4. Re: Visualizing Electrostatic Potential of *.grd format? > (Elaine Meng) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 06 Sep 2005 15:53:41 -0400 > From: <gtseng(a)mail2.vcu.edu> > Subject: [Chimera-users] creating a symmetric tetramer from a PDB file > for a monomer? > To: "chimera-users(a)cgl.ucsf.edu" <chimera-users(a)cgl.ucsf.edu> > Message-ID: <200509061953.PAA18668(a)despina.vcu.edu> > Content-Type: text/plain; charset=iso-8859-1 > > Dear Chimera creators: > Could you please let me know whether it is possible to create a > tetramer structure with 4-fold symmetry from a PDB file for a monomer? > Specifically, I want to create a structure of a voltage-gated K > channel which has 4 monomers surrounding a central pore symmetrically, > beginning with the PDB file for a monomer. There is no 'transformation > matrix' in the PDB file to allow me to create the tetramer easily. > Thank you very much for your help! > > Gea-Ny Tseng > > ------------------------------ > > Message: 2 > Date: Tue, 6 Sep 2005 13:48:50 -0700 > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] creating a symmetric tetramer from a PDB > file for a monomer? > To: <gtseng(a)mail2.vcu.edu> > Cc: chimera-users(a)cgl.ucsf.edu > Message-ID: <7485CA73-9B1A-492C-9F71-FB36FBF5B103(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed > > Hello Gea-Ny, > The Chimera features that generate multimers (the tools Unit Cell > and Multiscale Models) all use matrix information in the PDB file. > Multiscale Models uses BIOMT, MTRIX, SMTRY, and/or CRYST1 records, > and Unit Cell uses MTRIX, SMTRY, and/or CRYST1. > > It sounds like you don't have any of those in your PDB file. > > You could either > (A) figure out what information should be in such a matrix line > and edit it into your file before using one of the Chimera tools, > or > (B) open four copies of your monomer and try to position them > by hand. If you know what the axis of rotation should be, you > can use Constrained Move (Tools... Movement... Constrained Move > in recent versions) to define and use an axis of rotation. > http://www.cgl.ucsf.edu/chimera/1.2065/docs/ContributedSoftware/ > constrained/constrained.html > > Neither of these is very easy, but I don't know of any way to > automatically position the monomers without the matrix information. > It sounds like BIOMT (REMARK 350) records would be the most > appropriate. Even with an appropriate example, you would still > have to change the values. > > REMARK 350 is described at the PDB web site (you have to scroll > down to get to the description of REMARK 350): > http://www.rcsb.org/pdb/docs/format/pdbguide2.2/part_31.html > > Here is an example from 1fav (threefold): > REMARK 350 > REMARK 350 BIOMOLECULE: 1 > REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C > REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 > REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 > REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 > REMARK 350 BIOMT1 2 -0.500000 -0.866025 0.000000 35.81900 > REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 > REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 > REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 17.90950 > REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 31.02016 > REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 > > I hope this helps, > 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 > > > > On Sep 6, 2005, at 12:53 PM, <gtseng(a)mail2.vcu.edu> wrote: > >> Dear Chimera creators: >> Could you please let me know whether it is possible to create a >> tetramer structure with 4-fold symmetry from a PDB file for a monomer? >> Specifically, I want to create a structure of a voltage-gated K >> channel which has 4 monomers surrounding a central pore symmetrically, >> beginning with the PDB file for a monomer. There is no 'transformation >> matrix' in the PDB file to allow me to create the tetramer easily. >> Thank you very much for your help! >> >> Gea-Ny Tseng >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >> > > > ------------------------------ > > Message: 3 > Date: Wed, 07 Sep 2005 13:14:05 +0200 > From: Anna Feldman-Salit <anna.feldman-salit(a)eml-r.villa-bosch.de> > Subject: [Chimera-users] Visualizing Electrostatic Potential of *.grd > format? > To: chimera-users(a)cgl.ucsf.edu > Message-ID: <431ECB7D.8090203(a)eml-r.villa-bosch.de> > Content-Type: text/plain; charset=us-ascii; format=flowed > > Dear All, > > I would like to ask you a question regarding the visualization of > electrostatic potential on msms. For this purpose, of course, I need a > readable format for Potential Map. > In the past I used to work with DelPhi for potential calculations and > then visualize the outputted *.14 file by Chimera. > Today I calculate potentials by using UHBD program, while output files > are saved in /phi/ format with .grd extension (could be written either > in binary or ascii form). > Unfortunately, the Chimera doesn't recognize this format. > > Dear Chimera users, do you know the way to convert the *.grd files to > the *.phi ones readable by Chimera, or any other trick? > I can't recalculate the potentials by DelPhiController, because I have > only one dat-file for both radii sizes and charges (it also doesn't > work > in the simple way). > > I'd very appreciate any help of yours! > > Yours sincerely, > > Anna. > > ------------------------------ > > Message: 4 > Date: Wed, 7 Sep 2005 09:16:40 -0700 > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Visualizing Electrostatic Potential of > *.grd format? > To: Anna Feldman-Salit <anna.feldman-salit(a)eml-r.villa-bosch.de> > Cc: chimera-users(a)cgl.ucsf.edu > Message-ID: <6902E794-4AAB-438D-A8D8-FB8E8849D7D6(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed > > Hi Anna, > Actually, Chimera does read UHBD grids, the binary version. The older > approach to displaying potential on a surface, DelPhiViewer, is being > phased out in favor of the newer and more general tool, Surface Color > (Tools... Surface/Binding Analysis... Electrostatic Surface Coloring > or Tools... Volume Data... Surface Color both open this tool). > > Surface Color can color surfaces based on any of the volume data (3D > grid) formats that can be read by Volume Viewer (which include UHBD > binary): > http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/ > volumeviewer.html#formats > > Surface Color is relatively new. It is available in the snapshots > 1.2154 (linux, mac) and 1.2143 (windows). It is also available in > 1.2105, but I don't recommend using that one because we have made it > easier to use in the more recent snapshots. Here is the man page for > Surface Color in version 1.2154: > http://www.cgl.ucsf.edu/chimera/1.2154/docs/ContributedSoftware/ > surfcolor/surfcolor.html > > I hope this helps, > 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 > > On Sep 7, 2005, at 4:14 AM, Anna Feldman-Salit wrote: > >> Dear All, >> >> I would like to ask you a question regarding the visualization of >> electrostatic potential on msms. For this purpose, of course, I >> need a readable format for Potential Map. >> In the past I used to work with DelPhi for potential calculations >> and then visualize the outputted *.14 file by Chimera. >> Today I calculate potentials by using UHBD program, while output >> files are saved in /phi/ format with .grd extension (could be >> written either in binary or ascii form). >> Unfortunately, the Chimera doesn't recognize this format. >> >> Dear Chimera users, do you know the way to convert the *.grd files >> to the *.phi ones readable by Chimera, or any other trick? >> I can't recalculate the potentials by DelPhiController, because I >> have only one dat-file for both radii sizes and charges (it also >> doesn't work in the simple way). >> >> I'd very appreciate any help of yours! >> >> Yours sincerely, >> >> Anna. >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >> > > > ------------------------------ > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > End of Chimera-users Digest, Vol 29, Issue 5 > ********************************************

