March 2009 - Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] Making movies
by Elaine Meng 17 Mar '09

17 Mar '09

On Mar 16, 2009, at 10:13 PM, yimnai forlemu wrote: > Hello Elaine, > I have a quick question and was wondering whether I can use chimera > to archieve my goals.I have ran a BD simulation and saved > trajectories of my particles. My question is whether it is possible > for me to use chimera to create a movie from the BD simulations > trajectory data.If yes please could you just direct me to the > tutorial that can help me accomplish that goal. > Thanks > Neville Hi Neville, I don't know what "BD simulation" is. Chimera's "MD Movie" tool can read trajectory output from several programs: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.h… > If you have one of those formats, or can convert your output to one of those formats (for example, multiple PDB files), MD Movie can show the trajectory. You can control how the molecules look in Chimera as you normally do, then use "File... Record movie" from the MD Movie dialog to create a movie. This tutorial uses the MD Movie tool to do various things, including saving a movie: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembles2.html#p… > There are other ways to save a movie (not necessarily using the MD Movie tool). This page has more general information including links to example scripts and other movie-making tutorials: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/movies.html> I hope this helps, Elaine P.S. For a reliable response, please send mail to chimera-users(a)cgl.ucsf.edu rather than to me directly. If you send mail to only me and I'm run over by a bus, you will never get an answer!

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Session management suggestions
by Thomas Goddard 16 Mar '09

16 Mar '09

Matt Dougherty sent 4 session file management suggestions. 1) Session description text, browsable. 2) Copying camera positions between sessions. 3) Session version numbers with matching filename extensions. 4) Automated checkpoint session saving. Details below. Tom Matthew Dougherty wrote: > 1) I frequently have to use a lot of session files in combination with a > lot of command files to generate animations. > > One session file might be used with multiple command files. > > I try to pack as much information into the filename as a way to keep it > all organized, but this is becoming cumbersome. > the filenames are becoming cryptic to keep them short; plus I multiple > drafts I need to maintain in case the researcher wants to go back to a > prior visualization. > > It would be good to have a item in the' File' pull-down-menu to handle > summaries or descriptions. > > By activating it, I could type in a paragraph as to what is going on > with the session. > > In a bigger picture, it would be good to be able to start chimera, and > somehow peruse through these descriptions, but not have to load the > session to read the description. > > 2) many times in an animation project I start with a common session file > containing all the data sets in sync, and create multiple derivative > session files to handle different aspects of the animation, usually with > the unused datasets deleted for a particular animation session for > reasons of improving computation speed and loading for a particular > animation clip. > > sometimes I would like to move a set of camera positions created in one > of the daughter session files to another daughter session file. > > Matthew Dougherty wrote: > 1) optional automated versioning. Sometimes I when I am working on an > animation I need to keep the intermediate versions, particularly when I > am less certain about what I am doing and the complexity of the session > goes up. > > check box somewhere that causes saving to automatically prepend "_V22" > before ".py", for version 22 in this example, and _V23 for the next > save, etc. > > 2) optional automated checkpoint saving such that the interval time can > be set. sometimes when working on a complex session it get a crash and > I have not saved it, so I have lost all my work from the previous save, > which could be 1-4 hours.

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Octamer to dimer
by John Lowenstein 16 Mar '09

16 Mar '09

Dear Folks, In PDB 1ewj the structure comes up as an octamer. The physiological entity, in which I am interested, is a dimer. I can eliminate three of the for dimers, but I have not found a way to eliminate the six extra ligands (bleomycin) associated with the three eliminated dimers. (I want the dimer with two ligands.) Any suggestions? Thanks. Sincerely, John Lowenstein

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confocal stack
by Benoit Zuber 16 Mar '09

16 Mar '09

Hello, Is it possible to browse through the planes of more than 1 volume at a time? I have some confocal data and I want to browse along the X axis of the dataset; each volume corresponds to a confocal channel. Cheers, Ben

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adding CONECT records with nogui option
by shyamala 16 Mar '09

16 Mar '09

Hi Chimera users, I am sure there is a simple way to do this, but I need some help. I want to add CONECT records to a pdb file, given that the input file contains all necessary atom coordinate information. I need to do this within my shell script and I want to start chimera using the nongui option. Now, doing some google seach brought up this solution to add CONECT records (in the command line within CHIMERA gui) pdbrun nouser conect cat > filename.pdb where filename.pdb is the name of the output file with CONECT records added. the above mentioned command works when I pull up the file on GUI CHIMERA My question is then how would I use such a command when I want to use it in the nogui option. I have multiple files (>100) for which I need to add CONECT records and I want to do it with a script. Also, if someone could point me to a good resource for writing python scripts that can be then passed on to chimera, I would be grateful. Thanks, Shyamala Shyamala Iyer Graduate Student Department of Microbiology PO BOX 357242 University of Washington Seattle, WA, 98195

