id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
14511	Re: [chimerax-users] transparency around the model only	Elaine Meng	Tom Goddard	"{{{
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.  
}}}

[attachment:""tzone.cxs""]

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 window looked like this


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[[Image(Screen Shot 2024-01-31 at 9.03.52 AM.png)]]

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Upon session restore, looks like this


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[[Image(Screen Shot 2024-01-31 at 9.04.13 AM.png)]]

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> 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 
> 


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"	defect	closed	normal		Sessions		can't reproduce						all	ChimeraX