Hello there, I have a few technical questions about a movie I am trying to make with chimera. I have PDB files for three predicted structural elements of a larger protein whose structure my lab is resolving through cryo EM. I've converted these PDB files to MRC's of the desired resolution we are trying to obtain with the reconstruction. In an effort to produce animation which highlights structural elements of these three subdomains, I have encountered a couple difficulties translation the movie I envision through Chimera. I would like to start with the three subunits spaced across the X axis and rotating about the central y axis of each subunit. Then, one at a time, have a single unit grow and translate to the center, then while the other two subunits fade away, then return to it's original position. I've been able to script this type of motion for each of the individual subunits, but I hit a problem when I try to incorporate all three. - Is there a way to have multiple proteins roll about their own respective y axis instead of orbiting about the central y axis of the scene? - Is there a way to selectively show / hide (fade over specified number of frames) PDB's or MRC's like you can show / hide / fade text? Thank you in advance for your help. -Jared -- Jared A. Godar Graduate Student: Stewart Lab Vanderbilt University Medical Center Molecular Physiology & Biophysics Dept. Light Hall 708 Work: 615.322.7898 Fax: 615.322.7236
Hi Jared, You can make multiple models rotate about their own individual centers with the command "set independent" - I should probably add that to the movie commands list, thanks for the nudge. A related command you may also be interested in is "select" (the old function, selection for motion). Man pages for all these commands I mention can be accessed from here: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/framecommand.html We are planning to add more/better transitioning commands for movies, but Chimera is currently rather limited in that respect. If you are using Chimera commands, there are some icky ways for fading things in/out that involve repeating a command many times because a "frames" argument is not available: (1) the command "surftransparency" adjusts molecular surface (not volume surface) transparency. You can repeatedly use it to gradually make something 100% transparent. (2) the command "colordef" allows you to define your own colors and includes a transparency value. If you color something your new color, then you can repeatedly use colordef to redefine that color as more and more transparent. This would be rather painful for fading out multicolored things. The programmers among my colleagues may be able to generate Python scripts that would be much less icky. Finally, there are some experimental features of Chimera that can be downloaded separately from this page: http://www.cgl.ucsf.edu/chimera/experimental/experimental.html Look in this page for the one called "Animation Commands." I suspect it does not have everything you need, but some of these may be of interest: Vary volume data contour level. Make multiscale protein surfaces fly away radially. Smoothly change radius in icosahedral surface tool. I hope this helps, Elaine On Sep 15, 2006, at 12:56 PM, Jared Godar wrote:
Hello there, I have a few technical questions about a movie I am trying to make with chimera. I have PDB files for three predicted structural elements of a larger protein whose structure my lab is resolving through cryo EM. I've converted these PDB files to MRC's of the desired resolution we are trying to obtain with the reconstruction. In an effort to produce animation which highlights structural elements of these three subdomains, I have encountered a couple difficulties translation the movie I envision through Chimera. I would like to start with the three subunits spaced across the X axis and rotating about the central y axis of each subunit. Then, one at a time, have a single unit grow and translate to the center, then while the other two subunits fade away, then return to it's original position. I've been able to script this type of motion for each of the individual subunits, but I hit a problem when I try to incorporate all three. • Is there a way to have multiple proteins roll about their own respective y axis instead of orbiting about the central y axis of the scene? • Is there a way to selectively show / hide (fade over specified number of frames) PDB's or MRC's like you can show / hide / fade text? Thank you in advance for your help. -Jared
-- Jared A. Godar Graduate Student: Stewart Lab Vanderbilt University Medical Center Molecular Physiology & Biophysics Dept. Light Hall 708 Work: 615.322.7898 Fax: 615.322.7236_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
----- Elaine C. Meng, Ph.D. meng@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
On Sep 15, 2006, at 1:21 PM, Elaine Meng wrote:
The programmers among my colleagues may be able to generate Python scripts that would be much less icky.
If you know enough of the basics of Python to write a loop, then as Elaine pointed out these color transitions become less onerous. Also, you don't need to know the Python equivalent of every Chimera command you need, since you can: from chimera import runCommand to make the runCommand function available and then thereafter use it to execute a string with the command you want, e.g.: runCommand("open 1gcn") to open 1gcn. --Eric Eric Pettersen UCSF Computer Graphics Lab pett@cgl.ucsf.edu http://www.cgl.ucsf.edu
Hi Jared, You can use "set independent" and then "turn y 3 120" (120 steps of 3 degrees each) to rotate each model about its own center as Elaine mentioned. There is unforunately no command to face out maps or pdb models. An alternative approach to making animations in Chimera with a script and the Movie Recorder tools is to use the EMANimator extension. http://www.cgl.ucsf.edu/chimera/related/emanimator/emanimator.html This is a Chimera extension distributed by Steve Ludtke of the National Center for Macromolecular Imaging with his EMAN single particle reconstruction software. It allows you to move maps, spin them, fade them out, change surface thresholds, and control clipping. You create an animation timeline that you can play in Chimera and later save to a movie file. The main disadvantage of EMANimator is that it will not do much with PDB models. It cannot fade PDB models or control selection display of parts of those models. I'm going to add a command to the animation commands package on the Chimera experimental features page http://www.cgl.ucsf.edu/chimera/experimental/experimental.html to fade in/out maps, and if it proves easy, pdb models too. I'll send another email when that is available. Maybe later today or maybe next week. Tom
Hi Jared, I added commands to fade in and out volume surfaces, molecule models (PDB) and molecular surfaces to the experimental "animation commands" package. Documentation and the code to use with your existing Chimera is on the experimental features page toward the bottom. http://www.cgl.ucsf.edu/chimera/experimental/experimental.html Tom
participants (4)
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Elaine Meng -
Eric Pettersen -
Jared Godar -
Thomas Goddard