On Nov 19, 2008, at 9:37 AM, Bagchi, Angshuman wrote:
Hi, Could you please tell me how to produce animation in chimera. Actually, I have 2 proteins and would like to represent them as they are getting docked. What I mean is that I would like to move the proteins and then show that as if they are getting docked. Can this be done with chimera? Thanks Ang
Hi Ang, Yes, it can be done. Here is how I would do it: (1) create a Chimera session that includes saved/named positions of the proteins separated and the proteins docked. (2) figure out a set of commands that does the stuff you want in your animation, which would include "reset" to gradually change from one saved position to the other; put the commands in a file. Just opening the file will execute the commands. (3) after you are happy with what the Chimera command file does, just put a "movie record" command at the top of it and a "movie encode" command at the bottom, and execute it. Now with more details: (1) Open the structures of the two proteins from two separate files so that they can be moved separately. You can "freeze" a structure by deactivating it, so that the mouse moves only the other structure: <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/mouse.html#activedef
Save at least two positions, one with the proteins separated, another with the proteins docked together, as you want them to appear in your animation. The current position is saved using the command "savepos": <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/savepos.html
You could even save multiple positions for more control over the path the proteins will take as they are "docked" in the animation. There is a nice example in the online movie-making tutorial, see the "Ligand flying into unbound conformation" section: <http://www.cgl.ucsf.edu/chimera/tutorials/movies08/moviemaking.html> Get the display how you want it: background color, ribbons, ribbon style, which atoms are shown, atom display style, colors, etc. See "tips on preparing images": <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/ print.html#tips> You might also want to add a title using 2D labels (if so, leave room for it when you save the positions). <http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/2dlabels/2d...
Save the session (File... Save session As). It will include your saved positions and any 2D labels. Now you could exit and later restart the session without losing your work. (2) You could either try out commands by typing them individually, or by putting them in a text file (named *.com or *.cmd) and repeatedly opening the file after you adjust its contents and going back to the starting position. <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/indexcommand.html#cm...
The "reset" command is used to go from one saved position to another. It can be done abruptly in one frame or gradually over a specified number of frames. See movie-related commands for links to the manual page of "reset" and other commands that can do things over a specified number of frames. Besides the "reset," you might want to do other things like translate or rotate or fade in/out 2D labels with these commands. <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/movies.html#moviecom...
There are also links to a few example movie command files on that page. (3) Once you are happy with what the script does when you open it, then you can put a "movie record" command at the top and a "movie encode" command at the bottom. See the example movie command files and the "movie" command description: <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/movie.html
I prefer this process because at the end you have a session file and a command file that allow you to either reproduce the process efficiently, or to make some small change without a lot of duplicated effort. I am told that "reset" has had some problems which were just fixed, so if you get a bad behavior using that command, try getting a recent daily build from <http://www.cgl.ucsf.edu/chimera/alpha-downloads.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@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
Hi Elaine In continuation of the process (mentioned below) I have generated the helix that needs to be added. However it seems that the helix needs to be flexed in some points to get a better fit. Can yo let me know how do that? Thanks Andy On Wed, 19 Nov 2008 10:38:37 -0800 Elaine Meng <meng@cgl.ucsf.edu> wrote:
On Nov 19, 2008, at 9:37 AM, Bagchi, Angshuman wrote:
Hi, Could you please tell me how to produce animation in chimera. Actually, I have 2 proteins and would like to represent them as they are getting docked. What I mean is that I would like to move the proteins and then show that as if they are getting docked. Can this be done with chimera? Thanks Ang
Hi Ang, Yes, it can be done. Here is how I would do it:
(1) create a Chimera session that includes saved/named positions of the proteins separated and the proteins docked.
(2) figure out a set of commands that does the stuff you want in your animation, which would include "reset" to gradually change from one saved position to the other; put the commands in a file. Just opening the file will execute the commands.
(3) after you are happy with what the Chimera command file does, just put a "movie record" command at the top of it and a "movie encode" command at the bottom, and execute it.
Now with more details:
(1) Open the structures of the two proteins from two separate files so that they can be moved separately. You can "freeze" a structure by deactivating it, so that the mouse moves only the other structure: <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/mouse.html#activedef
Save at least two positions, one with the proteins separated, another with the proteins docked together, as you want them to appear in your animation. The current position is saved using the command "savepos": <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/savepos.html
You could even save multiple positions for more control over the path the proteins will take as they are "docked" in the animation.
There is a nice example in the online movie-making tutorial, see the "Ligand flying into unbound conformation" section: <http://www.cgl.ucsf.edu/chimera/tutorials/movies08/moviemaking.html>
Get the display how you want it: background color, ribbons, ribbon style, which atoms are shown, atom display style, colors, etc. See "tips on preparing images": <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/ print.html#tips>
You might also want to add a title using 2D labels (if so, leave room for it when you save the positions). <http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/2dlabels/2d...
Save the session (File... Save session As). It will include your saved positions and any 2D labels. Now you could exit and later restart the session without losing your work.
(2) You could either try out commands by typing them individually, or by putting them in a text file (named *.com or *.cmd) and repeatedly opening the file after you adjust its contents and going back to the starting position. <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/indexcommand.html#cm...
The "reset" command is used to go from one saved position to another. It can be done abruptly in one frame or gradually over a specified number of frames. See movie-related commands for links to the manual page of "reset" and other commands that can do things over a specified number of frames. Besides the "reset," you might want to do other things like translate or rotate or fade in/out 2D labels with these commands. <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/movies.html#moviecom...
There are also links to a few example movie command files on that page.
(3) Once you are happy with what the script does when you open it, then you can put a "movie record" command at the top and a "movie encode" command at the bottom. See the example movie command files and the "movie" command description: <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/movie.html
I prefer this process because at the end you have a session file and a command file that allow you to either reproduce the process efficiently, or to make some small change without a lot of duplicated effort.
I am told that "reset" has had some problems which were just fixed, so if you get a bad behavior using that command, try getting a recent daily build from <http://www.cgl.ucsf.edu/chimera/alpha-downloads.html>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@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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Dr. Anindito Sen (Ph.D) Research Associate , Dept. of Biochemistry and Molecular Genetics University of Virginia Box 800733 Charlottesville, VA 22908
Hi Andy, Elaine's earlier mailing list messages describe how to create the new alpha helix. If you have the alpha helix as part of the atomic model and need to move it and distort it to fit the map, here are suggestions. There are only two Chimera tools I can think of that are going to be of much use for this. The first is Movement Mouse Mode (menu Tools / Movement). It allows you to select any set of atoms and move them however you want with the mouse while the other parts of the model are frozen in place. That is going to produce bad bond geometry and the Minimize Structure tool (Tools / Structure Editing) may be able to fix those if the distortions are not too great. I don't have any experience trying that on hand-moved alpha-helices so don't know how likely it is to work. The Movement Mouse Mode tool will require moving a number of different subsegments of the alpha helix to introduce a bend. There are no specialized tools in Chimera that would bend an alpha helix in a continuous way. In general Chimera capabilities to fit flexible atomic models in maps are extremely primitive. Tom Anindito Sen wrote:
Hi Elaine
In continuation of the process (mentioned below) I have generated the helix that needs to be added. However it seems that the helix needs to be flexed in some points to get a better fit. Can yo let me know how do that?
Thanks Andy
participants (3)
-
Anindito Sen -
Elaine Meng -
Tom Goddard