Hi Xavier, In addition to Elaine's neon suggestion, if when you save an image you change the rendering from "Chimera" to "POV-Ray" then any dashed or dotted lines will be converted into equivalent cylinders and spheres in the POV-Ray image. I've attached an image that shows how a distance looks. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Aug 1, 2014, at 10:13 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:

Dear Xavier, Thanks for your kind words!

Unfortunately I can’t report any progress in this area. We did add a “spring” style, but other than manually calculating coordinates of small spheres and cylinders and then creating them with command “shape”, my only other idea for showing dashed lines as 3D objects via Chimera is to use the “neon” command (not available on Windows). It has many options and you can even control the lighting, but it is noninteractive and the parameters are mainly specified by parameter files neon.dat and conic.dat. It can be quite labor-intensive (iterative) to get what you want. Also, it does not include text labels, ribbons, or molecular surfaces: just spheres, ball-and-stick, sticks, and backbone “tubes.” I attach an image of the Chimera window and an image made with the command:

neon -o neon.tiff -c conic.dat

with parameter files conic.dat and neon.dat both in the current Chimera working directory. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/neon.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/neon1.html>

Sorry I don’t have a better answer, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

<neon.dat><conic.dat> Chimera window: <chimera.png>

neon.tiff using the settings in neon.dat and conic.dat <neon.tiff> On Aug 1, 2014, at 6:51 AM, F.Xavier Gomis-Rüth <xgrcri@ibmb.csic.es> wrote:

...

Dear CHIMERA team, I moved from SETOR to CHIMERA for preparing nice protein structure images for publication already some time ago and am totally happy. Thre is, however, one single feature that was possible in SETOR but I still miss in CHIMERA: to draw pseudobonds as dashed sticks or small spheres. Is it be really not possible to implement this nuisance? I known Elaine negatively answered a similar question some time ago within the BB but I would herewith strike a blow for it again. Best wishes and thanks for maintaining and devloping such a fantastic program, Xavier -- <fxgr_signanew.jpg>

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A few caveats of the Povray approach: In my tests (current daily build), it always makes cylinders with the same aspect ratio regardless of whether I am showing the lines as dotted or dashed in Chimera. Also, it is hard to tell they are cylinders unless you make the linewidth fairly large. Elaine On Aug 1, 2014, at 11:28 AM, Eric Pettersen <pett@cgl.ucsf.edu> wrote:

Hi Xavier, In addition to Elaine's neon suggestion, if when you save an image you change the rendering from "Chimera" to "POV-Ray" then any dashed or dotted lines will be converted into equivalent cylinders and spheres in the POV-Ray image. I've attached an image that shows how a distance looks.

--Eric