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Encoding movie by hand
by Tom Goddard 12 May '08

12 May '08

Anindito Sen wrote: > > Hi Tom > > How can we make a movie (not morphing) out of several still snaps > (.jpg) saved from of many density maps. > using chimera. > > Thanks > qandy > > Dr. Anindito Sen (Ph.D) > Research Associate , Dept. of Biochemistry and Molecular Genetics > University of Virginia > Box 800733 Charlottesville, VA 22908 Hi Qandy, You can create a movie directly from a set of images using the ffmpeg executable included in the Chimera distribution. When you make a movie using Chimera it runs the ffmpeg executable to make the movie file and the options used are printed to the Chimera reply log (Favorites / Reply Log). For example, in the reply log I see ARG_LIST IS ['-r', '25', '-i', '/tmp/chimovie_JgKl-%05d.ppm', '-y', '-f', 'mov', '-b', '2000', '-bufsize', '200', '/Users/goddard/chimera_movie.mov'] Movie saved to /Users/goddard/chimera_movie.mov so the ffmpeg command used was: ffmpeg -r 25 -i /tmp/chimovie_JgK1-%05d.ppm -y -f mov -b 2000 -bufsize 200 You could run a similar command from a shell to encode a movie outside of Chimera. The files are specified by the "-i" option. In the example they are ppm format but jpg will work too. The %05d means that the file names ended in a 5-digit number with leading zeros (e.g. chimovie_JgK1-00000.ppm, chimovie_JgK1-00001.ppm, ...). The -r option indicates frame rate (25 frames per second). The -f option is output format (mov = quicktime). The -b option is bit rate (Kbits/sec) and controls output quality. The -y option means to overwrite the output file if it already exists. For complete ffmpeg options see online docs: http://ffmpeg.mplayerhq.hu/ffmpeg-doc.html The Chimera copy of ffmpeg is in the distribution in chimera/bin (or on Mac in Chimera.app/Contents/Resources/bin). Tom

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Program won't open
by Abigail Lambert 12 May '08

12 May '08

Hello - I'm using a MacBook Pro, OS X (10.4.11), and I had been successfully using Chimera for a while. Then all of sudden, the program will no longer open. The Chimera icon blinks once in the taskbar, and then it disappears and the program does NOT open. I tried uninstalling and re-installing, but this does not help. Any suggestions? Thanks! - Abbie -

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Renaming chains in a PDB file with two chains
by Harinathachari Bahudhanapati 10 May '08

10 May '08

Hi Elaine, Thanks for all the answers you give to our questions. They are very helpful as I learn more everyday. I have a question. Is there anyway to rename a chain in a PDB file through the GUI? I have a few PATCHDOCK generated PDB files with two different chains named under Chain 'A' as #0.1 and #0.2. When I try to get the list of hydrogen bonds between these two chains, the chain name 'A' appears for all of the h-bonding pairs. So, I want to have them named Chain A and Chain B for easier analysis than scratching my head figuring out which h-bond pair is between the chains or with in the chain. I am attaching the pdb file. Please help me. (I thought of renaming the chains in the PDB file going through the PDB header (text file) and manually changing the name. But I am not a expert if anything goes wrong.) Sincerely Hari

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Dashed H-bond
by Ibrahim Moustafa 10 May '08

10 May '08

Dear Chimera Team, Few weeks ago I asked about how to make H-bonds with dashed line style, I got your great help in that. So, I can make the H-bond with the color and style I want; however, when saving the image (with POV true) I got the H-bond appeared with the new chosen color but not as dashed line shown in the display. But, if I save the image with POVray option false, I got the same style shown in the display (new color and dashed line). The question is why saving the image using ³POV true² does not give the image as it appears in the display? Again, it accepts the new color but not the dashed style. Thanks for your great help, Ibrahim -- Ibrahim M. Moustafa, Ph.D. Biochemistry and Molecular Biology Dept. 201 Althouse Lab., University Park, Pennsylvania State University PA 16802 Tel. (814) 863-8703 Fax (814) 865-7927

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Number of voxels?
by Kolodziej, Steven J 09 May '08

