[Chimera-users] Dashed H-bond

Elaine Meng meng at cgl.ucsf.edu
Fri May 9 09:20:07 PDT 2008

Dear Ibraham,
That is a known problem - the result from raytracing may be different  
from the Chimera display in some ways, as listed in the Limitations  
section of this page:

This problem is "pseudobonds always shown as sticks, even if shown as  
dashed lines in Chimera"

When you save an image in Chimera without raytracing, it will match  
the display, except the resolution is whatever you specified (usually  
better than the display).  However, when you turn on raytracing (POV- 
Ray option), Chimera writes a separate file describing the display,  
and that separate file is sent to the POV-Ray program.  The  
limitations reflect what information has been written to that  
separate file.  I am guessing it should be possible to describe the  
line as dashed in the file, but we have not written the code to do  
that yet.

In the image-saving dialog, when you turn on "raytrace with POV-Ray"  
there will also be a button "POV-Ray Options" - if you click that,  
there is an option to "Keep POV-Ray input files" if you want to see  
what that separate file looks like.  It is usually quite large.  It  
gets the same name as the saved image except ending in ".pov"  If you  
know a lot about POV-Ray, you could edit the file to contain the  
information you want and run POV-Ray on it separately, but it would  
not be easy.

Currently I can only recommend turning off raytracing to show dashed  
lines.  Also, if your display has a lot of details in it, often the  
image looks better without raytracing, in my opinion.
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

On May 9, 2008, at 8:58 AM, Ibrahim Moustafa wrote:

>    Dear Chimera Team,
>   Few weeks ago I asked about how to make H-bonds with dashed line  
> style, I got your great help in that.
>   So, I can make the H-bond with the color and style I want;  
> however, when saving the image (with POV true)
>  I got the H-bond appeared with the new chosen color but not as  
> dashed line shown in the display.
>   But, if I save the image with POVray option false, I got the same  
> style shown in the display (new color and dashed line).
>   The question is why saving the image using “POV true” does not  
> give the image as it appears in the display? Again, it accepts the  
> new color but not the dashed style.
>   Thanks for your great help,
>   Ibrahim

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