meng at cgl.ucsf.edu
Wed Apr 8 08:01:34 PDT 2009
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
If you want to specify certain pixel dimensions of the Chimera window,
use the "windowsize" command (command "help windowsize" will show its
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"
Some of the image tutorials include saving and restoring positions.
These are for version 1.4 (current daily build):
I hope this helps,
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
On Apr 8, 2009, at 3:49 AM, Bala subramanian wrote:
> 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.
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