09 May '08

I was wondering if anyone knows how to tell how many voxels within a bounding box can be assigned to protein signal instead of "empty space" at any given contour/density level? Thanks, Steve Kolodziej

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saving a stereo image
by Elaine Meng 09 May '08

09 May '08

On May 9, 2008, at 9:04 AM, Pallan, Pradeep S wrote: > > Hi Elaine, > I am trying to save a generate a stereo image by following the > instructions: > http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/tutorials/ > frameimages.html > > I captured left eye and right eye images separately, pasted > them side by side ~65 mm apart, and I see this do not appear as > stereo. Any comments and instructions? I can send you the image > if you want to take a look at it. > > Thank you very much, > Pradeep Pallan Hi Pradeep, I think you are looking at old documentation. I don't think the current documentation says anything about saving separate images for left eye and right eye. This is the current page: http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/ print.html#stereo Here is the blurb from that page, but it is probably better to go to the URL because there are helpful hyperlinks: Stereo. Wall-eye, cross-eye, and red-cyan stereo images can be saved by changing the graphics window to the corresponding camera mode with the Camera tool (or the command stereo) and using the "same as screen" Image camera mode in the Save Image dialog. Another way to save cross-eye stereo images is with the "stereo pair" Image camera mode; in that case, it does not matter what camera mode is being used in the graphics window, but the resulting image will be twice as wide as the specified size. Those approaches should work, assuming you also have a recent version of Chimera! (last production release Nov 2007 or newer) Best, 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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Selected residues already shown on the screen
by Ibrahim Moustafa 08 May '08

08 May '08

Dear Chimera team, How to include residues previously selected and shown on the screen with a new selection? For example, I did a selection for few residues and displayed them on the screen; then removed the selection. I wanted to run hbond on those residues already on display. How to do that? Thanks, Ibrahim -- Ibrahim M. Moustafa, Ph.D. Biochemistry and Molecular Biology Dept. 201 Althouse Lab., University Park, Pennsylvania State University PA 16802 Tel. (814) 863-8703 Fax (814) 865-7927

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MemoryError restoring session
by Eric Pettersen 07 May '08

07 May '08

Christian Rickert wrote: > At the university, I saved a huge project of mine containing a > density map and multiple (!) rigid-body fitted pdbs. > Although this system is a 32-bit Kubuntu 8.04 only (4 Gig of RAM > installed), I observed the same problems with my 64-bit SUSE 10.3 > (4 Gig of RAM installed as well) at work. > > Creating this project took me two days in total, so I really would > appreciate any suggestions from you ... Hi Christian, It's possible that your shell is imposing a limit on memory use by a single process. Before starting Chimera, remove the memory limit of your shell by typing: csh-type shell: unlimit sh-type shell: ulimit -v unlimited Let me know if this helps or not. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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how to use hbonds spec
by Miguel Ortiz-Lombardía 07 May '08

07 May '08

Hello, I'm trying to follow hydrogen bonds in a trajectory from amber. To do so, I would like to run a 'per frame' script with something like: hbonds spec :100 selRestrict cross relax false However, this fails because apparently no atoms are selected. This fails as well: hbonds spec #0:100 selRestrict cross relax false I can only see the hydrogen bonds if insert a select :100 before the hbonds command. I wouldn't like to see the green 'aura' of the selection, that's why I would like to make the selection within the hbonds command. I'm probably missing something, but cannot figure out what. Thank you! Miguel -- http://www.pangea.org/mol/spip.php?rubrique2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Je suis de la mauvaise herbe, Braves gens, braves gens, Je pousse en liberté Dans les jardins mal fréquentés! Georges Brassens

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Tile structure request
by Eduardo Sanz-Garcia 07 May '08

07 May '08

I noticed that the tile structure option arranges the models logically when there are 5 or less models opened. When there are 6 or more, the arrangement is a little bit chaotic, the models are not placed sequentially. Could this option be improved so the sequence is more logical? Thank you very much. Chimera is great!! PS: I am used to work with EM models, I don't know if the previously described behaviour also applies to atomic coordinates models.

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