- Chimera-users - RBVI Mailing Lists

Selecting from a surface area
by Miguel Ortiz-Lombardia 26 Jun '06

26 Jun '06

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi, I'd like to pick an area of a (msms) surface (like with a "lasso" tool) and from that area, select the atoms/residues from which it is built. I haven't found anything like this in the documentation, so I'm afraid it's not possible. Or is it? Best regards, Miguel - -- Miguel Ortiz Lombardía Centro de Investigaciones Oncológicas C/ Melchor Fernández Almagro, 3 28029 Madrid, Spain Tel. +34 912 246 900 Fax. +34 912 246 976 e-mail: molatwork(a)yahoo.es - ---------------------------------------------------------------------- Et ainsi ne pouvant faire que ce qui est juste fût fort, on a fait que ce qui est fort fût juste. Blaise Pascal, Pensées -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.1 (Darwin) iD8DBQFElFsPF6oOrDvhbQIRAiLYAJ9NHoF7sHbXJnZijo9Gfv8z9HJatQCfb9XQ 9q3hYNVjsZjVslF3Hv9+8ZU= =5dnB -----END PGP SIGNATURE-----

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Re: [Chimera-users] question
by Goel, Manisha 26 Jun '06

26 Jun '06

Hi Elaine, I too have been looking for a good protein-protein docking program, so I am jumping on the bandwagon .. Just small question regarding point 2 in the mail .. Does chimera do any minimization/optimization of the complex after we manually dock the two protein together ? Thanks a lot for your help.. Regards, -Manisha -----Original Message----- From: chimera-users-bounces(a)cgl.ucsf.edu [mailto:chimera-users-bounces@cgl.ucsf.edu] On Behalf Of Elaine Meng Sent: Monday, June 26, 2006 11:34 AM To: Jaya Bhatnagar Cc: chimera-users(a)cgl.ucsf.edu Subject: Re: [Chimera-users] question Dear Jaya, (1) Chimera will display whatever coordinates and residue names are present in the input file. It does not matter if the residues or the atoms in them are standard or not. However, you cannot define new residues to be built by Chimera with the "swapaa" or "addaa" commands. We have recently added a Build Structure tool (Structure Editing category) that lets you add arbitrary atoms and bonds to structures interactively. It is in the early stages of development, however, and is likely to change in the future. If you use this, you may want to check the bond lengths and adjust them in the "Set Bond Length" section of the Build Structure tool. The man page for Build Structure: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/ editing.html (2) Chimera does not do any automated docking. However, you can manually/interactively dock structures by moving one relative to the other (to freeze a structure and move only the others, you would uncheck its Active button in the Model Panel or its checkbox under the Command Line). The man page for the Model Panel: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html (3) I believe there is no limit on the number of amino acids present in the protein. There may be limitations due to the input file format (that is, the residue number column can only be a certain width in the input file format, usually PDB). However, in combination with use of different chain IDs this limit is quite high. For example, ribosome structures can be viewed in Chimera, although it may take a while for the structure to load. I hope this helps, Elaine On Jun 23, 2006, at 8:06 AM, Jaya Bhatnagar wrote: > Hi, > Is it possible in chimera to define a new amino acid residue? Also, > what > algorithms does it support involving docking of two proteins? And > is there > a limit on number of amino acids present in the protein? > > thanks a lot, > Jaya > > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users ----- 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 _______________________________________________ Chimera-users mailing list Chimera-users(a)cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

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Re: [Chimera-users] Chimera-users Digest, Vol 38, Issue 12
by Jonathan Hilmer 16 Jun '06

16 Jun '06

Thanks to all for the quick responses on interpolation. Here's a quick example showing what I was concerned about: arrows.bld ------------------ .color red .arrow 0 0 0 1 0 0 .color green .arrow 0 0 0 0 1 0 .color blue .arrow 0 0 0 0 0 1 ------------------ matrix2 ----------------- Model 0.0 0.505641 0.433743 -0.745785 -2.58211 -0.807506 0.542275 -0.232105 2.90884 0.303746 0.719587 0.624446 -0.194334 ----------------- matrix3 ---------------- Model 0.0 0.60158 -0.458982 0.653787 0.653219 0.190507 -0.712397 -0.675423 5.48737 0.775763 0.530872 -0.341124 0.0103466 ---------------- The first matrix is just unity. The 'reset'-based interpolation works great for going between 1 and 3 or 1 and 2 in both directions, as well as 3 to 2, but fails from 2 to 3. Since all this is new to me, I can't say for certain that this is due to gimbal lock, but that was my first guess. I haven't had the opportunity yet to try out Tom's axis-angle approach, but that should rule out any Euler problems. The other problem for me is that all my current methods are based upon a stepwise approach via commands (ungainly, but very functional when combined with shell scripts, imagemagick etc), and this is incompatible with the 'reset' interpolation. Perhaps it was misleading to mention the use of 'matrixset'. I appreciate that it is more trouble to deal with external files, but if it is not possible to easily implement the interpolation I'm looking for dynamically within Chimera's Python (due to required math libraries, etc) then I would have to hard-code the interpolation matrices into the .py script file anway, defeating the purpose. Thanks for the help: I'd love to hear about any future development in this area.

