[Chimera-users] md movie amber issue

Eric Pettersen pett at cgl.ucsf.edu
Mon Mar 5 11:58:37 PST 2007

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  
	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/ 
	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 Pettersen
                         UCSF Computer Graphics Lab
                         pett at 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 at 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 at 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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