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I figured it out. Key command does that.</div>
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It did not work at the beginning; then I realized I need a newer version of ChimeraX.</div>
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Thanks,</div>
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Ibrahim</div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Moustafa, Ibrahim M. <ria2@psu.edu><br>
<b>Sent:</b> Monday, March 15, 2021 3:14 PM<br>
<b>To:</b> Tom Goddard <goddard@sonic.net>; ChimeraX Users Help <chimerax-users@cgl.ucsf.edu><br>
<b>Subject:</b> Re: [chimerax-users] radial coloring cryo map</font>
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<span style="margin:0px; font-size:12pt; background-color:rgb(255,255,255)">Hi Tom,</span>
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<div style="margin:0px; font-size:12pt; background-color:rgb(255,255,255)"> Another related question:</div>
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<div style="margin:0px; font-size:12pt; background-color:rgb(255,255,255)"> How to create a key for the color radial?</div>
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<div style="margin:0px; font-size:12pt; background-color:rgb(255,255,255)"> Thank you,</div>
<span style="margin:0px; font-size:12pt; background-color:rgb(255,255,255)"> Ibrahim</span><br>
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<div id="x_divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> Tom Goddard <goddard@sonic.net><br>
<b>Sent:</b> Monday, March 15, 2021 2:31 PM<br>
<b>To:</b> ChimeraX Users Help <chimerax-users@cgl.ucsf.edu><br>
<b>Cc:</b> Moustafa, Ibrahim M. <ria2@psu.edu><br>
<b>Subject:</b> Re: [chimerax-users] radial coloring cryo map</font>
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<div class="" style="word-wrap:break-word; line-break:after-white-space">Hi Ibrahim,
<div class=""><br class="">
</div>
<div class=""> 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).</div>
<div class=""><br class="">
</div>
<div class=""><span class="x_x_Apple-tab-span" style="white-space:pre"></span>open 7294 from emdb</div>
<div class=""><span class="x_x_Apple-tab-span" style="white-space:pre"></span>color radial #1 center #1</div>
<div class=""><br class="">
</div>
<div class="">and here I also set the coloring distant range</div>
<div class=""><br class="">
</div>
<div class=""><span class="x_x_Apple-tab-span" style="white-space:pre"></span>color radial #1 center #1 range 130,180</div>
<div class=""><br class="">
</div>
<div class="">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.</div>
<div class=""><br class="">
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<div class=""> Tom</div>
<div class=""><br class="">
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<div class="">Image with color range and center (color radial #1 center #1 range 130,180):</div>
<div class=""><img id="x_x_CEB70380-9B8F-4A9C-9426-88CE709429BF" width="356" height="328" class="" data-outlook-trace="F:2|T:2" src="cid:A71372B3-E689-4C1F-A17F-74A0A6A5657C"></div>
<div class=""><br class="">
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<div class="">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.</div>
<div class=""><br class="">
</div>
<div class=""><img id="x_x_C537E4BA-2625-4B5E-AA66-C164E6B25110" width="356" height="328" class="" data-outlook-trace="F:2|T:2" src="cid:2C2E4437-0D43-49A4-8F31-535B3F17B51C"></div>
<div class=""><br class="">
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<div class="">Image with no center specified (color radial #1):</div>
<div class=""><br class="">
</div>
<div class=""><img id="x_x_459A0E96-0195-48E4-BC7E-F1BA0FA84F3B" width="356" height="328" class="" data-outlook-trace="F:2|T:2" src="cid:E1DE6EB0-4F0D-481D-9E2F-8EEC0FAF0B89"></div>
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<div><br class="">
<blockquote type="cite" class="">
<div class="">On Mar 15, 2021, at 10:10 AM, Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" class="">meng@cgl.ucsf.edu</a>> wrote:</div>
<br class="x_x_Apple-interchange-newline">
<div class="">
<div class="">Hi Ibrahim,<br class="">
I can't give the exact command because I don't know the center of your system. The command help is here:<br class="">
<br class="">
<<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%7Cf45df84dbbf346208d7308d8e7e09008%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637514298984118302%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=Sdty62d5qs673jM32wkImJ4JUhKg%2BDXrjmbdzXRiC1E%3D&reserved=0" originalsrc="https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#distance" shash="H8dieDX0mFHZnD0CojGSRCl12tN4+joJNTfF8+UnJylmJTVh6thFkxmgRq62jZwA7lHB15roXBYdnIgJmPKHT6VHpwOABWfRJVqgM5Tccx7c6jbQA+PkfvXmWgjrPc36SDDYEQeXa4AZ2Q0WYydv07UkHO0Y7Y+lsSACNsUWGN0=" class="">https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#distance</a>><br class="">
<br class="">
So the form of the command could be something like<br class="">
<br class="">
color radial <surf-model> center <center-spec> coordinateSystem <ref-model><br class="">
<br class="">
... where ways to specify the center are:<br class="">
<br class="">
<span class="x_x_Apple-tab-span" style="white-space:pre"></span>• x,y,z (three values separated by commas only) – an arbitrary point, interpreted in scene coordinates unless a different coordinateSystem is given<br class="">
<span class="x_x_Apple-tab-span" style="white-space:pre"></span>• an atom-spec – the center of the bounding box of the specified items<br class="">
<span class="x_x_Apple-tab-span" style="white-space:pre"></span>• cofr – the current center of rotation<br class="">
<span class="x_x_Apple-tab-span" style="white-space:pre"></span>• camera – the viewer position<br class="">
<br class="">
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 class="">
<<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%7Cf45df84dbbf346208d7308d8e7e09008%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637514298984128297%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=jRIBSY9dFIl5YQZhqlLS%2FRHa%2FBNhhX%2BZ9lmHXF%2F2drQ%3D&reserved=0" originalsrc="https://rbvi.ucsf.edu/chimerax/docs/user/commands/cofr.html" shash="JCdk68gvFQzOlzktwzQ2TtMvaHVug0L4UBB/syek/1lA9xEZvZjpvsWsrarf+RGb7e2h72zrgSuc2iay28EabAKI9I/I5qk3hNNl/+IDkrDzcCtTV4IWv/r70UVQUof8+ELk5LzdwhEYX2Pn9a88ESxugMCw3OX9iM4Pb7mFKXI=" class="">https://rbvi.ucsf.edu/chimerax/docs/user/commands/cofr.html</a>><br class="">
<br class="">
I hope this helps,<br class="">
Elaine<br class="">
-----<br class="">
Elaine C. Meng, Ph.D. <br class="">
UCSF Chimera(X) team<br class="">
Department of Pharmaceutical Chemistry<br class="">
University of California, San Francisco<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
<blockquote type="cite" class="">On Mar 15, 2021, at 9:36 AM, Moustafa, Ibrahim M. <<a href="mailto:ria2@psu.edu" class="">ria2@psu.edu</a>> wrote:<br class="">
<br class="">
Dear all,<br class="">
<br class="">
I am trying to color a cryoem map radially in ChimeraX (to get something similar to surface color by radius in chimera).<br class="">
<br class="">
I used the following comand:<br class="">
<br class="">
color radial #model <br class="">
<br class="">
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 class="">
<br class="">
What is the correct command/options to do radial coloring in ChimeraX? <br class="">
<br class="">
Thanks for help,<br class="">
Ibrahim<br class="">
<br class="">
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</blockquote>
<br class="">
<br class="">
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