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Chimera paper virus models
by Thomas Goddard 16 Jun '06

16 Jun '06

Hi Ulrich, This week I made 5 paper virus models using the Chimera flatten icosahedron tool. You can have the images I created: http://www.cgl.ucsf.edu/home/goddard/temp/viper-gallery-jun2006/ The image files are named according to the Protein Data Bank (PDB) 4 letter id code. The page http://www.cgl.ucsf.edu/home/goddard/temp/viper-gallery-jun2006/vipergaller… shows images of the approximately 200 known virus capsids taken from the VIPER web site. http://viperdb.scripps.edu/ I added some comments to the flatten icosahedron documentation a few days ago describing "tiling" of the Chimera image to handle capsid proteins that are cut in half -- so they appear on both sides of the cut. http://www.cgl.ucsf.edu/chimera/experimental/flatten_icosahedron/flaticos.h… I printed my images on standard photopaper. The images above will need to be scaled to fit on a piece of paper. I just asked my web browser to scale them to fit when I printed. One additional note about my images -- I turned on "silhouette edges" to give the black outlines around the proteins. This is done using Chimera menu entry Tools / Viewing Controls / Effects. Tom

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Chimera movies in PowerPoint
by Thomas Goddard 16 Jun '06

16 Jun '06

Hi Xinchao, Several people have asked exactly your question of how to get a Chimera movie to play in PowerPoint on Windows without being jerky. I don't have a Windows machine to test on today but I investigated on the web and have a theory. I believe the jerky playback is because Chimera is encoding the movie using the -qscale option to the ffmpeg encoder causing variable bit rate (VBR) encoding. When you play the movie it becomes jerky because the player software does not handle the variable bit rate well -- it doesn't buffer up enough data and then can't handle the passages when alot is changing in the video. Another issue is choosing a format that PowerPoint on Windows accepts. Here are two suggestions. The first is to reencode the movie using the ffmpeg program included in Chimera: chimera/bin/ffmpeg -i mymovie.qt -f avi -vcodec msmpeg4 -b 2000 mymovie.avi This command produces an AVI file using msmpeg4 encoding at a bit rate of 2000 Kbits / sec (about 12 Mbytes / minute) from a quicktime file created by Chimera. You can increase the bit rate to get better quality or lower it to get smaller file size and worse quality. From what I read on the web Windows XP will be happy with AVI format and msmpeg4 encoding. You may find it hard to run this command unless you are familiar with running command-line programs on Windows. You could use a Windows Command Prompt window or Run Command, but you may need to provide full paths to the ffmpeg program and movie file. An alternative is to modify the Chimera Movie Recorder code chimera/share/MovieRecorder/ffmpeg_encoder.py putting comment characters (#) in front of lines 106-111: arg_list.append('-qscale') qsc = param_dict['Q_SCALE'] if qsc: arg_list.append(str(qsc)) else: arg_list.append('1') so they become # arg_list.append('-qscale') # qsc = param_dict['Q_SCALE'] # if qsc: # arg_list.append(str(qsc)) # else: # arg_list.append('1') This change is eliminating the -qscale option when Chimera runs ffmpeg to encode your movie. Instead we will explicitly request the encoding bit rate with the -b ffmpeg option. Now restart Chimera and record a movie with the Movie Recorder using "Custom" video format to select bit rate (which controls movie quality and file size). The Custom video format settings are under the Movie Options panel, swich on "Use preset video format" and select "Custom" from the Presets menu. Then set the resolution to match your Chimera window size (shown in the upper right corner of the Movie Recorder dialog, choose the encoding format and set the bit rate (in kilobits per second). If you don't make these Custom settings then Movie Recorder will use ffmpeg's standard very low bit rate of 200 kbits/second making a very low quality and small file size movie. Let me know if you found either of these suggestions to produce usable movies for PowerPoint on Windows. Then I can change Chimera Movie Recorder to make it easy to use such settings. Tom > To: goddard(a)cgl.ucsf.edu > Subject: Chimera Movie format > Date: Fri, 16 Jun 2006 15:33:52 -0400 > From: Xinchao Yu <yxinchao(a)bu.edu> > > Dear Tom: > I am a graduate student working with Dr. Christopher Akey at Boston > University. Recently, I have been trying to make some movies for large > compplexes with multiple domains. My problem is that if I use MPEG as the > output movie format, the movement can get very jerky in the movie. While I > don't have this problem with .mov format (compressed to the same extent as > the .MPEG files). But .mov file is not readily incorporated into powerpoint > presentations. Did you have similar observations? Or do you have some > suggestions concenning this problem. Thanks a lot! > > > Xinchao Yu > Department of Physiology & Biophysics > Boston University, School of Medicine > 700 Albany Str., Boston, MA, 02118 >

