November 2008 - Chimera-users - RBVI Mailing Lists

volume planes tool
by Jeff Triffo 22 Jun '16

22 Jun '16

hi folks, anyone know if the volume plane tool will support arbitrary orientation of the plane any time soon? -Jeff

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color scale bar
by Yao Cong 17 Jul '09

17 Jul '09

Hello Chimera developer, I am rendering a PDB file colored according to B-factor value by "render by attribute" tool. How can I generate a color scale bar besides the structure labeling the color scale used? Many thanks, Yao Cong

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using EMAN/AIRS/SSEHunter
by Peter Hildebrand 10 Dec '08

10 Dec '08

Hallo there, we have installed the AIRS (EMAN 1.8) Package for Chimera (build 2470), but have difficulties to get it run. steps to reproduce: launch Chimera load .mrc file calling tools/AIRS/SSEHunter there is no file to select in the 'MRC file' selection box. If we provide parameters for Angstrom, Resolution and threshold and press 'Apply' we get this: ================================================================= UnboundLocalError Exception in Tk callback Function: <function command at 0x89f67d4> (type: <type 'function'>) Args: () Traceback (innermost last): File "CHIMERA/lib/python2.4/site-packages/Pmw/Pmw_1_2/lib/PmwBase.py", line 1747, in __call__ None File "CHIMERA/share/chimera/baseDialog.py", line 238, in command None File "/usr/local/EMAN/chimeraext/Airs/ssehunter.py", line 89, in Apply targetPath=airsIO.getPath(target) File "/usr/local/EMAN/chimeraext/Airs/airsIO.py", line 62, in getPath return path UnboundLocalError: local variable 'path' referenced before assignment ================================================================= Are we using this module in the wrong way (wrong parameters e.g.) or is it a bug (where?). Thanks in advance, jan and peter

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The Macromolecular Modeling Blog
by Nir London 06 Dec '08

06 Dec '08

Hi all, We've started a new blog on all that is related to Macromolecular Modeling http://rosettadesigngroup.com/blog/ We opened this blog in order to provide the modeling community with a helpful resource. Keep updated with what's new in the modeling world, read executive summaries of the latest literature and stay in touch with pears. On its background there is an image of a protein-protein complex I've created using chimera, can any of you suggest a nicer figure for the background ? The best image anyone will send me will be used as background (with due credits :) please check it out and tell me what you think... Cheers, Nir London. Rosetta Design Group http://rosettadesigngroup.com

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Image use permission request from Jones and Bartlett Publishers in Boston
by Asuka Ohsawa 05 Dec '08

05 Dec '08

Dear Sir or Madam: My name is Asuka Ohsawa, and I am a freelance photo researcher for Jones and Bartlett Publishers, Inc., in Boston, MA. We're currently working on an educational textbook by Dr. Benjamin Lewin titled Essential Genes, 2nd Edition, and the author has requested to use the image that appears on the following website: http://www.cgl.ucsf.edu/chimera/ImageGallery/entries/rnabases/ rnabases.html At your earliest convenience, could you please let me know who owns the copyright to the image in question, and how I can get in touch with him/her? In order for us to publish the image properly, we need to acquire a signature from the author of the image. Your kind assistance in this matter will be much appreciated. Should you have any questions or require additional information, please do not hesitate to contact me. Thank you, and I look forward to hearing from you. Best, Asuka Ohsawa Freelance Photo Researcher Jones and Bartlett Publishers, Inc. Email: asukabunny(a)gmail.com Phone: 718/349-0393

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"docking" animation
by Elaine Meng 05 Dec '08