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Rotation Angle
by Huang, Zhong 07 Sep '05

07 Sep '05

Hi, dear chimera developers' I am a Chimera user of UT Medical school at Houston . Here I want to know how chimera rotates the loading structure. I wish to know what the rotation parameters mean? Which coordinate sysmtem they refere to? I check the on-line tutorial. Unfortunately, I didn't get the answer. Best Zhong Huantg

2 1

[Chimera-users] Visualizing Electrostatic Potential of *.grd format?
by Anna Feldman-Salit 07 Sep '05

07 Sep '05

Dear All, I would like to ask you a question regarding the visualization of electrostatic potential on msms. For this purpose, of course, I need a readable format for Potential Map. In the past I used to work with DelPhi for potential calculations and then visualize the outputted *.14 file by Chimera. Today I calculate potentials by using UHBD program, while output files are saved in /phi/ format with .grd extension (could be written either in binary or ascii form). Unfortunately, the Chimera doesn't recognize this format. Dear Chimera users, do you know the way to convert the *.grd files to the *.phi ones readable by Chimera, or any other trick? I can't recalculate the potentials by DelPhiController, because I have only one dat-file for both radii sizes and charges (it also doesn't work in the simple way). I'd very appreciate any help of yours! Yours sincerely, Anna.

2 1

Suggestion re Docking Results
by Philip Crawford 06 Sep '05

06 Sep '05

Hi. I like Chimera and hit a limit yesterday. (Windows version.) We are running DOCK using the ZINC databases, which produces very large output_scored.mol2 files. I tried using Chimera to open and sort one of these. After an hour, I killed Chimera. John Irwin suggested (via the Dock-fans list) that I recommend you set a limit on the size of output file to be opened. An alternative may be to set a limit on the number of records which will be read, regardless of file size. Thanks for a useful product. Cheers, Philip Crawford __________________________________________________ Philip Crawford, B. Comp. Sc., MIEEE Structural BioInformatics and Drug Design Group http://www.sbio.med.unsw.edu.au/sbio School of Medical Sciences The University of NSW Phone: +61-2-9385 2564 Mobile: +61-419-294 698 Fax: +61-2-9385 1059 Email: <mailto:p.crawford@unsw.edu.au> p.crawford(a)unsw.edu.au __________________________________________________

2 1

changing the rendering of distanced dotted lines
by Boaz Shaanan 06 Sep '05

06 Sep '05

Hi, Distances between pairs of atoms are marked as dotted lines by the 'distances' panel. Is it possible to make those dots bigger by scaling them up somehow so that they are seen more clearly ? They obviously get larger when I zoom in but sometimes I'd rather stay in the zoom-out view but make the dots more visible. Please let me know. Thanks, Boaz

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[Chimera-users] Save pdb files only have 5 subunits at 5-fold at virus?
by Jason 04 Sep '05

04 Sep '05

Hi all Is it possible to save pdb files that only have 5 subunits at 5-fold after using mulitscale tools buliding virus paritle. And this pdb file can open at other programs too, ex: DeepView, PyMOL. When I use File/Save PDB chimera can save pdb file, but this file(model) only can show correctly at chinera. If I opened this file at PyMOL or DeepViewit only show the origional 3(A, B, C)chain model thanks Jason

4 3

Using the Chimera Tutorial
by Gea-Ny Tseng 31 Aug '05

31 Aug '05

Dear Chimera creators: I am trying to learn how to use Chimera by using your on-line Tutorial. Is there a printable version of the Tutorial and User's Guide? I am not sure how to read the Tutorial and then try out the commands using one single monitor (that is all I have). Or did I miss something obvious? Your help is highly appreciated? Gea-Ny Tseng, PhD Physiology Virginia Commonwealth University

2 1

helices display in latest snapshots
by Boaz Shaanan 30 Aug '05

30 Aug '05

Hello, I the latest snapshots (Windows 2143 and linux 2154) helices show up as thin worms when I ask for 'ribbons' under action (they used to look like nice ribbons in previous releases). I found the tools/depiction/ribbons display and managed somehow to change the look of the ribbons (still, they looked nicer before) but failed to change the look of the helices. Where can I do this now ? Thanks, Boaz

3 2

[ViewDock] wrong bonds
by Aurelien GROSDIDIER 29 Aug '05

29 Aug '05

Hi all ! I'm currently trying to use the ViewDock plugin to visualize results coming from our in house docking program, which dumps PDB files. These PDBs are them transformed into in a DOCK3/DOCK4 compliant format. First, I should say I haven't seen a clear description of this format, and the script gathering together PDB files is very empirical. The problem I see might come from a mistake of our docking program. Urls to fock3/4 specifications are thus welcome :) Problem context: ---------------- The problem happens when dealing with ligands having several distinct residue numbers or if the docking coordinates do not consist only of a ligand, but also a set of sidechains of its receptor (also with distinct residue number). Problem symptoms: ----------------- The representation loaded using ViewDock show bonds between each and every atoms of the ligand (and the sidechains, if any), no matters their atom type or how far they are. This is kinda of weird, as the representation is perfect when these PDB are loaded from individual PDB files (not using ViewDock). I am a newbie on this mailing list, and unfortunately this problem should be solved withing a few days or so. I would like to apologize in advance in case this help request should go somewhere else. And in case you need a clearer description of the problem (with figures, input files and so on), feel free to contact me either directly or using the ML :) Thanks a lot for your help, Aurélien Grosdidier

