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
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> 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> 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
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fplato.cgl.ucsf.edu%2Fmailman%2Flistinfo%2Fchimerax-users&data=04%7C01%7Cria2%40psu.edu%7C2aa4b7fefc1d4e64109e08d8e7d53457%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637514250190228328%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=3K6QRJQadaU0SdCLyEZsc7W6NtcuyR3OgFrgXmzd538%3D&reserved=0
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): 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. Image with no center specified (color radial #1):
On Mar 15, 2021, at 10:10 AM, Elaine Meng <meng@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>
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>
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
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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@sonic.net> Sent: Monday, March 15, 2021 2:31 PM To: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Cc: Moustafa, Ibrahim M. <ria2@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@cgl.ucsf.edu<mailto:meng@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@psu.edu<mailto: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 _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu<mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu<mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Tom, Another related question: How to create a key for the color radial? Thank you, Ibrahim ________________________________ From: Tom Goddard <goddard@sonic.net> Sent: Monday, March 15, 2021 2:31 PM To: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Cc: Moustafa, Ibrahim M. <ria2@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@cgl.ucsf.edu<mailto:meng@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@psu.edu<mailto: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 _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu<mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu<mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
I figured it out. Key command does that. It did not work at the beginning; then I realized I need a newer version of ChimeraX. Thanks, Ibrahim ________________________________ From: Moustafa, Ibrahim M. <ria2@psu.edu> Sent: Monday, March 15, 2021 3:14 PM To: Tom Goddard <goddard@sonic.net>; ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] radial coloring cryo map Hi Tom, Another related question: How to create a key for the color radial? Thank you, Ibrahim ________________________________ From: Tom Goddard <goddard@sonic.net> Sent: Monday, March 15, 2021 2:31 PM To: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Cc: Moustafa, Ibrahim M. <ria2@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@cgl.ucsf.edu<mailto:meng@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@psu.edu<mailto: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 _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu<mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu<mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Ibrahim, The Color Key gui was just added (so you would need to get a current daily build for that), and I have not yet written documentation. However, if you get it, it may be mostly self-explanatory. Start from menu: Tools... Depiction... Color Key. The command version was added earlier, a few weeks ago, and it has documentation as well as an example in the tutorial (linked to the image in the documentation): <https://rbvi.ucsf.edu/chimerax/docs/user/commands/key.html> 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 12:14 PM, Moustafa, Ibrahim M. <ria2@psu.edu> wrote:
Hi Tom, Another related question: How to create a key for the color radial? Thank you, Ibrahim
Thanks Elaine, Got it! Ibrahim ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Monday, March 15, 2021 3:30 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, The Color Key gui was just added (so you would need to get a current daily build for that), and I have not yet written documentation. However, if you get it, it may be mostly self-explanatory. Start from menu: Tools... Depiction... Color Key. The command version was added earlier, a few weeks ago, and it has documentation as well as an example in the tutorial (linked to the image in the documentation): <https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Fkey.html&data=04%7C01%7Cria2%40psu.edu%7C0476452bab254a86618d08d8e7e8d130%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637514334414685859%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=3NVuliTRhasmxxeSKDlUeQPDT7Lw7kORqqh4dfJA7ug%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 12:14 PM, Moustafa, Ibrahim M. <ria2@psu.edu> wrote:
Hi Tom, Another related question: How to create a key for the color radial? Thank you, Ibrahim
participants (3)
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Elaine Meng -
Moustafa, Ibrahim M. -
Tom Goddard