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 ³POV true² 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 -- Ibrahim M. Moustafa, Ph.D. Biochemistry and Molecular Biology Dept. 201 Althouse Lab., University Park, Pennsylvania State University PA 16802 Tel. (814) 863-8703 Fax (814) 865-7927
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@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
POV-Ray does not support dashed lines directly. There is a POV-Ray macro for dashed lines called Stippellijn described in <http://www.stack.nl/~brian/LookingAtNothing_WordPress/wp-content/uploads/2007/08/povray_workshop_snippets.pdf> that you might try. I'll look into adding something like that to chimera's POV-ray output. Greg Couch UCSF Computer Graphics Lab On Fri, 9 May 2008, Elaine Meng wrote:
From: Elaine Meng <meng@cgl.ucsf.edu> Sender: chimera-users-bounces@cgl.ucsf.edu To: Ibrahim Moustafa <I.moustafa@psu.edu> Cc: "chimera-users@cgl.ucsf.edu" <chimera-users@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: 169.230.27.3 is authenticated by a trusted mechanism) Received-SPF: pass (cgl.ucsf.edu: 169.230.27.3 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@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
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
Dashed line support for POV-Ray will be in the next successful daily build. - Greg On Fri, 9 May 2008, Greg Couch wrote:
POV-Ray does not support dashed lines directly. There is a POV-Ray macro for dashed lines called Stippellijn described in <http://www.stack.nl/~brian/LookingAtNothing_WordPress/wp-content/uploads/2007/08/povray_workshop_snippets.pdf> that you might try. I'll look into adding something like that to chimera's POV-ray output.
Greg Couch UCSF Computer Graphics Lab
participants (3)
-
Elaine Meng -
Greg Couch -
Ibrahim Moustafa