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regarding coloring
by moumita dutta 24 Aug '05

24 Aug '05

Dear Sir, How can I use more than one color to highlight different area using the UCSF chimera software in a 3d refined model of a virus ? Regards, M.Dutta --------------------------------- Start your day with Yahoo! - make it your home page

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problems reading delphi phi map under XP
by Boaz Shaanan 24 Aug '05

24 Aug '05

Hello, When I try to read a delphi phi map under XP I get the error message: Return code: -2147483641 and the program exits. The same map would be read OK under linux and under Win2k. I'm using the latest win32 snapshot (the same happens with the official release though). I would appreciate if you could let me know what has gone wrong. Thanks, Boaz

2 1

ATI catalyst 5.7 drivers with R9600SE video card crash winxp when creating surfaces (or running surface benchmark) in chimera-1.2143
by Sabuj Pattanayek 22 Aug '05

22 Aug '05

Hi, I had upgraded ATI's catalyst drivers from 5.4 (or 5.5) to 5.7 for my R9600SE video card under winxp sp2. In Chimera-1.2143 when I tried to create a surface representation or tried the surface benchmark the screen would go black (monitor led goes from green to orange) and the system would crash (no longer responds to pings). Downgrading to catalyst 5.6 fixed the problem. I sent a trouble ticket to ATI. Has anyone had a similar problem with Radeon (non-firegl) cards? Thanks, Sabuj Pattanayek

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Re: [chimera-dev] accelerators and stereo
by Eric Pettersen 18 Aug '05

18 Aug '05

Hi Justin, Chimera doesn't have a function to directly save a stereo image. Instead, what you do is save separate left-eye and right-eye images and place them appropriately in your presentation or paper -- for a cross-eye image that would be the left-eye on the right and vice versa. You save the images by bringing up the Side View (under Favorites) and clicking on the "Camera" tab. There is a "camera mode" menu under that tab that lets you select left-eye/right-eye views. Then just use the regular image-saving process. This is also described in the Images tutorial (near the end): http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ frameimages.html We want to make this easier to do but haven't gotten to it yet. Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu On Aug 18, 2005, at 7:06 AM, Justin Wu wrote: > Hi > Would you please let me know how to make a cross-eye figure from > Chimera? I do not where to look for this function. > Thanks > Justin > ************************************************ > Justin Wu > Rm 752, Biological Science Building > 484 West 12th Ave, > Columbus, OH 43210 > Tel: (614)247-5040, Fax: (614)292-6773 > ************************************************ > > _______________________________________________ > Chimera-dev mailing list > Chimera-dev(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev >

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Re: [Chimera-users]
by Eric Pettersen 09 Aug '05

09 Aug '05

Hi Sabuj, It is the indentation. In Python, indentation is meaningful and statements at the same "level" have to have the same indentation. I've appended the critical part below. Note the the "self.rulerTexts..." and "x += ..." statements are indented one space further than the preceding if/else and "text = ..." statements. To Python, the extra space starts a new indented block of statements, which is only legal after 'if' statements and so forth. Take a space away from the front of the last two statements and I think things will work. --Eric for chunkStart in range(self.seqOffset, end, 10): seq1index = self.seqs[0].gapped2ungapped (chunkStart) if seq1index is None: dispText = "?" else: dispText = str(seq1index+1) text = self.mainCanvas.create_text(x, y, anchor='s', font=self.font, text="%s" % (dispText)) self.rulerTexts.append(text) x += self.chunkGap + 10 * (self.fontPixels[0] + self.letterGaps[0])

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by Pattanayek, Sabuj 09 Aug '05

09 Aug '05

Hi all, Is there a modification I can do to the multi-align viewer code so that "-" (gaps) characters are not counted in the alignment numbering (but are still displayed for alignment purposes) from a fasta file in the multi-align viewer? The numbering should correspond to the first sequence found in the fasta file (i.e. I don't care about the numbering due to gaps in the second, third, etc sequences). Thanks, Sabuj Pattanayek

3 2

Making and Breaking bonds in Chimera
by David Chenoweth 04 Aug '05

04 Aug '05

Dear Chimera users, Does anyone know how to make a new bond or delete a bond between two atoms within a PDB file using chimera? -Thanks DC

2 1

Coloring by Delphi potential in Chimera
by Elaine Meng 29 Jul '05

29 Jul '05

Hi Zach, DelPhiViewer got removed because other tools can do the same things in a more general and flexible way. Unfortunately in the latest snapshot (1.2129, June) it is confusing to get to these newer features, but they are all there, and I'll explain how. I'll assume you are using that latest snapshot and that you have an electrostatic potential file in the format from DelPhi. ------------------- First, open the electrostatic potential file with File... Open. If the file is named ending in .phi you can set the File type to "all (guess type)" or "DelPhi or GRASP potential". This will automatically start Volume Viewer. (A) IF you want to look at contour (isopotential surfaces), keep using Volume Viewer. Open the Volume Viewer man page by clicking the Help button on the dialog. You probably want to go to the "Surface or Mesh" section of the man page, under "Display Panel". Otherwise... (B) IF you want to color the molecular surface or GRASP surface based on the potential, click the Unshow button on Volume Viewer and then the Close button on Volume Viewer. Open the molecule and show its surface that you want to color, or open the GRASP surface you want to color (this can also be opened with File... Open). The tool for coloring a surface by potential is Surface Color (Tools... Surface/Binding Analysis... Surface Color). Pick the surface of interest from the menu next to "Color surface" and choose the electrostatic potential data from the menu next to "Using volume data or geometry". You probably want to change the "Color scheme" to "3 color symmetric" - then you have something similar to the DelPhiViewer surface coloring interface. Click the Help button on the Surface Color dialog if you want to see the man page. -------------------- We realized this is pretty confusing and have tried to make it better (and the improvements will show up in the next release). The improvements are that you will be able to color a surface according to electrostatic potential by choosing Tools... Surface/Binding Analysis... Electrostatic Surface Coloring, and then you can open the electrostatic potential using a Browse button on that tool (avoiding Volume Viewer entirely). It will also start with the 3-color scheme when opened this way. I hope this helps, 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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[Chimera-users] coloring of nearly identical protein sequences in multialign viewer
by Sabuj Pattanayek 29 Jul '05

