[Chimera-users] batch production of images

Tom Goddard goddard at sonic.net
Fri Apr 19 09:12:01 PDT 2013


Hi Ben,

   You can use the Mac Chimera to run a batch job rendering images.  
Just start the normal graphical Chimera, open your batch script, iconify 
Chimera, and maybe your images are ready later in the day or the next 
day.  Chimera needs to have a window on the display in order to render 
and save images using the OpenGL graphics.  So you can't log out before 
it is done.  You would use the "headless" Linux Chimera when you need 
the processing to run when you are not logged in, or you need it to run 
on a server that has no display.

   Yep, just use runCommand("copy ...") in your Python batch processing 
script to save the images.

   To get the same view point for every image I would open the first 
model and by hand get the view point you want, then undisplay that model 
(using Model Panel, or command ~modeldisp #0).  Save this session so you 
will be able to retrieve the exact view point used in the future if you 
need to create more images. Now load your Python batch processing script 
which should load a model, save an image, then close that one model, and 
iterate over all models.  All the while, the original model you opened 
by hand is still open and undisplayed.  The reason you keep it open and 
undisplayed is because as long as one model stays open Chimera keeps the 
current view point.  If you close all models, then open one, it resets 
the view to show that one.

   There is a basic primer on Chimera Python scripts in the Programmer's 
Guide that shows batch image saving

http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html

   Tom


-------- Original Message --------
Subject: [Chimera-users] batch production of images
From: Benjamin SCHWARZ
To: UCSF Chimera Mailing List
Date: 4/19/13 7:52 AM
> Dear list,
>
>     I am considering to use chimera to render (a tons of) pictures of models that I generated and issued in nice markerSet (.cmm) files.
>
> 1. If I understand well, the only way to do that is through the linux headless version, and there is no way to do that under MacOS X for the moment
>
> 2. I should then use the "copy" command. Something like : chimera --nogui --script "myscript.py"
>    where myscript.py should contain something like  "from chimera import runCommand; runCommand('copy file pipo.png')"
>
> 3. All my models were produced in a same cartesian, and I'd like to keep the orientation and "picture frame" similar for all pictures. What I mean here, is that I'd like to be able to set my camera somewhere, looking in a specified direction, which I would probably do under the chimera GUI; and then, shoot all my pictures from that point of view on a batch mode.
> How shall I do that (set a point of view for the camera and use it on a batchmode) ?
>
>            Thanks a lot again for your great job, and your constant answers
>
> 		--Ben
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