[Chimera-users] Color zone with transparency
goddard at cgl.ucsf.edu
Thu Aug 14 10:27:16 PDT 2008
Elaine Meng wrote:
Currently to make the color zone transparent, you have to make the atoms
defining the zone transparent, see:
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
Color atoms that will be defining zones - could be transparent or
nontransparent colors as desired.
Select those atoms.
Use Color Zone.
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
> 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
> Tom Goddard wrote:
>> 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?
>> Daniel Wilson wrote:
>>> 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,
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