December 2008 - Chimera-users - RBVI Mailing Lists

Maintaining Color and Formatting Selections for New Molecules
by Eric Ganz 08 Dec '08

08 Dec '08

Now that I have formatted and colored one molecule, I would like to maintain the color and formatting selections for a series of new molecules. How should I do this?

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Re: [Chimera-users] Labeling the surface representation
by Elaine Meng 07 Dec '08

07 Dec '08

Hi Mehdi, I misunderstood your question. I thought you meant the atomspec balloons that temporarily pop up when you put the mouse over the atoms, and the previous instructions apply to those. Your picture shows the regular residue labels. To show a residue label, the residue's ribbon or some of its atoms must be displayed. It is OK for the surface to also be shown, but then the problem is that the surface usually covers up the residue labels so you can't see them. You can make the surface transparent to see the labels inside (see "Actions... Surface... transparency..." in the menu or use the command "surftransparency"). <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/surftransparency.html > If you are displaying these labels to make a figure, another suggestion is to use 2D Labels. You have to enter the text of a 2D label yourself, but you can move it to any position in the window. 2D Labels are independent of the structure and how it is displayed. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/2dlabels/2dlabels.… > 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 Dec 7, 2008, at 11:31 AM, Mehdi wrote: > Thank you for your detailed information. I could not still figure > out how to label the residues on surface representation. I have > attached the figure (for instance) showing the ribbon representation > with a few amino acids labeled but if I want to achieve the labeling > on the surface the labels,unlike the ribbon, do not appears on it. I > also followed the tutorial but the atomspec balloons were not > observed on the surface as soon as the ribbon or simple stick > representation are hided.Do I have to keep the simple bond or ribbon > representation in order to keep the atomspec balloon and labels > observable?

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show CA as sphere and ribbon
by lvyuan zhang 07 Dec '08

07 Dec '08

Hi, I want show one of the CAs in a single protein chain as a sphere. But it looks like that I have to hide the ribbon to let the sphere show. Is there anyway that I can show the CA as sphere and also allow the ribbon to remain? I looked at the gallery and I didn't find anything that can help me, so here I am to ask for help from you again. Thanks first! Cheers! Luyuan

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I got it.
by lvyuan zhang 07 Dec '08

07 Dec '08

I saved the CA atoms as another pdb file, and then import it, and show atoms as sphere. ________________________________ From: lvyuan zhang <gleanerly(a)yahoo.com> To: chimera-users(a)cgl.ucsf.edu Sent: Sunday, December 7, 2008 4:42:20 PM Subject: show CA as sphere and ribbon Hi, I want show one of the CAs in a single protein chain as a sphere. But it looks like that I have to hide the ribbon to let the sphere show. Is there anyway that I can show the CA as sphere and also allow the ribbon to remain? I looked at the gallery and I didn't find anything that can help me, so here I am to ask for help from you again. Thanks first! Cheers! Luyuan

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Labeling the surface representation
by Mehdi 07 Dec '08

07 Dec '08

I am a new user of chimera, I would like to know how to label the residues in surface representation like the same action for ribbon! It simply works for ribbon but unfortunately I could not get it to work for surface. Mehdi

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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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Chimera on Linux PPC
by Tom Goddard 05 Dec '08

05 Dec '08

Hi Justin, We do not currently build Chimera for Linux with PowerPC processors. Chimera includes more than 30 third-party libraries which we build automatically on each supported platform (Windows, Mac, Linux...). Compiling all those libraries is the real problem. Many of those libraries require special patches to build on all our platforms (Windows, Linux, Mac). It would likely take weeks of work for Linux PPC for someone very experienced in compiling open source packages from source code. We do not have the resources to do that for such an obscure platform. The next platform we will likely support is Mac 64-bit (Intel) sometime in the next year, after that 64-bit Windows. The latest Chimera can be compiled without the proprietary molecular surface code. We don't have that latest source code on the web site, but if you manage to build all the third-party packages (called "foreign" packages on our source code download page) I'd put the latest source code on the web and tell you how to disable the molecular surface compilation. Tom Justin A. Lemkul wrote: > > Dear Sir, > > I am installing a few machines in our lab that are running Ubuntu > Linux (8.04) on PowerPC architecture. They are iMac G5 desktop > machines, a little old, but new to us. I have thus far been unable to > install Chimera on these machines, being that it is such an odd setup, > and PPC is rapidly falling out of use. I came across a message in the > chimera-users archive that made me wonder if installing Chimera on > these systems was even possible: > > http://www.cgl.ucsf.edu/pipermail/chimera-users/2005-December/000607.html > > Are you aware of anyone that has installed Chimera on such a system? > Do you think it is even possible? We would really like to be able to > use Chimera on these machines (it is installed on all our other > machines, and has become a staple in our lab). Any advice you could > give me would be greatly appreciated. > > If I can resolve all of the dependencies, would Chimera install > without MSMS? I don't believe I can install MSMS on these machines, > given the available installation packages. > > Thank you very much for your time and attention. > > -Justin >

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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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Chimera-users December 2008