[Chimera-users] md movie amber issue

[Elaine Meng]

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
>>> _____________________________
>>>
>>>
>>>
>>
>
>