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:
_____________________________







_______________________________________________
Chimera-users mailing list
Chimera-users@cgl.ucsf.edu
http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users