29 Jul '05

Hi all, I have a clustal aln file or a fasta file with two nearly identical aligned protein sequences. When I view them in the multialign viewer I would like to change the color of the consensus style. That is, residues which are both identical should be just black (rather than red and capitalized) and residues that are not identical should be red (or some other color that contrasts against black). Is there anyway to do this? Better yet would it be possible to not use the consensus at all and color the entire non-matching column a color of my choice? Thanks, Sabuj Pattanayek

3 4

gopenmol files in chimera?
by syma 25 Jul '05

25 Jul '05

HI, I was just wondering if it is possible to import gopenmol plt files in chimera either directly or by going through a (freely available) conversion code? Thanks in advance for your help, -Syma *************************************************** Dr Syma Khalid Lab. of Molecular Biophysics, Department of Biochemistry, University of Oxford South Parks Road, Oxford OX1 3QU U.K. ***************************************************

4 4

insertion codes and residue selection
by Moo Cow 11 Jul '05

11 Jul '05

I would be very grateful for advice. Some coordinates contain residue 51 residue 51A (a residue with an insertion code) If I select #0:51 then both residues are selected. Is there any way to persuade chimera to just select residue 51, but not 51A ? Many thanks -- ___________________________________________________________ Sign-up for Ads Free at Mail.com http://promo.mail.com/adsfreejump.htm

3 2

How to append functional groups to a residue
by C. Parry 01 Jul '05

01 Jul '05

Hi Chimera Peoples - My question is how does one append a functional group (say, nitro, bromine, ..., or metal) to a residue (say, tyrosine, ..., adenine). This would involve replacing some atom or group. I am aware of 'swapa,' 'swapna' commands but these are straight forward one-for-one changes of whole residues. Thanks. C. Parry __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

2 1

Exporting 3D File Formats
by peter allen 30 Jun '05

30 Jun '05

Hello, Does your software have any way of exporting 3d file formats. DXF OBJ 3DS IGES STL DWG etc Many Thanks Peter Allen

2 1

Gallery PDB source
by David Piper 24 Jun '05

24 Jun '05

Chimera Folks, I was looking at the gallery images and noticed that one is of the FlAsH molecule. Are the PDB coordinate available somewhere for this molecule? Or ReAsH? Thanks, David

2 1

Electron density
by C. Parry 22 Jun '05

22 Jun '05

Could anyone help with loading and displaying CNS or XPLOR electron density maps in Chimera. I have tried many times and also the dialog boxes in the user guide do not exactly correspond to the version (12/2004) of Chimera I have. Thanks. ____________________________________________________ Yahoo! Sports Rekindle the Rivalries. Sign up for Fantasy Football http://football.fantasysports.yahoo.com

3 2

mutation tool?
by ROBERT LAVIERI 17 Jun '05

17 Jun '05

I am exploring/using the program and I was wondering if there was any sort of point mutation tool? Such that one could graphically see say a mutation like ser23trp? Thanks, Robert R Lavieri

2 1

how to open bug-report dialog in v1.2105
by Sabuj Pattanayek 13 Jun '05

13 Jun '05

Hi, In v1.2105 (irix) the report a bug command under the help menu is not available (as stated in the current development documentation I assume for v1.2129). How do I open the bug report submission dialog from the command line or from the menus even if a crash or error has not occurred? Thanks, Sabuj Pattanayek

2 1

Stereo monitors
by Thomas Goddard 06 Jun '05

06 Jun '05

Steve Ludtke reports what his lab is using for hardware stereo. Tom ------- Start of forwarded message ------- Date: Mon, 6 Jun 2005 12:59:39 -0500 (CDT) From: Steve Ludtke <stevel(a)blake.3dem.bioch.bcm.tmc.edu> Reply-To: sludtke(a)bcm.tmc.edu To: Thomas Goddard <goddard(a)cgl.ucsf.edu> Subject: Re: Chimera Suggestion We have the Sharp 15" one. As I said, it works ok as long as you stay in the sweet spot, but gives me a nasty headache (which the glasses do not). We haven't tried any of the high-refresh LCD's yet. We still use CRT's for that at the moment. We're about to try a homebrew polarized glasses solution. We do actually have a (800x600) high refresh projector for use with the shutter glasses which works well. - ---------------------------------------------------------------------------- Steven Ludtke, PhD | Baylor College of Medicine sludtke(a)bcm.tmc.edu | Asst. Professor & Co-Director stevel(a)alumni.caltech.edu | National Center For Macromolecular Imaging V: (713)798-9020 | Dept of Biochemistry and Mol. Biol. F: (713)798-1625 | instant messenger: sludtke42 | Those who Do, Are http://ncmi.bcm.tmc.edu/~stevel | The converse also applies On Mon, 6 Jun 2005, Thomas Goddard wrote: > Hi Steve, > > Our stereo monitor that requires no glasses was a 20" flat panel > type display from Opticality (formerly X3D). I just found out we have > returned it because it worked so poorly. I'd be curious what > make/model you have. Also have you tried any normal flat panels with > fast refresh rates and LCD glasses? > > Tom > ------- End of forwarded message -------

