[Chimera-users] Silhouette edges around dashed wire-style bonds

[Elaine Meng]

Hi Thomas,
If you are on a non-Windows system, you could try the "neon" command  
-- this generates a static, shadowed image in which any dashed lines  
are shown as a series of short cylinders (actually more like medicine  
capsules since they have rounded ends).

The "neon" command is actually built on top of the "conic" command.   
Both make static images (not interactively rotatable) and share a  
large number of command-line options, but conic was meant to show CPK  
or spacefill, while neon extends it to showing tubes and sticks.

<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/neon.html>
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/neon1.html>
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/conic.html>
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/conic1.html>

There are several potential caveats besides the unavailability of neon  
on Windows:

- the distance value is not shown
- dashed line style (dot-dash, spacing etc.), background color,  
lighting directions etc. are not taken directly from the Chimera  
settings but specified separately...
- there are many many options for both conic and neon, and neon reads  
a "neon.dat" control file

I guess the latter is really a double-edged sword, in that it is nice  
to have so many options, but potentially time-consuming to figure out  
how to deploy them.  As a first stab you could just try the defaults,  
not specifying any options.  I attach two images of a short peptide  
with distance measurement:  image saved the normal way in Chimera and  
the result of using the command (on Mac):

neon -f tiff -o ~/Desktop/junk.tiff -s

Or, if you are on Windows it is all moot (sorry!) but perhaps other  
users would be interested.
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

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