thanks Tom. Actually I wanted to use the cone option in the BILD format. According to the documentations there is not cone option using the Chimera command file, am i missing something? thanks again, Keren. On Nov 4, 2011, at 9:29 PM, Tom Goddard wrote:
Hi Keren,
The BILD graphics rendering in Chimera daily builds is broken. I get the same results as you where the specified color is not used and the transparency does not work.
In the Chimera 1.5.3 production release the color works but the transparency works very poorly and this is a known deficiency (although not explained in the documentation). In 1.5.3 I believe that transparency works by adding the color (red,green,blue) of your sphere multiplied by (1-transparency) to the image. This is often very wrong. For instance if you show a transparent sphere on a white background it will be invisible -- you'll just see solid white. The problem is that the stuff behind the transparent sphere is not dimmed.
I suggest giving up on BILD if transparency is important and instead use a Chimera command file. The following command will make a sphere with correct transparency.
shape sphere center 0,0,0 radius 10 color 1,0,0,0.3 modelId #0
Put it in a file with a ".cmd" suffix. If you want to make many spheres and have them be part of the same Chimera model then be sure to specify the modelId parameter. Otherwise the spheres will end up as separate Chimera models.
Tom
hello:
I am trying to use the transparency option in the bild format. it seems that: .transparency 0.3 .sphere 0 0 0 10 results in a sphere
however .color 1 0 0 .transparency 0.3 .sphere 0 0 0 10
results in a black image, it only works if transparency is set to 0.
any suggestions what i am doing wrong?
thanks, keren.