[Chimera-users] Color zone with transparency

Tom Goddard goddard at cgl.ucsf.edu
Thu Aug 14 10:27:16 PDT 2008

Elaine Meng wrote:

Hi Daniel,
Currently to make the color zone transparent, you have to make the atoms 
defining the zone transparent, see:



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.


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:
>> 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:
>>> 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

More information about the Chimera-users mailing list