[Chimera-users] Silhouette edges around dashed wire-style bonds
pett at cgl.ucsf.edu
Wed Dec 23 10:30:14 PST 2009
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...
UCSF Computer Graphics Lab
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.
> 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 C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the Chimera-users