[chimerax-users] radial coloring cryo map

Mon Mar 15 11:42:57 PDT 2021

Thank you Tom for your reply.

Defining the center with #model worked too.

color radial #model center #model

  Just to mention, when I tried to specify the center by the exact map center it did not work as intended:

  color radial #model center x,y,z

 Ibrahim

________________________________
From: Tom Goddard <goddard at sonic.net>
Sent: Monday, March 15, 2021 2:31 PM
To: ChimeraX Users Help <chimerax-users at cgl.ucsf.edu>
Cc: Moustafa, Ibrahim M. <ria2 at psu.edu>
Subject: Re: [chimerax-users] radial coloring cryo map

Hi Ibrahim,

  The trick is to specify the center of your EM virus map which apparently is not at 0,0,0.  Here is how to tell it to use the center of the bounding box of the map surface (that might be slightly off from the true center).

open 7294 from emdb
color radial #1 center #1

and here I also set the coloring distant range

color radial #1 center #1 range 130,180

You could instead adjust your map origin so that the center of the map is at 0,0,0 using menu Tools / Volume Data / Map Coordinates and adjusting the "Origin Index" -- usually it would need to be 1/2 the map size -- for instance in the above example the map is 280 by 280 by 280 grid points so origin index 140 might put the center at 0,0,0.  But the right value might be 139.5 or even 139 -- depends on how the map reconstruction was done, which grid point it used for the center of symmetry.

  Tom

Image with color range and center (color radial #1 center #1 range 130,180):
[cid:A71372B3-E689-4C1F-A17F-74A0A6A5657C]

Image with center but no range (color radial #1 center #1) so it uses the full range from center of map to most radially distant point.

[cid:2C2E4437-0D43-49A4-8F31-535B3F17B51C]

Image with no center specified (color radial #1):

[cid:E1DE6EB0-4F0D-481D-9E2F-8EEC0FAF0B89]

On Mar 15, 2021, at 10:10 AM, Elaine Meng <meng at cgl.ucsf.edu<mailto:meng at cgl.ucsf.edu>> wrote:

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://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#distance<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%7Cf45df84dbbf346208d7308d8e7e09008%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637514298984118302%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=Sdty62d5qs673jM32wkImJ4JUhKg%2BDXrjmbdzXRiC1E%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://rbvi.ucsf.edu/chimerax/docs/user/commands/cofr.html<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%7Cf45df84dbbf346208d7308d8e7e09008%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637514298984128297%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=jRIBSY9dFIl5YQZhqlLS%2FRHa%2FBNhhX%2BZ9lmHXF%2F2drQ%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<mailto: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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