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

[Eric Pettersen]

Unfortunately another issue is that neon knows nothing about metal- 
coordination pseudobonds and will not depict them.  So you would have  
to put distance monitors wherever you want dashed lines...

--Eric

                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         http://www.cgl.ucsf.edu

On Dec 23, 2009, at 10:03 AM, Elaine Meng wrote:

> 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
>
> <image1.png><image.tiff>
>
>
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