[Chimera-users] Combining ribbons and ball-n-stick using neon

Elaine Meng meng at cgl.ucsf.edu
Wed Mar 9 10:11:08 PST 2005

On Mar 8, 2005, at 3:07 PM, Todd Weaver wrote:
> Wondering if there is a way to combine ball-n-stick rendered with neon 
> and
> displaying distances as dashed lines with ribbons for other parts of 
> the
> protein. I have attached an image captured with save, all looks good 
> except
> the distances are not displayed as black lines because it has not gone
> through neon.  If I run neon the ribbons do not show up.  I would like 
> to
> have both in the final image.

Hi Todd,
I think you can accomplish everything without neon (except there will
not be shadows).  You can change the appearance of the distance monitor
by opening the Pseudobond Panel (under Tools... Inspectors), clicking 
line for the distance monitor, and then clicking "attributes" on the 
This will bring up an attributes panel in which you can change the 
length of dashes, etc.  However, you can't get rid of the number (the 
so another possibility is to create a pseudobond with PBReader (under
Tools... Utilities), and then edit that pseudobond's attributes in the 
way.  PBReader just takes an input file listing the atom pairs you want
lines drawn between.  I attach an image with one pseudobond I made this
way and one that is a distance monitor.  Of course, it's not  your same
structure.  It is pdb entry 1zik, and here is the input to PBReader I 

:27.a at nz :22.b at oe2 black

The color is optional, and you can change it in the attributes.  Other 
I did was to make the background white, and in the Effects tool, turn 
depth cuing and increase subdivision quality, but it seems like you have
a handle on those things.

Caveat:  there is currently a bug that results in compressed dashed
lines in the image you get after supersampling.  You can try making the
dashes extra long within Chimera to compensate for now.  For this image,
the dashes looked normal in Chimera but as you can see, they look more
like hashed solid lines in the image.
Hope this helps!
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

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