1 0

Red / blue stereo
by Thomas Goddard 06 Jun '05

06 Jun '05

Steve Ludtke would like red / blue stereo. Tom ------- Start of forwarded message ------- Date: Sat, 4 Jun 2005 02:13:29 -0500 (CDT) From: Steve Ludtke <stevel(a)blake.3dem.bioch.bcm.tmc.edu> Reply-To: sludtke(a)bcm.tmc.edu To: Thomas Goddard <goddard(a)cgl.ucsf.edu> Subject: Chimera Suggestion We've had a minor resurgance of stereo work in the lab recently. We have a couple of SGI's still with the standard shutter-glasses, and a single PC with a CRT and an active stereo capable projector. We tried the Sharp autostereographic monitor, but it works only so-so, and gives me a headache almost instantly. It would be really useful to have simple stereo set up for occasional use on all of the desktop machines in the lab (which have normal LCD panels now). Anyway, I was just wondering if you guys thought about implementing analglyph (red/blue glasses) stereo ? I've done this manually for snapshots using the 'left eye' and 'right eye' mode in chimera to get the separation right, and it works surprisingly well as long as you don't mind sacrificing color. It would be very useful to have this available for interactive use. Any chance ? (it's also very useful for posters, since many people can't do the eye-crossing thing). Just a suggestion :^) - ---------------------------------------------------------------------------- Steven Ludtke, PhD | Baylor College of Medicine sludtke(a)bcm.tmc.edu | Asst. Professor & Co-Director stevel(a)alumni.caltech.edu | National Center For Macromolecular Imaging V: (713)798-9020 | Dept of Biochemistry and Mol. Biol. F: (713)798-1625 | instant messenger: sludtke42 | Those who Do, Are http://ncmi.bcm.tmc.edu/~stevel | The converse also applies ------- End of forwarded message -------

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Selection question in --nogui mode
by Miguel Ortiz Lombardia 26 May '05

26 May '05

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hello. I'm trying to execute this: $chimera --nogui cmd:findselhbonds where the file findselhbonds contains: open 01.pdb select :59-62 hbonds selRestrict any saveFile tmp.bonds In the graphic mode those instructions work as expected, however in the - --nogui mode I get this error: Opening 01.pdb... warning: Ignored bad PDB record found on line 1 warning: Ignored bad PDB record found on line 2 Computed secondary structure assignments (see reply log) Model 0 (01.pdb) appears to be a protein with no secondary structure assignments. Computing assignments for it using the ksdssp algorithm (Kabsch and Sander Define Secondary Structure of Proteins) with an energy cutoff of - -0.5, minimum helix length of 5, and minimum strand length of 4. If these parameters don't produce good results for this structure, you can rerun the algorithm with different settings using the 'compute SS' button in the model panel (under 'infrequent' actions) or via the 'ksdssp' command in the Midas emulator. The model panel will also allow you to save new default parameters. 1 model opened Opened 01.pdb containing 1 model, 632 atoms, and 62 residues Error while processing cmd:forchimera: NameError: global name 'selMode' is not defined (see reply log for Python traceback info) Traceback (most recent call last): File "/usr/local/linux_prg/Chimera/share/__main__.py", line 59, in ? value = chimeraInit.init(sys.argv) File "CHIMERA/share/chimeraInit.py", line 287, in init prefixableType=1) File "CHIMERA/share/chimera/__init__.py", line 1043, in open File "CHIMERA/share/Midas/ChimeraExtension.py", line 17, in func File "CHIMERA/share/Midas/midas_text.py", line 88, in processCommandFile File "CHIMERA/share/Midas/midas_text.py", line 62, in makeCommand File "CHIMERA/share/Midas/midas_text.py", line 1039, in doSelect File "CHIMERA/share/Midas/__init__.py", line 620, in chimeraSelect File "CHIMERA/share/chimera/tkgui.py", line 1604, in selectionOperation NameError: global name 'selMode' is not defined Any clues? Thank you very much! Miguel - -- 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 email: miguel.ortiz(a)cnio.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 >>> And the boring bits follow... -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.2.6 (GNU/Linux) iD8DBQFCleiGF6oOrDvhbQIRAi6cAJ415IJkwKrdjmhOofNbff34aEM3OQCeMdHj GNtxhKnI0DVyUDenbeAHOmw= =VDTj -----END PGP SIGNATURE----- **NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en su caso los ficheros adjuntos, pueden contener información protegida para el uso exclusivo de su destinatario. Se prohíbe la distribución, reproducción o cualquier otro tipo de transmisión por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies.

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Dipole
by Miguel Ortiz Lombardia 18 May '05

18 May '05

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi all, Maybe a silly question, but I couldn't find anything in the docs. Given one structure pdb and an electrostatic potential calculated by delphi, can Chimera display the resulting dipole as a vector? Thank you very much! Cheers, Miguel - -- 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 email: miguel.ortiz(a)cnio.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 >>> And the boring bits follow... -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.2.6 (GNU/Linux) iD8DBQFCi3u+F6oOrDvhbQIRAsvpAJ40rweZtnhVlp3HPYt8sVDODfzEjgCfdAyq efdpkP4wOqyWcrCTT23aJCM= =rxYo -----END PGP SIGNATURE----- **NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en su caso los ficheros adjuntos, pueden contener información protegida para el uso exclusivo de su destinatario. Se prohíbe la distribución, reproducción o cualquier otro tipo de transmisión por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies.

