Hi Tom, Until Movie Recorder directly supports supersampling and assuming you are willing to assemble the frames into a movie yourself, what you can do is use the Per-Frame->Define Script menu item of MD Movie to create supersampled image frames. In the dialog that comes up choose a "Chimera commands" script and enable the "Use leading zeroes..." check box. For your script, just type in: copy file frame<FRAME>.png png supersample 5 which will produce 5x5 supersampled frames named frame0001.png (etc.). You could use 'raytrace' instead of 'supersample 5' to get ray-traced frames. The ray-tracing stuff is brand new so you might want to make one image and see how it looks (choose "Raytrace..: true " off the File->Save Image dialog) before making a bunch of frames. The issues we are aware of (and will be working on for future releases) are a zoom-factor difference between Chimera's view and the ray-traced view (which you can compensate for by over-zooming the Chimera window) and jagged self-shadowing of ribbons (i.e. as the ribbon curves away from the light source, the resulting shadow edge is jagged). Playing through the trajectory will record the frames. You may want to disable trajectory looping (the "Loop" check box next to the play buttons). Another thing is that since you're on a Mac (problem would be the same on Windows), the frames that 'copy' produces will come out in Chimera's "current directory", wherever the heck that is (possibly your home directory). Let's say you've made a folder named "frames" as a subdirectory of your home directory and you'd like the frames to be saved there. There are three approaches I can think of: 1) Use the Unix command line (Terminal.app) and launch Chimera (Chimera.app/Contents/Resources/bin/chimera) from the frames folder. If you already know how to do this, it's pretty simple. If not, you probably want to use one of the next two... 2) Instead of just giving the name "frame<FRAME>.png" in the copy command, use the full path to the folder, e.g. "/Users/tRo/frames/ frame<FRAME>.png" 3) Force Chimera to go to the frames folder. In the Chimera command line (Favorites->Command Line) type "cd /Users/tRo/frames" before doing the recording. --Eric Eric Pettersen UCSF Computer Graphics Lab pett@cgl.ucsf.edu http://www.cgl.ucsf.edu On Mar 4, 2007, at 9:30 AM, Elaine Meng wrote:
Hi Tom, Recording a movie uses the screen resolution. In contrast, image saving uses "supersampling": a bigger image is saved initially and then sampled back down to the requested size, and that gets rid of jagged edges. Currently, movie recording cannot save the image frames with supersampling, but we plan to add that in the future.
If you are recording a trajectory in MD Movie, use the "recording" feature in MD Movie. There is no advantage to using Movie Recorder (under Utilities) or the command "movie" because they use exactly the same underlying mechanism to save frames and assemble them into a movie, and are subject to identical resolution issues. All the same flags that can be used with the "movie" command can be entered in the recording dialog called from MD Movie. The difference is (as you noted) the Movie Recorder is not synchronized well with trajectory playback.
See http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/ movie.html#recording
and the "encode" options in: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/movie.html
In neither case would you have to assemble the individual frames yourself (unless you wanted to for some reason) - on Movie Recorder, clicking the "Make movie" button encodes the saved frames into a movie file.
Settings that affect the final movie appearance are Chimera window size (adjust this before saving image frames) and the encoding options mentioned above. I hope this helps, Elaine ----- 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 Mar 4, 2007, at 4:20 AM, Thomas Caulfield wrote:
Hi again Elaine,
(I) So I have a MD movie trajectory working (NAMD style, not AMBER), but my question now goes to rendering a movie. I noticed that under the MD trajectory window (which plays the frames), that the net resolution afterward is pretty low (whether I choose MPEG-1/2/4 or quicktime.mov). But when I do renderings of images the quality is amazing. (II) I also went to Utilities under tools and movie recording, where it seems some preferences are listed (like resolution etc.), but when I hit record under that option the trajectory doesn't play, so It starts taking high-resolution screenshots into a folder with the name qui*blah-1,2,3,4,... and so on. If this were to play the trajectory that would be fine, because I could use graphic converter to make a movie of that. When I tried to do it manually and the make the movie, it was better resolution, but jerky skipping tons of frames at a time.
Is there an easier way to do it in (I) and set some preference to the desired resolution (it looked all bitmappy and fuzzy by the end), rather than trying to take 1000+screeshots from method (II)?
Thanks again.
-Tom
PS I will try getting this to that other email you gave before thanks.
On Mar 3, 2007, at 1:26 PM, Elaine Meng wrote:
Hi Tom, For some reason the mail came to me and not Eric! It may be because his address was typed with a one instead of an ell (should be cgl not cg1) - but no harm, I've forwarded it to him. He will have to address the first question, but I'll tackle the other.
In single-PDB input, the frames should be indicated with MODEL and ENDMDL records. For an example, see any NMR structure in the PDB that has more than one set of coordinates (1plx is a nice small example). Best, Elaine ----- 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 Mar 3, 2007, at 1:06 AM, Thomas Caulfield wrote:
Hi Eric,
I wanted to know about using Amber prmtop with Chimera movie md traj. I used it and my initlal frame looks fine, but then it starts bouncing out of camera and back, and my final molecule looks a mess. But in VMD it looks just fine. I'd rather use Chimera for rendering since everything looks so nice in it, however I don't know why it is doing this.
I also tried using a series of PDBs instead (to circumvent this issue), but I cannot load it as a single PDB (with multiple frames in it), since the program complains there is only 1 structure in the file. I removed all END and added numbers between the files to try and get it to realize there were frames.
What can I do to fix this?
Thanks a bunch!
-Tom
_____________________________ Tom Caulfield, Ph.D. Candidate School of Chemistry & Biochemistry Cherry Emerson Bldg., RM 329 Georgia Institute of Technology Atlanta, GA 30332-0400 Harvey Laboratory: http://rumour.biology.gatech.edu _____________________________
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