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Problem adjusting sphere quality in script
by Marhoefer, R (Richard) 16 Mar '09

16 Mar '09

Dear Chimera Users, I want to adjust the quality of spheres, cylinders and ribbons in a script. From the moviemaking tutorial script I learned that I must use some lines of Python. Therefore, I used the code as found in the example: import chimera chimera.LODControl.quality = 20 When I open this script like in the tutorial, the value of "subdivision quality" in the "Effects" panel is indeed set to 20. However, the quality of spheres and cylinders remains untouched. From that point in time any further modifications of the value in the "Effects" panel do not have any effect. If I change the value of "subdivision quality" in the "Effects" panel before opening the Python code, anything works fine. Did anybody succeed with changing the sphere quality in a script? Kind regards, Richard Mit freundlichen Grüßen / With kind regards Dr. Richard Marhoefer Senior Scientist BioChemInformatics Intervet Innovation GmbH Zur Propstei 55270 Schwabenheim, Germany E-Mail: richard.marhoefer(a)sp.intervet.com Phone: +49 (6130) 948 204 Fax: +49 (6130) 948 517 Mobile: +49 175 723 081 4 Home http://www.intervet.com Sitz der Gesellschaft: Schwabenheim Amtsgericht Mainz, HRB 23 166 Geschäftsführer: Dr. Peter Schmid -------------------------------------- This message and any attachments are solely for the intended recipient. If you are not the intended recipient, disclosure, copying, use or distribution of the information included in this message is prohibited -- please immediately and permanently delete. --------------------------------------

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command line
by Sirano Dhe-Paganon 16 Mar '09

16 Mar '09

After entering a command in the "command line" of UCSF-Chimera, I would like the command that I pasted to disappear. Currently, it does not disappear; how can I make it disappear after I press the enter button?

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Chimera needs your vote.
by Nir London 16 Mar '09

16 Mar '09

There is a poll going on at the macromolecular modeling blog "What is your favorite molecular viewer?" http://rosettadesigngroup.com/blog/284/what-is-your-favorite-molecular-view… PyMOL is currently at the lead, but you might make the difference, go ahead and show your support for Chimera (or choose one of the other viewers if you like them more) but most importantly drop a comment as to why YOUR viewer is the best. Disclaimer: for fairness, similar messeges are sent to the other competitors mailing lists as well, but we like yours the most ;) Nir London. Rosetta Design Group. http://rosettadesigngroup.com/blog/

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centering on an atom
by Sirano Dhe-Paganon 16 Mar '09

16 Mar '09

In UCSF-Chimera, I would like to center on an atom of a molecule without zooming-in towards the atom. I found the "focus" command, which centers the atom, but the command includes a zooming-in step; is there a "focus" or "center"-like option that does not zoom-in? Also, most visualization programs have a simple, one-click mouse-button to center on an atom; I cannot find this option in UCSF-Chimera. Sirano

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Re: [Chimera-users] window size
by Elaine Meng 13 Mar '09

13 Mar '09

Hi Jean-Paul, For a more reliable response, please send questions to chimera- users(a)cgl.ucsf.edu rather than to me directly -- I might be out (sick or vacation), or others may know the answer when I don't! There is no preference for window sizes and locations. However, there is a startup option "--geometry" for the main window (but not other tools, sorry): <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/options.html#geometry> How to specify startup options depends on your type of computer: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/startup.html> Some related things... After you start Chimera, you can use the "windowsize" command to specify the pixel dimensions of the main window. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/window.html> If you save a session, it should restore with the same main window size. I don't think the location is saved, however. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/sessions.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 On Mar 13, 2009, at 11:16 AM, Jean-Paul Armache wrote: > hello, > i have a question. is there a way of saving the window sizes and > windows positions in chimera ? whenever i start chimera the default > all the windows have always the same position and sizes. i always > adjust it to the same position and size, but maybe there is a way to > save it as a preference ? i checked the preferences file, nothing > there. > thank you, > best regards, > jean-paul armache

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Chimera-users March 2009