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Re: [Chimera-users] New 64-bit Linux version of Chimera
by Thomas Goddard 17 May '05

17 May '05

The 64-bit Linux Chimera 1.2123 installer was broken. A packaged file did not have execute permission. The fixed version is on the download page now with the same version number and date. If you got the broken version (by downloading in the past 8 hours), please try again. Sorry for the gaff. Tom

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Draw user specified object
by Reza Khayat 17 May '05

17 May '05

Hi, I was wondering if there is a way to draw a user specified object. For example, draw a cylinder (bond) from vertex x to vertex y. Thank you. Reza rkhayat(a)scripps.edu

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New 64-bit Linux version of Chimera
by Thomas Goddard 17 May '05

17 May '05

A new 64-bit Linux Chimera snapshot (version 1.2123) is available on the Chimera download page. http://www.cgl.ucsf.edu/chimera/download.html Unless you are viewing large data sets (> 1 Gb), we suggest you use 32-bit versions of Chimera on 64-bit Linux systems. 32-bit versions will likely run faster and use less memory. The 32-bit versions are more likely to be compatible with your Linux distribution. We are not yet making regular distributions for 64-bit linux so our 32-bit version will usually be newer. Tom

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Re: [Chimera-users] Exporting VRML of MSMS surfaces
by Thomas Goddard 16 May '05

16 May '05

The VRMLoutput/__init__.py I posted in my previous two emails worked for the newly added MSMS surface output, but was broken for volume contour surfaces. Here is the corrected code. Tom ---- VRMLoutput/__init__.py follows: # ----------------------------------------------------------------------------- # Output displayed _surface models as VRML. # # ----------------------------------------------------------------------------- # def surfaces_as_vrml(surface_models): surf_vrml = ['#VRML V2.0 utf8\n', 'Transform {', ' children ['] import _surface import chimera for m in surface_models: if m.display: if isinstance(m, _surface.Surface_Model): glist = filter(lambda g: g.display, m.surface_groups()) for g in glist: vrml = surface_group_as_vrml(g) surf_vrml.append(vrml) elif isinstance(m, chimera.MSMSModel): vrml = msms_surface_as_vrml(m) surf_vrml.append(vrml) surf_vrml.extend([' ]', '}']) vrml = '\n'.join(surf_vrml) return vrml # ----------------------------------------------------------------------------- # def surface_group_as_vrml(g): vertex_rgba = g.vertex_colors() solid_rgba = g.color() m = g.model() mat = m.material shine = mat.shininess / 128.0 srgb = mat.specular if g.display_style() == g.Solid: v, vi = g.geometry() n = g.normals() ts = g.two_sided_lighting() vrml = surface_vrml(v, vi, n, vertex_rgba, solid_rgba, ts, shine, srgb) else: v, vi = g.edges() # Mesh lighting not supported in VRML97. vrml = mesh_vrml(v, vi, vertex_rgba, solid_rgba) return vrml # ----------------------------------------------------------------------------- # def msms_surface_as_vrml(m): vertex_rgba, solid_rgba, mat, shine, srgb = msms_colors(m) # TODO: Use m.drawMode (Filled, Mesh, Dot) to control vrml style vfloat, vint, tri = m.triangleData() v = vfloat[:,:3] n = vfloat[:,3:6] vi = tri[:,:3] ts = True vrml = surface_vrml(v, vi, n, vertex_rgba, solid_rgba, ts, shine, srgb) return vrml # ----------------------------------------------------------------------------- # def msms_colors(m): if m.colorMode == m.Custom: vertex_rgba = colors_to_rgba(m.customColors) elif m.colorMode == m.ByAtom: vfloat, vint, tri = m.triangleData() alist = m.atomMap() vatoms = map(lambda i: alist[i-1], vint[:,1]) vertex_rgba = colors_to_rgba(map(atom_color, vatoms)) else: vertex_rgba = None mol = m.molecule if mol: c = mol.surfaceColor if c == None: c = mol.color solid_rgba = c.rgba() mat = c.material else: solid_rgba = (1,1,1,1) import chimera mat = chimera.MaterialColor(0,0,0).material shine = mat.shininess / 128.0 srgb = mat.specular return vertex_rgba, solid_rgba, mat, shine, srgb # ----------------------------------------------------------------------------- # def colors_to_rgba(color_list): rgba = map(lambda c: c.rgba(), color_list) import Numeric rgba_f32 = Numeric.array(rgba, Numeric.Float32) return rgba_f32 # ----------------------------------------------------------------------------- # def atom_color(atom): c = atom.surfaceColor if c == None: c = atom.color if c == None: c = atom.molecule.surfaceColor if c == None: c = atom.molecule.color return c # ----------------------------------------------------------------------------- # def surface_vrml(vertices, vertex_indices, vertex_normals, vertex_rgba, solid_rgba, two_sided_lighting, shininess, specular_rgb): vrml_template = \ '''Shape { appearance Appearance { material Material { diffuseColor %s transparency %.3f shininess %.3f specularColor %s } } geometry IndexedFaceSet { coord Coordinate { point [ %s ] } normal Normal { vector [ %s ] } coordIndex [ %s ] %s solid %s } } ''' pts = tuple_string(vertices, '%.6g %.6g %.6g') ns = tuple_string(vertex_normals, '%.6g %.6g %.6g') m = polygon_size(vertex_indices) vi_format = ' '.join(['%d'] * m + ['-1']) ci = tuple_string(vertex_indices, vi_format) if vertex_rgba: clrs = tuple_string(vertex_rgba[:,:3], '%.3f %.3f %.3f') cspec = 'color Color {\n color [\n%s]\n }\n' % clrs else: cspec = '' srgb, trans = material_colors(vertex_rgba, solid_rgba) specular = '%.3f %.3f %.3f' % specular_rgb if two_sided_lighting: solid = 'FALSE' else: solid = 'TRUE' vrml = vrml_template % (srgb, trans, shininess, specular, pts, ns, ci, cspec, solid) return vrml # ----------------------------------------------------------------------------- # VRML does not handle normals for lines. # def mesh_vrml(vertices, vertex_indices, vertex_rgba, solid_rgba): vrml_template = \ '''Shape { appearance Appearance { material Material { emissiveColor %s transparency %.3f } } geometry IndexedLineSet { coord Coordinate { point [ %s ] } coordIndex [ %s ] %s } } ''' pts = tuple_string(vertices, '%.6g %.6g %.6g') m = polygon_size(vertex_indices) vi_format = ' '.join(['%d'] * m + ['-1']) ci = tuple_string(vertex_indices, vi_format) if vertex_rgba: clrs = tuple_string(vertex_rgba[:,:3], '%.3f %.3f %.3f') cspec = 'color Color {\n color [\n%s]\n }\n' % clrs else: cspec = '' srgb, trans = material_colors(vertex_rgba, solid_rgba) vrml = vrml_template % (srgb, trans, pts, ci, cspec) return vrml # ----------------------------------------------------------------------------- # def material_colors(vertex_rgba, solid_rgba): if vertex_rgba: srgb = '0 0 0' trans = 1 - max(vertex_rgba[:,3]) else: srgb = '%.3f %.3f %.3f' % solid_rgba[:3] trans = 1 - solid_rgba[3] return srgb, trans # ----------------------------------------------------------------------------- # def polygon_size(vertex_indices): if vertex_indices: return len(vertex_indices[0]) return 0 # ----------------------------------------------------------------------------- # def tuple_string(tuples, format): tuple_strings = [] for t in tuples: tuple_strings.append(format % tuple(t)) tstring = '\n'.join(tuple_strings) return tstring # ----------------------------------------------------------------------------- # def surface_models(): import chimera import _surface mlist = chimera.openModels.list(modelTypes = [_surface.Surface_Model, chimera.MSMSModel]) return mlist # ----------------------------------------------------------------------------- # def write_surfaces_dialog(): import os.path dir = os.path.dirname(__file__) help_path = os.path.join(dir, 'helpdir', 'vrml_output.html') help_url = 'file://' + help_path filters = (('VRML', ('*.wrl', '*.vrml'), '.vrml'),) import OpenSave od = OpenSave.SaveModeless(title = 'Save Surfaces as VRML', filters = filters, defaultFilter = 0, command = write_surfaces_cb, multiple = 0, help = help_url) od.enter() # ----------------------------------------------------------------------------- # def write_surfaces_cb(okayed, dialog): if okayed: paths = dialog.getPaths() if len(paths) == 1: write_surfaces_as_vrml(paths[0]) # ----------------------------------------------------------------------------- # def write_surfaces_as_vrml(path): mlist = surface_models() vrml = surfaces_as_vrml(mlist) f = open(path, 'w') f.write(vrml) f.close()

