[Chimera-users] Chimera frame storage director

Elaine Meng meng at cgl.ucsf.edu
Fri Aug 14 13:13:59 PDT 2009

On Aug 14, 2009, at 12:34 PM, Tom Guu wrote:

> Dear Dr. Meng,
> This is Tom Guu from Rice University.  I am using chimera to make  
> some animation for my virus structure, that I would like to present  
> at my defense ten days from today.  I encountered a problem with  
> Chimera with the image storage issues.
> I am able to make movies, but they are generally very short, last  
> for a few seconds, and the frames are generally stored at a /tmp  
> folder.  Since the /tmp folder in our computer server has quite  
> limited spaces, once I perform a more complex animation, errors  
> messages would pop up (each ppm is about 4MB and sometime that's  
> over 300 frames will fill up the tmp dictory).  I am thinking about  
> storing frame files onto an external hard drive (200-300GB), which  
> can handle many more frames.  So I go into 'movie recorder" under  
> which there is a "frame options".  I specified the dictory for  
> frames to my external dirve (also clicked on "Set Input  
> Location").  Then re-execute my command (Open, click on cmd file  
> which cotains the script), well... the frames seemed to be stored  
> at the same /tmp location (nothing was written onto my external  
> drive).  Is there a way that I can do to make the frames stored at  
> the external drive?  If the frames are stored on the external  
> drive, is it going to affect the encoding process?
> In addition, I am also trying Chimera on my windows system  
> (Vista).  I was able to excute the command (cmd files) without any  
> problem.  The molecule is spinning as it should in the chimera.  
> However, when I opened up the encoded movie, it is just a blank  
> screen (with no molecule in sight). I check the directory (also  
> another /tmp directory), and I can see the ppm files were being  
> written.  Then a screen popped up on my computer, C:\Program Files 
> \Chimera\bin\ffmpeg.exe  The screen was on for at lesat 20-30 secs,  
> then the movie is made.  However, as I said, I didn't see any movie  
> on my computer screen though  I did find the "help command" and I  
> am currently don't seem to be able to find the answers to my  
> problems.  Any suggestion?
> Thanks for such a long email.  I much appreciate your help.
> Regards,
> Tom

Hi Tom,
If you are using the movie command to record the movie, you should  
use the movie command options to specify the directory (for example,  
a command something like "movie record directory my-directory-path").

The "frame options" in the Movie Recorder graphical interface only  
affect recording with that graphical interface, not with the  
command.  However, if you *are* using the Movie Recorder to record  
and it seems to be ignoring your setting, please use "Help... Report  
a Bug" in the Chimera menu to send us a problem report.  Include a  
description, and if you want feedback, your email address.

I am not sure I understand your second issue.  All I can say is that  
even though a movie file may appear, it takes a while for the ffmpeg  
program to fully create it, so you have to be patient and wait until  
ffmpeg is done before you can open the movie and play it back.  Was  
the movie OK after ffmpeg was done?  If not, again you may want to  
use "Help... Report a Bug" and include any relevant information.   
This mechanism also allows files to be attached to the report.

Besides "help command" for commands (for example, "help movie" to see  
your local copy of the URL given above), the Chimera Help menu  
provides several routes into the documentation (including "Help...  
Search documentation") and you can click the Help button on most  
dialogs to see the corresponding manual pages.

For future reference, it is better to send Chimera questions to  
chimera-users at cgl.ucsf.edu than to me personally, unless you are  
including private data.  This allows others to benefit from the  
information, and other staff to answer your question if I am  
unavailable or don't know the answer.

Best wishes for success and triumph at your defense!
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

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