[Chimera-users] high quality pictures for publication

Thomas Goddard goddard at cgl.ucsf.edu
Wed Jun 24 15:05:20 PDT 2009

Hi Elaine,

   I agree with your advice.  I seldom use raytracing to produce 
publication images.  I do always use glossy lighting.  Glossy lighting 
is not enabled by the publication presets as far as I know.  It has to 
be turned on separately in the Lighting panel (Tools / Viewing Controls 
/ Lighting).


Elaine Meng wrote:
> 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:
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/print.html#tips>
> 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.
> <http://www.cgl.ucsf.edu/chimera/ImageGallery/>
> <http://www.cgl.ucsf.edu/chimera/features.html>
> 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:
> <http://www.cgl.ucsf.edu/home/meng/icompare/icompare.html>
> 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 smoother
> (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:
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/raytracing.html>
> I hope this helps,
> Elaine
> -----
> 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
>                      http://www.cgl.ucsf.edu/home/meng/index.html
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