Dear Tom,

Thanks for your great help. I made my image without ray tracing, it is indeed nice too. But not as nice as ray-tracing….  J

Thanks,

Best,

Maya

From: Tom Goddard [mailto:goddard@cgl.ucsf.edu]
Sent: Wednesday, October 07, 2009 7:44 PM
To: maya shcushan
Cc: 'Chimera BB'
Subject: Re: Chimera pov-tracing question

Hi Maya,

  Your mesh is transparent in the povray image (zoom in on the image and look at the mesh lines) but I guess is much less transparent than in the Chimera window.  I ran some test images with the current Chimera 1.4 daily build which also showed the povray mesh looked much different (darker, thicker and less transparent) than in the Chimera window.  While we have improved the match between povray images and what you see in the Chimera window it is still very bad.  Dozens of messages on the chimera-users mailing list relate to the poor quality of Chimera Povray images.

http://www.google.com/search?hl=en&q=povray+site%3Awww.cgl.ucsf.edu%2Fpipermail%2Fchimera-users+-filetype%3Agz+site%3Awww.cgl.ucsf.edu%2Fpipermail%2Fchimera-users+-filetype%3Agz&aq=f&oq=&aqi=

As suggested in the following message, with these poor quality povray results a better presentation can almost always be obtained by not using povray:

http://www.cgl.ucsf.edu/pipermail/chimera-users/2009-June/004030.html

Attached are 5 test images showing some of the problems. 1mwm chain A, molmap 6 angstroms.

test.png - povray transparent mesh 0.24, appears very dark
test2.png - povray transparent mesh 0.04, black specks all over the mesh
test4.png - povray transparent surface 0.24, ugly multilayer mosaic
test5.png - no povray, transparent surf 0.24, glossy lighting, silhouette edges
test6.png - no povray, same as test5 but mesh.

    Tom


-------- Original Message --------
Subject: Chimera pov-tracing question
From: maya shcushan
To: 'Thomas Goddard'
Date: 10/7/09 9:59 AM

Dear Dr Goddard,

You previously assisted me with other problems with Chimera, so now I am asking your help again.

I have a density map and a structure mapped on it. I showed the map as transparent mesh, and tried to pov-ray the image. However, the picture came up with the map not transparent (attached). Do you have any idea how to resolve this issue, making the map transparent in the image as it is in the main window

Thanks,

Best,

Maya Schushan

Department of Biochemistry

George S. Wise Faculty of Life Sciences
Tel Aviv University