[Chimera-users] high quality pictures for publication

Fabian Glaser fglaser at technion.ac.il
Thu Jun 25 07:05:36 PDT 2009

Thanks you all for your kind and informative answer, indeed the glossy 
representation is very nice, I wasn't aware of it.

Best regards,


Thomas Goddard said the following on 06/25/2009 01:05 AM:
> 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:
>> <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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Fabian Glaser, PhD

Bioinformatics Knowledge Unit,
The Lorry I. Lokey Interdisciplinary
Center for Life Sciences and Engineering
Technion - Israel Institute of Technology
Haifa 32000, ISRAEL

Web:   http://bku.technion.ac.il
Email: fglaser at tx.technion.ac.il
Tel:   +972-(0)4-8293701
Cel:   +972-(0)54-4772396

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