Hi Bala,
For (2):  there is no way to tell Chimera to save the image for only  
part of what is shown.  Instead you need to adjust the view so that  
the window contains the same thing as you want in the image.  Then,  
with File... Save Image you can specify as many or as few pixels as  
desired (the image can be at higher, lower, or same resolution as the  
Chimera window).

If you want to specify certain pixel dimensions of the Chimera window,  
use the "windowsize" command (command "help windowsize" will show its  
manual page).

I know it is common to have one figure that is zoomed out and another  
that is a closeup in the same rotational orientation.  You can save  
positions with the "savepos" command and restore them with the "reset"  
command.  If you prefer not to use the mouse to zoom (scale) or  
translate when creating these positions because it is easy to  
accidentally change the rotation, you can use the "scale" and "move"  
commands instead.

Some of the image tutorials include saving and restoring positions.   
These are for version 1.4 (current daily build):
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/frameimages.html

<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/convergent.html

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 Apr 8, 2009, at 3:49 AM, Bala subramanian wrote:

Friends,

Kindly help me with the following queries.

1) How to output the 2drms created for a md. trajectory using MD  

movie tool.

2) Is there any way to select a square box of a particular length  

around the molecule and save the image for publication with the  

desired resolution. I have seen in the chimera archieve that window  

size can be adjusted. I am not sure if this is the right way to get  

my job done.

Thanks,

Bala

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