Re: [chimerax-users] transparency around the model only

[Elaine Meng]

I guess this is a session bug:  tested in UCSF ChimeraX version: 1.8.dev202401220544 (2024-01-22)

 After the 3 commands below, 

> For example, if I have atomic structure #1 fitted into map surface #2 and I want the surface within 6 Angstroms of the atoms to be transparent cyan:
> 
> color #1 cyan transparency 50
> color zone #2 near #1 distance 6
> color #1 tan transparency 0


I saved a session tzone.cxs, attached.  

tzone.cxs​

 window looked like this

Upon session restore, looks like this

> On Jan 31, 2024, at 8:54 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
> 
> Hi Dmitry,
> The only way I can think of is somewhat stupid, i.e., more trouble than it should be:
> 
> (1) make the atomic structure the transparent color that you actually want for that part of the surface
> (2) use color zone to make the surface near the atomic structure match the atomic structure (which includes its transparency)
> (3) then change the atomic structure to the nontransparent color(s) that you really want it to have
> 
> For example, if I have atomic structure #1 fitted into map surface #2 and I want the surface within 6 Angstroms of the atoms to be transparent cyan:
> 
> color #1 cyan transparency 50
> color zone #2 near #1 distance 6
> color #1 tan transparency 0
> 
> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#zone>
> 
> At first I thought I could use "select zone" instead and then just do the coloring of the nearby surface directly rather than via the atomic structure, but that seems to select the entire isosurface if any of it is within the zone.
> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/select.html#zone>
> 
> Another related command "surface zone" just does hide/show rather than coloring.
> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html#zone>
> 
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Resource for Biocomputing, Visualization, and Informatics
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
>> On Jan 31, 2024, at 2:19 AM, Dmitry Semchonok via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
>> 
>> Dear colleagues, 
>> 
>> I have a cryo-EM 3D map and model.
>> 
>> A model is fitted for only part of my cryo-EM map.
>> 
>> Is there a command to make the map transparent only where the model is fitted in?
>> 
>> Thank you.
>> 
>> Kind regards,
>> Dmitry 
> 

[Elaine Meng]

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[Elaine Meng]

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[Elaine Meng]

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[Tom Goddard]

I tried the steps you did to make this session and the session restores correctly. You saved junk.cxs first then later opened it and saved tzone.cxs, and I tried that too, still worked for me. I would need a reproducible test case to track down this bug.

Here is what I tried that worked:

open 2gbp
molmap #1 8
close #1
open 1zik
fit #1 in #2
color #1 cyan transparency 50
color zone #2 near #1 distance 6
color #1 tan transparency 0
save test2.cxs
close
open test2.cxs
color #1 salmon transparency 50
color zone #2 near #1 distance 6
color #1 tan transparency 0
save test3.cxs
close
open test3.cxs

[Elaine Meng]

Hi Tom,
I reproduced it twice, first with junk.cxs and then with tzone.cxs.  But now when I start over and do the whole thing over again, I don't have this problem.   It restores as cyan.

Yet, when I open tzone.cxs it is not cyan even though ChimeraX showed it as cyan when I saved it.  However, in agreement with your findings, when I start from tzone.cxs and giving these commands again does not show the problem.

color #1 cyan transparency 50
color zone #2 near #1 distance 6
color #1 tan transparency 0
save tzone2.cxs
close
open tzone2.cxs  

Color me confused. So I guess I can't reproduce it either, although I'm annoyed that I spent all that time reproducing it and reporting it in the first place.  I encountered it when I figured out this series of commands for Dmitry and saved the session and was surprised that when I reopened the session, it was a different color. Argh.

[Tom Goddard]

Yeah, it is frustrating. Likely there is a bug but I need a set of commands that reproduces it, the session file is not enough.