1 0

matching scale for different sessions
by jinghua＠ucsd.edu 16 May '05

16 May '05

to our friendly developer, Is there a way to specify the physical size for a view, so that different sized molecule or map is shown at the same physical scale from different sessions. By the way, is there a command to specify the pixel size of the window? the shrink to fit or grow to fit doesn't work well. many thanks! Jinghua <<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>>< Jinghua Tang, Ph.D. Phone: 858-534-5852(o) 4107 Natural Sciences Bldg, MC-0378 858-597-2056(h) Department of Chemistry & Biochemistry Fax: 858-534-5846 University of California, San Diego E-mail: jinghua(a)ucsd.edu La Jolla, CA 92093-0378 http://cryoem.ucsd.edu/~jinghua <<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><

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by Klinkhardt＠em.uni-frankfurt.de 13 May '05

13 May '05

Hello, I have a question concerning the surface resolution of multiscale models. My intention was to create a surface from pdb data, export it as vrml and reimport it in maya for further animation, shading etc. It works quite well (I had to convert the vrml file in ascii with Deep Explorer first) but the problem is, that I do not get a fine surface with all its convexities and sites for binding. This is important for my work because I would like to animate receptor binding and subsequent signaling in maya. I am looking for a fine surface like these MSMS main surface from pdb data. I do not need many copies of single pdb surfaces but I guess I will only get a #real# surface using the multiscale models tool?? I tried to change the surface resolution (the best result was with resolution: 3, threshold atom density 0.00, smoothing factor 0.5 and smoothing interations 2/3) but I was not able to create a really fine surface. Is there any possibility to get a finer surface (like MSMS main surface) for VRML export? If not, do you have an idea if there are other tools to do that? It would be rally great if you could give me a short reply. Thanks a lot in advance (and sorry for my english...). Best regards Ute

2 2

Scale bar in Chimera
by Haixiao Gao 09 May '05

09 May '05

Hi, I have a problem with the "scale bar" option in Chimera. I was trying to show the scale bar together with a EM density map in spider/brix format. Howerver, it seems that when I changed zoom in/out position, the size change of the "scale bar" is not proportional to the size change of the density map? My chimera version is win32, bata version from 12/15/2004. Thanks for the help! -Haixiao

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Re: [Chimera-users] os x tiger
by Thomas Goddard 05 May '05

05 May '05

We've put code in the Chimera 1.2121 snapshot (released May 5, 2005) to work around a bug in the Apple OpenGL driver that caused Chimera to crash when displaying molecule ribbons. You need to use Chimera 1.2121 or later on Mac OS 10.4. Tom

1 0

beta version of Sequence.py
by Bryan W. Lepore 05 May '05

05 May '05

i'm trying out the secondary structure matching stuff that Eric wrote, and i'm wondering if there is a updated Sequence.py package (that has the StructureSequence functions)? b/c the new MatchMaker/__init__.py trys to import StructureSequence, but its not in chimera/Sequence.py. -bryan

2 1

os x tiger
by Grant Geske 04 May '05

04 May '05

has anyone tried running chimera on the new mac os tiger?? i did and it did not work. does anyone have any suggestions?? grant ________________________________ Grant Geske Blackwell Group University of Wisconsin-Chemistry 1101 University Ave Madison, WI 53706 PH: 608-262-9043 email: chemg(a)mac.com

2 2

circular permuation
by Bryan W. Lepore 04 May '05

04 May '05

i want to test my understanding about the "circular permuation" during matching: is this for proteins that result from gene duplication? -bryan

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Fwd: [Chimera-users] writing alignment
by Elaine Meng 04 May '05

04 May '05

Begin forwarded message: > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Date: Wed May 4, 2005 1:56:54 PM US/Pacific > To: "Bryan W. Lepore" <lepore(a)brandeis.edu> > Subject: Re: [Chimera-users] writing alignment > > > On Wednesday, May 4, 2005, at 01:41 PM, Bryan W. Lepore wrote: >> however i'd like to ask if mmaker is in fact not written to handle >> specific stretches of a model - e.g you can do #1:.a at the least? >> e.g., not something like #1:.a1-10,a15-20... to prune out areas to >> ignore. >> >> -bryan >> > > Hi Brian, > You can specify which chains (like in that example you included > in a previous mail) to construct an alignment with, but not > subparts of those chains. > > However, remember that the structure matching will only use > residues that are actually aligned in the initial sequence alignment. > So, it doesn't matter if the sequences have other parts > that are essentially unalignable. > Elaine >