05 Dec '08

On Nov 19, 2008, at 9:37 AM, Bagchi, Angshuman wrote: > Hi, > Could you please tell me how to produce animation in chimera. > Actually, I have 2 proteins and would like to represent them as they > are getting docked. What I mean is that I would like to move the > proteins and then show that as if they are getting docked. Can this > be done with chimera? > Thanks > Ang Hi Ang, Yes, it can be done. Here is how I would do it: (1) create a Chimera session that includes saved/named positions of the proteins separated and the proteins docked. (2) figure out a set of commands that does the stuff you want in your animation, which would include "reset" to gradually change from one saved position to the other; put the commands in a file. Just opening the file will execute the commands. (3) after you are happy with what the Chimera command file does, just put a "movie record" command at the top of it and a "movie encode" command at the bottom, and execute it. Now with more details: (1) Open the structures of the two proteins from two separate files so that they can be moved separately. You can "freeze" a structure by deactivating it, so that the mouse moves only the other structure: <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/mouse.html#activedef > Save at least two positions, one with the proteins separated, another with the proteins docked together, as you want them to appear in your animation. The current position is saved using the command "savepos": <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/savepos.html > You could even save multiple positions for more control over the path the proteins will take as they are "docked" in the animation. There is a nice example in the online movie-making tutorial, see the "Ligand flying into unbound conformation" section: <http://www.cgl.ucsf.edu/chimera/tutorials/movies08/moviemaking.html> Get the display how you want it: background color, ribbons, ribbon style, which atoms are shown, atom display style, colors, etc. See "tips on preparing images": <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/ print.html#tips> You might also want to add a title using 2D labels (if so, leave room for it when you save the positions). <http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/2dlabels/2… > Save the session (File... Save session As). It will include your saved positions and any 2D labels. Now you could exit and later restart the session without losing your work. (2) You could either try out commands by typing them individually, or by putting them in a text file (named *.com or *.cmd) and repeatedly opening the file after you adjust its contents and going back to the starting position. <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/indexcommand.html#c… > The "reset" command is used to go from one saved position to another. It can be done abruptly in one frame or gradually over a specified number of frames. See movie-related commands for links to the manual page of "reset" and other commands that can do things over a specified number of frames. Besides the "reset," you might want to do other things like translate or rotate or fade in/out 2D labels with these commands. <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/movies.html#movieco… > There are also links to a few example movie command files on that page. (3) Once you are happy with what the script does when you open it, then you can put a "movie record" command at the top and a "movie encode" command at the bottom. See the example movie command files and the "movie" command description: <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/movie.html > I prefer this process because at the end you have a session file and a command file that allow you to either reproduce the process efficiently, or to make some small change without a lot of duplicated effort. I am told that "reset" has had some problems which were just fixed, so if you get a bad behavior using that command, try getting a recent daily build from <http://www.cgl.ucsf.edu/chimera/alpha-downloads.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

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Vista Video Card Error
by Devon Cayer 04 Dec '08

04 Dec '08

Hello, I'm currently attempting to model some viral capsid proteins using your software. Unfortunately, when I attempt to use the "side view" option I get a video card error, and I'm told to update my video card drivers. I've contacted the manufacturer and they have told me my laptop, a Gateway MT6821, is up to date with all the latest drivers. What else could be a possible problem do you think? I look forward to any input, Sincerely, Devon C Devon M Cayer Graduate Student The Scripps Research Institute Ghadiri Lab devcayer(a)scripps.edu

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building a alpha helix
by Anindito Sen 04 Dec '08

04 Dec '08

Dear All I was wondering if there is any tool by which can generate an alpha helix, as an extension of a truncated crystal structure docked in the density map. The possibility of the truncated portion of the protein behaving as an alpha helix has been predicted by different groups. The density map shows some empty regions (after the crystal structure has been docked) just good enough for an alpha helix to fit in. Best Andy Dr. Anindito Sen (Ph.D) Research Associate , Dept. of Biochemistry and Molecular Genetics University of Virginia Box 800733 Charlottesville, VA 22908

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Software(Drug Design)
by Tarit Mitra 04 Dec '08

04 Dec '08

28, Ashfield Green Yateley Hants GU46 6AL UK Dear Sir, I am a retired scientist, and working on an honorary basis for the University of London. I work from home and go to the University in regular interval. I would very much like to use your software for drug design. I was wondering whether you would grant me a free academic licence to the software. I shall only use the software for academic purpose and not for any financial reason whatsoever. I have both Linux(Ubantu) and Windows XP. My computer has 40GB hard disk with 756MB RAM I shall be grateful if you will kindly consider my case favourably. Yours faithfully T. K. Mitra, B.Sc(London), Ph.D(London)

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Chimera rotational matrix
by Bui Khanh Huy 01 Dec '08

01 Dec '08

Hi, I notice that Chimera has slightly different in calculation of transform when I tried to rotate my EM density (200x200x200 mrc file) using Chimera. The origin of the density reported by Volume Viewer is 0,0,0 First, I print out the homologous transform matrix using: >>> om = chimera.openModels >>> mlist = om.list() >>> m = mlist[0] >>> print m.openState.xform The transformation is: 1 0 0 0 0 1 0 0 0 0 1 0 If I rotate the model using command: roll z -30 1 Then print out the transform matrix again: 0.866025 0.5 0 -36.8852 -0.5 0.866025 0 61.2937 0 0 0 1 That would be weird because I didn't do any translation. So what is really happening in Chimera when I rotate the model? Best, Huy

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Chimera-users November 2008