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matrixget/set, keyframes, and interpolation
by Jonathan Hilmer 16 Jun '06

16 Jun '06

Does anyone have experience making movies in Chimera used more advanced motions, besides the standard roll, rock, etc? My general idea is to use matrixget to output a series of matrices, interpolate them in my standard Python environment (which is related to the question from Vol 38, Issue 10), and create as output a Chimera script composed of hundreds of 'matrixset' matrices. The Python Computer Graphics Kit (http://cgkit.sourceforge.net) will give me the functions for quaternions, as would ScientificPython or pythonOpenGL, but a quick review of their documentation suggests that in any package it will be necessary to interpolate the rotation separately from the translation: obviously it would be more convenient if there is a package that can transparently interpolate the matrices as provided by Chimera. Has anyone gone through this issue before, hopefully with some tips for me? Thanks, Jonathan

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how to tell chimera to use the local python installation
by Sabuj Pattanayek 15 Jun '06

15 Jun '06

Hi, With the release of xorg-7.1.1 and mesa-6.5 I finally have direct rendering for my i855gm/i810 intel video device under linux. However I get lots of flickering of an object inside of the chimera display window when I rotate or move the object. I don't have this issue with pymol (compiled against the system python) and vmd (compiled against C/C++ opengl bindings?) or even glxgears. Perhaps I can workaround this problem by telling Chimera to use the local python installation? How is this done? Thanks, Sabuj

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saved image discoloration
by Megan Grabenauer 13 Jun '06

13 Jun '06

I've successfully used Chimera in the past to make beautiful images for publication. However I recently installed v1.2199 for Mac OS X and now whenever I try to save an image I get discolored boxes throughout the saved image. (see attached) The position of the boxes varies slightly each time. I have the image width set to 1050 pixels, 300 pixels per unit, and supersample at 3x3. Any suggestions would be appreciated. I do have an older computer, is this possibly a hardware issue? Megan

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Dock PDB into low resolution EM map.
by Puey Ounjai 12 Jun '06

12 Jun '06

Dear all, I am trying to dock atomic coordinate of a protein derived from 3D X-ray crystal (PDB format) into lower resolution (about 20-25 A resolution) EM map (BRIX, XPLOR ASCII or SITUS format) from 2D crystal. 1. Does Chimera have this kind of fitting tool (PDB to volume) or I have to fit the coordinate by hand? If chimera can do this task, Which command should I use? 2. Does Chimera have any statistical evaluation for manual fitting? 3. How can you evaluate the % matching of 2 models in Chimera? Best regards, Puey Ounjai

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Fish-eye view
by Thomas Goddard 12 Jun '06

12 Jun '06

Hi Gabe, Fish-eye would be handy for presentation images. I submitted a request for this in 2003 to the Chimera bug/feature tracking system. Unfortunately it has not seen the light of day since. But I make fish-eye images once in while. I've attached one I just made for you as a test looking inside reovirus (1ej6). The trick is to bring up the Chimera Python shell, menu entry Tools / General Controls / IDLE and type a few things: >>> c = chimera.viewer.camera >>> c.viewDistance 30.0 >>> c.screenWidth 13.0 >>> c.viewDistance = 2 >>> The parameters that control the field of view are "viewDistance" (default 30) and "screenWidth" (default 13). I think view distance means how far your face is from your screen and screen width is how wide the Chimera window is -- maybe the defaults refer to centimeters. The defaults (narrow screen and far view) give a field of view of 25 degrees. Setting viewDistance = 2 gives a field of 150 degrees. Tom > To: Thomas Goddard <goddard(a)cgl.ucsf.edu> > From: Gabriel Lander <glander(a)scripps.edu> > Subject: odd request > Date: Fri, 9 Jun 2006 13:03:11 -0700 > > Hi Thom, > The P22 paper I presented at the biophysics conference in Salt Lake > City will be published on June 23rd in Science, so when that happens > I'll send the movie I made with Chimera your way. > We actually got the cover of the issue, and I worked with a graphics > artist here at scripps to put it together using his fancy graphics > software. One thing that really made the structure very visually > striking was the implementation of a fisheye lens. Although this > feature is not scientifically very useful, it would be a great artistic > addition to Chimera. I have no idea how difficult this would ever be > to implement or if it'd be worth it, but it's just a thought. I know > you get like a million suggestions a day, so obviously this would go > somewhere in the utmost bottom list of things to do. > I've attached the mockup we made for the cover to give you an idea of > what I'm talking about. > Cheers, > -gabe > > *** removed image ***

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