[Chimera-users] high quality pictures for publication

Elaine Meng meng at cgl.ucsf.edu
Wed Jun 24 12:47:06 PDT 2009

Dear Fabian,
For publication images, to some extent different people will prefer  
different things.  I will describe what I think is important, but keep  
in mind others may have artistic differences!  The User's Guide  
includes a more comprehensive "image tips" page, also available by  
clicking the Tips button on the image-saving dialog:

It seems like many people think POV-Ray is always the fancier/better  
option, whereas the Chimera rendering without raytracing only has the  
advantage of being faster.  I disagree.  For my own presentation/ 
publication images, I always use the Chimera rendering as I can get  
much better results that way.  This may be due in part to my lack of  
expertise with POV-Ray, but it is also because there are options only  
available with the Chimera rendering, and because the shadows from  
raytracing tend to add to the complexity of an image and make it  
harder to understand.  Of course, the faster turnaround and somewhat  
more WYSIWYG nature of the Chimera rendering also helps in making  
nicer images.  Most of the Chimera images in the gallery and all  
currently in the feature highlights page were made directly in  
Chimera, without raytracing.

For images primarily containing opaque molecular surfaces, I would use  
Chimera (non-raytraced) rendering with settings:  white background,  
increase molecular surface vertex density to 10, turn off depth  
cueing, turn on sihouette edges, and either use glossy lighting, or if  
that is not available on your computer, increase the shininess and  
brightness parameters.

  ** If you simply use the publication preset #1 or #2 (see Preset  
menu) it will do all of the above for you! **

Example image from using publication preset #1 is attached at the  
bottom of this message.  Just now, I also made a page with more images  
showing the settings being changed individually:

However, let's say you have decided to use raytracing because you want  
shadows.  My suggestions for raytracing surfaces would be:

(a) increase molecular surface vertex density to make the surface  
(b) if white background, make the surface some other color (silhouette  
edges would better demarcate the boundary, but they are not available  
with raytracing)
(c) for faster rendering increase the POV-Ray Option "antialias  
threshold" from the default of 0.3 to at least 0.5, but 1.0 or even  
higher may still look as good and be much faster
(d) if shadows are too dark, try decreasing the "key-to-fill" ratio in  
Lighting.  Your shadows look much darker than what I got when  
raytracing today with the default ratio of 2.0.  The default used to  
be higher, but that was a long time ago (changed before production  
release 1.2540 July 2008).
(e) if shadows are in the wrong place, try moving the "key" light  
position in Lighting
The latter two as well as quick shadow location previewing are  
mentioned in the raytracing page:

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

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