[Chimera-users] Nice postscript output from chimera.

J B Procter procter at zbh.uni-hamburg.de
Sat Jun 26 09:58:49 PDT 2004

On Fri, 25 Jun 2004, Greg Couch <gregc at cgl.ucsf.edu> wrote:

> Just to be clear, the answer is no.  PostScript's imaging model does

This was what I thought - I had to ask just in case I'd missed some
buried extension in the tool menu.

> ...
> the image data for that resolution, so there is no advantage in the
> general case.

Certainly true - and chimera rendering works fine when you use the
file->save image.. function.  The difference between molscript and
chimera output is in the simplicity of molscript's ribbon diagrams,
which are very familiar representations, and make for very efficient
postscript. It is not that chimera can't do this, but that one has to
set up the styles carefully. 

> What aspect of the MolScript diagram do you really want?  

The only real difference is in the ribbon representations, as was
pointed out by Elain Meng (thanks!), where molscript has an inner and
outer ribbon style. For publication, I would use chimera's rounded
ribbons, which seem to give a better impression of depth than the
default single-plane ribbon. Its probable that the molscript model gives
a similar effect by using distinct inner/outer shadings.

> Generating 
> molscript input for a single molecule looks like it would be fairly
> easy, so you could use chimera as an interactive version of the
> MolAuto program. A python script that generate MolScript input from
> the current chimera state would be a welcome contribution.  :-) 

That is what I was getting at when I asked the question !  Chimera
already does much more than molscript, but generating molscript
diagrams would be a great extension. If I don't get around to it myself,
the main steps involved in doing this would be:

 - resolving coordinate file paths (or writing temporary files)
 - transforming the translation and rotation matrices  
 - translating the per-residue(and perhaps per-atom) styles 
   to molauto commands.  
 - forking the molauto|molscript process and either handling
   errors or putting the postscript where the user suggested.


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