[Chimera-users] projection view for publication

Elaine Meng meng at cgl.ucsf.edu
Thu Jul 30 11:30:48 PDT 2009

Hi Tom,
My sense is that most published images use perspective, and only  
fairly expert Chimera users are aware there is also an orthographic  
option.  In deciding what to use for your own system, is is partly  
"artistic license" and partly what you are trying to illustrate.

I used perspective in most of my published images, but not all.   
Examples where I used orthographic:

- looking at a helix bundle end-on, I did not want the near ends to  
look so much larger than the far ends, and I did not want the bundle  
to appear splayed when it really wasn't

- I had structures side-by-side and thought that it seemed to be a  
more accurate comparison in the orthographic view. Probably they  
weren't equidistant from the center of the window, or one was taller  
or wider than the other, and I didn't want the additional (albeit  
slight) distortion of perspective

The above may sound disparaging of perspective, but it is another cue  
along with shading and depth-cueing that aids perception of the 3- 
dimensional scene -- that's why I use it in most cases.  I haven't  
used the Camera settings to magnify the perspective to any extremes  
(very large field of view would be somewhat like fish-eye), but I have  
never seen anything about perspective in journal image instructions.

Since taste factors into the decision, others may have different  

I hope this helps,
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jul 30, 2009, at 11:07 AM, Tom Duncan wrote:

> I have seen some good recent comments on settings for saving  
> publication-quality images, but I wonder if there is a general  
> preference (by users or or journals) for use of perspective versus  
> orthographic projection when generating images for publication.

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