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mmaker
by Bryan W. Lepore 03 May '05

03 May '05

i'm confused about the command "mmaker". `chimera --nogui mmaker` causes a "no such file or directory" error, so i tried `chimera --nogui --mmaker` which isnt' right either. also tried just `mmaker` even though its not in bin/ lib/. so do i make a heredoc script? i suspect i am missing a fundamental point (that i didn't find with `google: mmaker site:www.cgl.ucsf.edu/chimera`) i've tried both the latest official release and the lastest snapshot. -bryan

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by Ihms, Elihu C 02 May '05

02 May '05

I noted that Apple still has X11 availible for download, just that it's not publicized. http://a1408.g.akamai.net/7/1408/1388/20030317/akamai.info.apple.com/X11/us… Keep up the good work on Chimera! -- Elihu Ihms [ ihms(a)tamu.edu ]

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Chimera Surface Area/Volume
by Elaine Meng 27 Apr '05

27 Apr '05

Hi Dieter, Just a few add-ons to Tom's reply: Another approach to getting the surface area of the receptor buried by the ligand is to run Surface Area/Volume (a) on the complex of ligand and receptor (must delete water and anything else first). Then use Attribute Calculator to sum the surface areas of the receptor atoms only. (b) after deleting ligand, run it again on the receptor. The total is all from the receptor, so it is not necessary to use Attribute Calculator. Subtract the value from (a) from this value. Tom gave a link to the development documentation, which is slightly ahead of the Chimera version you have. It is almost the same, except that the Tools menu has been reorganized. Probably in the version you have, both Attribute Calculator and Surface Area/Volume are in the Utilities submenu of the Tools menu. To get the documentation that goes with your version, use the Help buttons on those dialogs or open the User's Guide from the Help menu. If you have the latest snapshot (1.2105, March) there is an "Attributes" tutorial (Help... Tutorials). Part 2 has one example of using Surface Area/Volume and Attribute Calculator. Finally, if anything is confusing or hard to find in the documentation, please feel free to complain to me! 8-) 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

1 0

buried surface area
by Thomas Goddard 27 Apr '05

27 Apr '05

Hi Dieter, The surface area / volume tool (menu entry Tools -> Utilities -> Surface Area / Volume) could give buried surface areas if you ran it for the unbound receptor, unbound ligand, and then the complex, and then calculated { Area(receptor) + Area(ligand) - Area(receptor+ligand) } / 2 When you use this tool it reports the total area to the Reply Log (menu entry Favorites / Reply Log) and atoms are assigned an attribute saying how much area they contribute. It is a bit of a pain to run it 3 times and do the math yourself. The surface area is calculated by a web server as described in the Chimera User's Guide http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfvol/surfvol.ht… so you will need an internet connection to use it. The Chimera User's Guide is only available in HTML as far as I know. It is written in HTML. Tom > From: "Dieter Blaas" <dieter.blaas(a)meduniwien.ac.at> > To: Thomas Goddard <goddard(a)cgl.ucsf.edu> > Date: Wed, 27 Apr 2005 21:38:46 +0200 > Subject: buried surface area > > Hi Tom, > two quick questions: 1/ can Chimera calculate/display > the surface area buried by e.g. a ligand when bound on > a receptor? 2/ is there a documentation other than htlm > (e.g. pdf file)? > Thanx, Dieter >

1 0

Resize a molecule
by Thomas Goddard 27 Apr '05

27 Apr '05

Here is some code to scale a molecule size by a given factor. That is all atoms have their coordinates multiplied by a factor. Tom ------- Start of forwarded message ------- Date: Wed, 27 Apr 2005 11:05:55 -0700 (PDT) From: Thomas Goddard <goddard(a)cgl.ucsf.edu> Hi Jinghua, By "virus cage pdb file" I guess you mean you placed atoms at icosahedral positions, and want to show them connected up to show some icosahedral pattern. I think the easiest approach is to open your old session, run a command to change the diameter of the cage, then save a new session. Below is some Python code that provides a "scalemol" Chimera command. Make a directory chimera/share/scalemol in your Chimera distribution and put the code below in file chimera/share/scalemol/ChimeraExtension.py. Then start Chimera, open the cage PDB model, use menu entry Favorites/Command line, and type a command: scalemol 0 1.5 to make model number 0 bigger by a factor of 1.5. If you have more than one model open you can see the model numbers using Favorites / Model Panel, the model number is shown in the left hand column. Tom - ---- scalemol/ChimeraExtension.py code follows: # ----------------------------------------------------------------------------- # def scale_molecule(cmdname, args): from Midas.midas_text import error fields = args.split() try: model_num = int(fields[0]) factor = float(fields[1]) except: error('Syntax error: scalemol <model-number> <factor>') return import chimera mlist = chimera.openModels.list(id = model_num) if len(mlist) == 0: error('scalemol: No model number %d' % model_num) return for model in mlist: for a in model.atoms: x, y, z = a.coord().xyz.data() c = chimera.Coord() c.x, c.y, c.z = (factor*x, factor*y, factor*z) a.setCoord(c) # ----------------------------------------------------------------------------- # import Midas.midas_text Midas.midas_text.addCommand('scalemol', scale_molecule) ------- End of forwarded message -------

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get to lighting adjustment
by jinghua＠ucsd.edu 26 Apr '05

26 Apr '05

to whom it may concern, How could I get to the adcanced feature of lighting adjustment? Can I add more lights with different directions? Thanks! Jinghua <<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>>< Jinghua Tang, Ph.D. Phone: 858-534-5852(o) 4107 Natural Sciences Bldg, MC-0378 858-597-2056(h) Department of Chemistry & Biochemistry Fax: 858-534-5846 University of California, San Diego E-mail: jinghua(a)ucsd.edu La Jolla, CA 92093-0378 http://jinghua.ucsd.edu <<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><<>><

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