Elaine Meng wrote: Hi Daniel, Currently to make the color zone transparent, you have to make the atoms defining the zone transparent, see: http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-January/002249.html Best, Elaine Hi Daniel, Me again. I guess you were mainly asking about the part of the surface not within the zone distance. With a volume surface, I was able to separately control the transparency and color of the zone and non-zone parts as follows: Select surface of interest with mouse. Use Actions... Surface... transparency... [whatever you want for the nonzone part] Color atoms that will be defining zones - could be transparent or nontransparent colors as desired. Select those atoms. Use Color Zone. Best, Elaine Daniel Wilson wrote:

Hi Tom,

yes, you are right. I find the same thing except did you notice that you now cannot turn the transparency off! You need to uncolor zone and then it will work. Likewise, when you colorzone first, then try transparency it does not work, i.e. the colorzone is preventing subsequent changes in transparency. In anycase, my issue is more with the fact that you cannot make the region you colored transparent, which is what most people are probably going to what to do since this is the but that is being highlighted,

Best regards Daniel

Tom Goddard wrote:

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Hi Daniel,

When I make a transparent surface for a volume by pressing the volume dialog color button and making opacity 0.5 and then use color zone to color part of the surface (using a PDB model), the transparent part far from the zone remains transparent. Also works if select the volume surface and use the Actions / Surface / Transparency menu then color zone. What are the exact steps you use when it fails to preserve transparency?

Tom

Daniel Wilson wrote:

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Hi Tom,

For what we want, the combination of one transparent model with one mesh is working. However, I will play around with the raytracing a few examples with povray and see if it looks better. Seems to make more sense before you invest time in a script.

The other thing I noticed is that you lose transparency on a whole volume when you color zone one region of it? or am I making something wrong? Is it not possible to have a single volume with two different colours and transparent?

Thanks for you advice and kind offer, regards Daniel