[chimerax-users] radial coloring cryo map

[Moustafa, Ibrahim M.]

Thank you Elaine,

  The following command worked:

color radial #model center cofr coordinateSystem #model

  Many thanks,
   Ibrahim
________________________________
From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: Monday, March 15, 2021 1:10 PM
To: Moustafa, Ibrahim M. <ria2 at psu.edu>
Cc: ChimeraX Users Help <chimerax-users at cgl.ucsf.edu>
Subject: Re: [chimerax-users] radial coloring cryo map

Hi Ibrahim,
I can't give the exact command because I don't know the center of your system.  The command help is here:

<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Fcolor.html%23distance&data=04%7C01%7Cria2%40psu.edu%7C2aa4b7fefc1d4e64109e08d8e7d53457%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637514250190228328%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=EnE24w7oY%2BDC10GZfgaUVLCdQtKGAcCNs%2F0qp1Dmcn8%3D&reserved=0>

So the form of the command could be something like

color radial <surf-model> center <center-spec> coordinateSystem <ref-model>

... where ways to specify the center are:

        • x,y,z (three values separated by commas only) – an arbitrary point, interpreted in scene coordinates unless a different coordinateSystem is given
        • an atom-spec – the center of the bounding box of the specified items
        • cofr – the current center of rotation
        • camera – the viewer position

None of those are the same as center of screen, unless you are using the center-of-rotation method that tracks center of view:
<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Fcofr.html&data=04%7C01%7Cria2%40psu.edu%7C2aa4b7fefc1d4e64109e08d8e7d53457%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637514250190228328%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=eSAV6P64zVtRsYXOmGVekX3a4Ojb39D5WoFsrJVKIyc%3D&reserved=0>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco




> On Mar 15, 2021, at 9:36 AM, Moustafa, Ibrahim M. <ria2 at psu.edu> wrote:
>
> Dear all,
>
>   I am trying to color a cryoem map radially in ChimeraX (to get something similar to surface color by radius in chimera).
>
> I used the following comand:
>
> color radial #model
>
>  However, the map is colored from one side to the other instead of radial coloring starting from the center. I tried to specify the center of the screen as 0,0,0 but that did not help.
>
>     What is the correct command/options to do radial coloring in ChimeraX?
>
>   Thanks for help,
>   Ibrahim
>
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