Thank you Elaine, The following command worked: color radial #model center cofr coordinateSystem #model Many thanks, Ibrahim ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Monday, March 15, 2021 1:10 PM To: Moustafa, Ibrahim M. <ria2@psu.edu> Cc: ChimeraX Users Help <chimerax-users@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@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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