- Chimera-users - RBVI Mailing Lists

python scripts
by christopher lau 07 Apr '09

07 Apr '09

Dear Madam/Sir I am new to Chimera and this forum so I apologize in advance if I my question is inappropriate. I want to start writing python scripts such that I can run the script and the color code, orientation, etc of the molecule opened can be automated. Do you know of any good tutorials that teach what commands are available to use in python for chimera and how to run some basic python scripts in chimera? I have figured out enough to open the Python Shell in Chimera, but that is all. An example python script would be helpful. Thanks everyone, Chris Lau

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chimera help
by Ines COLLINGS 07 Apr '09

07 Apr '09

Dear Madam/Sir, I would like to add the coordinates direction x,y,z in Chimera so that I may know the orientation of the unit cell. Could you let me know how to do this. Thank you very much in advance, Ines Collings

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Re: [Chimera-users] Map Morphing questions
by Thomas Goddard 06 Apr '09

06 Apr '09

Hi Julio, While it is possible to rotate models and use Morph Map at the same time there isn't currently a command to do the morph part. This makes it difficult to record an animation since the morph has to be started by hand from the dialog. The turn command would look like "turn y 3 120" to turn around the y axis in 3 degree steps for 120 steps. Here's the Chimera 1.4 (daily build) "turn" documentation: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/turn.html I would like to make a morphmap command so it can be used in animation scripts. Can you explain a bit more your case involving more than 2 maps? Tom Dr .Julio Ortiz wrote: > Hi Tom, > I have been using recently the Morph Map function in Chimera. It is > really helpful! I would like to prepare several movies using this tool. > Three questions: > > 1)Is it possible to combine the morphing with some basic rotations, like > for example around Y axis?. > > 2)I am sure that is doable making some script, but actually..I am so > sorry..I haven't had time to sit down and read carefully how to make > your scripts. > Could you provide me with an initial script to do the rotation of the > morph map which I can start to modify in the future? > > 3) Would it be possible to add more than two maps for the morphing > automatically, and give a sequence of which pairs need to be morphed > instead of make sequential steps? > > Thanks for your help. I hope we can meet again in the near future I > would love to have an update of wht is possible with your wonderful > program. > > Greetings, > Julio >

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Rosetta Academic Training Webinar
by Nir London 06 Apr '09

06 Apr '09

The Rosetta Design Group is proud to present the first webinar in the Rosetta Academic Workshop Series. For the first webinar, we have selected to focus on Protein-Protein Docking based on the answers to the interest poll. We hope this will be the first in a line of helpful and inspiring webinars to kick-off our Rosetta Academic Workshop Series. What: Protein-Protein Docking When: May 4th 2009, 0800-1000 AM EST Where: Your office! Click here for more details and registration (For non html emails: http://rosettadesigngroup.com/RDGLS/index.php?sid=54479&lang=en) Pleas note: This is not a promotional webinar. Rosetta is open-source and freeware for academic and non-profit organizations and can be downloaded here from University of Washington's TechTransfer Digital Ventures. The majority of the webinar is concerned with Rosetta 2.3.0. Rosetta 3.0 is still a beta version. Hope to see you there, Nir London. Rosetta Design Group | http://rosettadesigngroup.com/

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delay in starting the program
by Eaazhisai Kandiah 03 Apr '09

03 Apr '09

Hi Chimera-Developers, Recently, my work-computer was upgraded from MaC-OS 10.4 to 10.5. I installed the Chimera X-windows version for 10.5. Apparently, while starting the program, it takes almost 2min for the program to get activated. While checking the activity monitor, chimera tries to use 'OSASCRIPT' which together with Chimera, showed as 'not-responding'. I couldn't troubleshoot the reason for this huge delay in start and hence rectify it. Any help would be appreciated. Thank you, Eaazhisai Kandiah Laboratory of Structural Biology NIAMS, National Institutes of Health, Room 1511,Bldg 50 9000 Rockville Pike, Bethesda, MD-20892 kandiahe(a)mail.nih.gov Off: 301 451 2281 Fax: 301 480 7629

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calculating centroid of atoms
by Bala subramanian 02 Apr '09

02 Apr '09

Friends, I want to choose certains atoms and get the x,y,z coordinates of the center. Kindly write me how to do it in chimera. Bala

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chimera help
by Terrance Chiang 02 Apr '09

02 Apr '09

Hi, I am trying to show a structural change between two proteins that differ by one amino acid, is this possible with chimera? I was unable to display the transformation I desired, so I looked into other ways to show changes between two overall similar molecules. I found that it is possible to show a change in the surface between two similar molecules, but I am unable to utilize the function because it requires a different file format. I would like to do both... that is, to show the conformational change from one protein to another, as well as show the change in surface from one protein to another, but I keep hitting these road blocks. Any help would be highly appreciated! Thanks, Terrance Chiang

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save reply log via command line?
by Sebastian Kruggel 01 Apr '09

01 Apr '09

dear chimera team / users, i was looking for a way to save the content of the reply log to a text file via command line, because i wanted to embed and process some results given in the reply log in a small cmd/py-script without. thanks in advance, sebastian -- Sebastian Kruggel Institut für Pharmazie Bundesstr. 45 | Raum 112 (406) D 20146 Hamburg Tel +49 (0)40 42838-3626 (-3484) kruggel(a)chemie.uni-hamburg.de

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Re: [Chimera-users] write selected command
by Elaine Meng 01 Apr '09

01 Apr '09

Hi Ed, Are there conformational changes in this process, or do chains simply move as rigid bodies? I had thought there were conformational changes within chains, but now looking at your movie again, I'm not sure. If each rigid body is a separate model, you would simply save the different configurations of the entire set as named positions with the command "savepos". Then you can reset to successive named over a specified number of frames with "reset" or smoothly interpolate over multiple saved positions with "fly". There have been recent improvements including addition of "fly" so I'd recommend a recent daily build if it sounds like this approach is doable. The process would then be scripted in a Chimera command file rather than appearing as playback in MD Movie. Once the command file generates the desired movie content, you could put a "movie record" command at the top and "movie stop" and "movie encode" commands at the bottom. example command files: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/movies.html#examples 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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write selected command
by Edward Brignole 01 Apr '09

01 Apr '09

Elaine and co, I have a mess of models that I'm opening, repositioning a ligand using match to various positions in each model. No problem there. For each model and ligand position I select the correct chains from that model with the repositioned ligand models but can't manage to save coordinates. Obviously there's the save pdb dialog but for all these models and ligands this will be more convenient scripted into chimera commands. I've got it all working except this: select #6:.a-p #8 #9 write selected relative 0 #6,8,9 /path/to/file.pdb ~select The part it doesn't like is the model_numbers and I've tried various permutations without success. The only way I can get it to work is if I only specify one model number. Can you please help me figure out how to phrase this command correctly? An example or two on that commands page might make the syntax easier to decipher. Thank you for your excellent program and support. Ed ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Edward Brignole NIH Kirschstein Postdoctoral Fellow Francisco Asturias Lab, CB227 Center for Integrative Molecular Biosciences The Scripps Research Institute www.scripps.edu/~brignole brignole(a)scripps.edu 443-653-2070 (cell) 858-784-8598 (lab)

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