<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=Windows-1252">
<style type="text/css" style="display:none;"> P {margin-top:0;margin-bottom:0;} </style>
</head>
<body dir="ltr">
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
Thank you Elaine,</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
The following command worked:</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
color radial #model center cofr coordinateSystem #model</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
Many thanks,</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
Ibrahim</div>
<div id="appendonsend"></div>
<hr style="display:inline-block;width:98%" tabindex="-1">
<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Elaine Meng <meng@cgl.ucsf.edu><br>
<b>Sent:</b> Monday, March 15, 2021 1:10 PM<br>
<b>To:</b> Moustafa, Ibrahim M. <ria2@psu.edu><br>
<b>Cc:</b> ChimeraX Users Help <chimerax-users@cgl.ucsf.edu><br>
<b>Subject:</b> Re: [chimerax-users] radial coloring cryo map</font>
<div> </div>
</div>
<div class="BodyFragment"><font size="2"><span style="font-size:11pt;">
<div class="PlainText">Hi Ibrahim,<br>
I can't give the exact command because I don't know the center of your system. The command help is here:<br>
<br>
<<a href="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">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</a>><br>
<br>
So the form of the command could be something like<br>
<br>
color radial <surf-model> center <center-spec> coordinateSystem <ref-model><br>
<br>
... where ways to specify the center are:<br>
<br>
• x,y,z (three values separated by commas only) – an arbitrary point, interpreted in scene coordinates unless a different coordinateSystem is given<br>
• an atom-spec – the center of the bounding box of the specified items<br>
• cofr – the current center of rotation<br>
• camera – the viewer position<br>
<br>
None of those are the same as center of screen, unless you are using the center-of-rotation method that tracks center of view:<br>
<<a href="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">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</a>><br>
<br>
I hope this helps,<br>
Elaine<br>
-----<br>
Elaine C. Meng, Ph.D. <br>
UCSF Chimera(X) team<br>
Department of Pharmaceutical Chemistry<br>
University of California, San Francisco<br>
<br>
<br>
<br>
<br>
> On Mar 15, 2021, at 9:36 AM, Moustafa, Ibrahim M. <ria2@psu.edu> wrote:<br>
> <br>
> Dear all,<br>
> <br>
> I am trying to color a cryoem map radially in ChimeraX (to get something similar to surface color by radius in chimera).<br>
> <br>
> I used the following comand:<br>
> <br>
> color radial #model <br>
> <br>
> 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.
<br>
> <br>
> What is the correct command/options to do radial coloring in ChimeraX? <br>
> <br>
> Thanks for help,<br>
> Ibrahim<br>
> <br>
> _______________________________________________<br>
> ChimeraX-users mailing list<br>
> ChimeraX-users@cgl.ucsf.edu<br>
> Manage subscription:<br>
> <a href="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">
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</a><br>
<br>
</div>
</span></font></div>
</body>
</html>