September 2005 - Chimera-users - RBVI Mailing Lists

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

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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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