[Chimera-users] Dashed H-bond

Greg Couch gregc at cgl.ucsf.edu
Fri May 9 11:23:31 PDT 2008

POV-Ray does not support dashed lines directly.  There is a POV-Ray macro 
for dashed lines called Stippellijn described in 
that you might try.  I'll look into adding something like that to 
chimera's POV-ray 

 	Greg Couch
 	UCSF Computer Graphics Lab

On Fri, 9 May 2008, Elaine Meng wrote:

> From: Elaine Meng <meng at cgl.ucsf.edu>
> Sender: chimera-users-bounces at cgl.ucsf.edu
> To: Ibrahim Moustafa <I.moustafa at psu.edu>
> Cc: "chimera-users at cgl.ucsf.edu" <chimera-users at cgl.ucsf.edu>
> Date: Fri, 9 May 2008 09:20:07 -0700
> Subject: Re: [Chimera-users] Dashed H-bond
> Received-SPF: pass (cgl.ucsf.edu: is authenticated by a trusted
>     mechanism)
> Received-SPF: pass (cgl.ucsf.edu: is authenticated by a trusted
>     mechanism)
> 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:
> http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/raytracing.html
> 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.
> Best,
> Elaine
> -----
> 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
>                      http://www.cgl.ucsf.edu/home/meng/index.html
> 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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