[Chimera-users] high quality pictures for publication

Elaine Meng meng at cgl.ucsf.edu
Wed Jun 24 16:22:36 PDT 2009

My understanding of glossy lighting vs. increased shininess/brightness:

Glossy lighting, if available on your system, has the advantage of  
making surfaces of all kinds look smoother and shinier even at fairly  
low vertex density (and ribbons, spheres, sticks at fairly low  
subdivision quality).  However, glossy lighting is not available for  
some proportion of users.  At least in my experience, and as shown in  
the image comparisons here,

>> <http://www.cgl.ucsf.edu/home/meng/icompare/icompare.html>

you can get a just-as-nice appearance by increasing the shininess and  
brightness, but at the cost of also needing to increase the vertex  
density and subdivision quality.  That increases the triangles in the  
scene and thus computational demands.  The publication presets  
increase molecular surface vertex density, subdivision quality,  
shininess and brightness -- but they do not adjust vertex density of  
nonmolecular surfaces.  For those other surfaces, how to smooth or if  
they even can be smoothed depends on how they were created (e.g.  
volume surfaces could be subdivided and smoothed using options in the  
Volume Viewer tool) and you would have to do that separately.  At  
least for a volume surface, that is sort of like massaging the data  
and probably wouldn't be good to have a preset do automatically.  So  
another advantage of the glossy lighting is that it makes all the  
surfaces look smoother without changing the actual triangulation.

The image comparisons page mentioned above doesn't include a  
comparison of with and without glossy lighting at low vertex density/ 
subdivision quality, but users with that feature available can try it  
for themselves.


On Jun 24, 2009, at 3:05 PM, Thomas Goddard wrote:

> 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).
> 	Tom
> 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:
>> 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

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