May 2010 - Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] Save session for movie
by Eric Pettersen 18 May '10

18 May '10

Hi Francesco, On Apr 19, 2010, at 12:29 AM, Francesco Pietra wrote: > If at all, I did not understand if a continuous trace of the centroid > (instead of a series of balls) can be obtained in the context of the > protein. That would improve the presentation further. Otherwise, the > series of balls for the centroid, with appropriate choice of radius > and step size, shows the pathway of the ligand through the protein > adequately. Nothing simple comes to mind. One way that's a bit of work would be to save the centroid information to a file (the 'Save' button on the Axes/Planes/Centroids interface) and the use a text editor to create a BILD file (BILD format) showing lines/cylinders connecting the centroid centers. > As a minor point, I was unable to render helices transparent. > Transparency would help to to see the centroid trajectory in between > helices. Should be possible unless there's something wrong with your graphics cards. Try this: Select->Structure->secondary structure->helix Actions->Color->from editor This will bring up a color editor. Try making a transparent red. For me, the editor looks like this when I do that: (note the "Opacity" box is checked) and the structure looks like this: --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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accessing atom information
by Bala subramanian 17 May '10

17 May '10

Friends, I have just begun to explore the chimera-python linkage. I loaded a pdb file using chimera.openModels function. Then i tried to loop through the residues and display atom information based on a condition. >>>for r in mymodel.residues: *#this works for me* if r.type=='ARG': print r.atoms >>>for r in mymodel.residues: *#this dose not work. I know there is a ARG residue with id 151.* if r.id=='151': print r.atoms I dnt understand how atom attributes are packaged within a residue. Kindly write me few examples of accessing atom information from a residue. Thanks, Bala

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clip planes in vrml
by Daniel Gurnon 17 May '10

17 May '10

Hi all, I'm thinking of the 3D printing of physical models, and how informative clipping planes can be....would it be feasible to add capped-clip planes to vrml output? I also ran into a problem when I exported a surface to vrml and tried to view it with Adobe 3D reviewer. The color information didn't transfer. This isn't a problem when saving ribbons or bonds as vrml. Dan -- ____________________________ Daniel Gurnon, Ph. D. Assistant Professor of Chemistry DePauw University Greencastle, IN 46135 p: 765-658-6279 e: danielgurnon(a)depauw.edu

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Re: [Chimera-users] Creating movies
by Tom Goddard 15 May '10

15 May '10

Hi Matthew, The movie images including the command-line is very weird -- never heard of that happening before. It is almost certainly a graphics driver problem. You can try a Chimera daily build which uses a different image capture method. Also you can report the bug with the version you are using Chimera menu entry Help / Report a Bug.... That will give us information about your graphics card and driver that may help us advise you further. Tom > Tom, > > Thanks for the note -- regarding "all my commands show during the > movie" -- > > When I use the command line interface, the entire chimera window gets > recorded, not the viewing window with the protein. When I play back > the movie, I see the tool bar complete with the command line. I > even get to watch the text appear in the command line as it was > entered. I am using the linux version and will take the opportunity > to try the daily build. > Thanks for the help. I'll keep you updated. > > Cheers, > Matthew > > > > > Tom Goddard wrote: >> Hi Matt, >> >> Not sure what you mean by "all my commands show during the movie". >> Your second problem sounds like part of the image is corrupted and >> that is most likely a graphics driver problem causing the saved >> images to be wrong. You might want to try a Chimera daily build >> instead of the Chimera 1.4.1 production release because the daily >> builds use a different image capture method that may work better on >> your machine. >> >> You might also look at the 2009 movie course material which is more >> up-to-date than the 2008 material. >> >> http://www.cgl.ucsf.edu/chimera/tutorials/movies09/moviemaking.html >> >> Both 2008 and 2009 materials primarily use command scripts and that >> is the recommended approach. >> >> Tom >> >> >>> Hello, >>> >>> I am fairly new to using chimera and created my first movie using >>> command line syntax. I am mostly pleased with the results, except >>> for two things: >>> (1) I used the 'movie record' option and all my commands show during >>> the movie. >>> (2) the right hand side of the image looks like 'snow'. >>> >>> I followed similar instructions to the tutorial for ligand flying >>> into unbound conformation from: >>> http://www.cgl.ucsf.edu/chimera/tutorials/movies08/moviemaking.html >>> >>> Should I be using a script instead? Is there a better way to do this? >>> >>> Thanks for any help. >>> Matt Skeels >>

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Creating movies
by Matthew Skeels 15 May '10

15 May '10

Hello, I am fairly new to using chimera and created my first movie using command line syntax. I am mostly pleased with the results, except for two things: (1) I used the 'movie record' option and all my commands show during the movie. (2) the right hand side of the image looks like 'snow'. I followed similar instructions to the tutorial for ligand flying into unbound conformation from: http://www.cgl.ucsf.edu/chimera/tutorials/movies08/moviemaking.html Should I be using a script instead? Is there a better way to do this? Thanks for any help. Matt Skeels

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Energy Minimization
by Eric Pettersen 13 May '10

13 May '10

Dear All, Using Minimize command, I can minimize the the energy of the protein. But is there a way by which I can check the energy the protein before I perform the minimization and after minimization or least after minimization. Thanks and Regards Monisha (originally sent to chimera-bugs)

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Solvate RNA-protein Complex
by Andrew Tran 12 May '10

12 May '10

Hi Chimera support, I am trying to analyze a protein-RNA complex and would like to neutralize the phosphate backbone with ions and solvate the complex. When I try to do this using Chimera (through AMBERtools?), the complex dissociates. Is there a way to add ions and solvate without dissociation of the complex? Andrew Tran Brown University Biochemistry and Molecular Biology

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error
by zxd 11 May '10

11 May '10

Hi, I'm helping Chinese Academy of Sciences test 3D Stereo display with your Chimera-1.4.1. We are using the Samsung Syncmaster 2233 monitor, Nvidia 3D Vision kit (transmitter plus glasses). I'm able to open the software. When I select, tools->camera->sequential stereo, the application will enounter an error and exit. Attached are the snapshots of the error message and details of our computer. Xiaodong Zhao 2010-05-11 zxd

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Chimera failed abnormally
by emirate14 10 May '10

10 May '10

Hi, I've downloaded the chimera-1.4.1-win32.I am succeeded to run it for several times. However, the program had a error named as "Chimera failed abnormally; the exit code was: 1. use the --debug command line option for the full error message." and I can not start it anymore (same as Johan Börjesson, http://www.cgl.ucsf.edu/pipermail/chimera-users/2005-November/000578.html) I notice there is a note in debug box "Type=screen distance must be positive", does it cause the problem? I am looking forward to your reply. Thank you very much. Best regards . Qian Wang Zhejiang University, Hangzhou, China

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ksdssp assignments
by Tom Duncan 10 May '10

10 May '10

I noticed that the secondary structure assignments for a specific protein by ksdssp (default parameters) show a few significant differences versus the DSSP assignments shown at the PDB (file = 1aqt). Any idea why? Thanks, Tom

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