Silhouette edges around dashed wire-style bonds
Hello! In some of my structures, I need dashed bonds to indicate hydrogen bonding or metal complexation. As I understand it, in order for bonds to be displayed as dashed, they need to be wire-style. I wondered if silhouette edges could also be extended to these wire-style bonds? Alternatively, could stick-style bonds possibly be displayed in a dashed fashion? Maybe as a series of cylinders, each separated by a certain distance, or eg. as a series of equally spaced small spheres. Thank you, Thomas
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
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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Unfortunately, the current silhouette edge technique doesn't work with lines. So the alternative is more likely. I've filed an enhancement request so you'll be notified when it is in the daily builds. - Greg On 12/22/2009 06:06 AM, Dipl.-Ing. Thomas Mitterfellner wrote:
Hello! In some of my structures, I need dashed bonds to indicate hydrogen bonding or metal complexation. As I understand it, in order for bonds to be displayed as dashed, they need to be wire-style. I wondered if silhouette edges could also be extended to these wire-style bonds?
Alternatively, could stick-style bonds possibly be displayed in a dashed fashion? Maybe as a series of cylinders, each separated by a certain distance, or eg. as a series of equally spaced small spheres.
Thank you,
Thomas
participants (4)
-
Dipl.-Ing. Thomas Mitterfellner -
Elaine Meng -
Eric Pettersen -
Greg Couch