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Hi Elaine, Thank you so much, this is exactly what I was looking for; I have residues colored the way I like now. I appreciate your answer, and I will be sure to join the ChimeraX mailing list as well. Best wishes,
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Hi Elaine,</div>
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<br>
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Thank you so much, this is exactly what I was looking for; I have residues colored the way I like now. I appreciate your answer, and I will be sure to join the ChimeraX mailing list as well.</div>
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<br>
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Best wishes,</div>
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Marcell<br>
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<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, April 11, 2022 5:34 PM<br>
<b>To:</b> Zimanyi, Marcell <Marcell.Zimanyi@ucsf.edu><br>
<b>Cc:</b> chimera-users@cgl.ucsf.edu <chimera-users@cgl.ucsf.edu>; ChimeraX Users Help <chimerax-users@cgl.ucsf.edu><br>
<b>Subject:</b> Re: [Chimera-users] Chimera X color by attribute middle range value</font>
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<div class="PlainText">Hi Marcell!<br>
In ChimeraX, you can control which colors go with which values in the "palette" option of the "color byattribute" command. This option can take color/value pairs, and the "range" option is not needed in your situation (if I understand correctly). As you found,
if you only give the range, it will spread out the colors evenly. <br>
<br>
Here's an example of value,color pairs if you want to color by attribute named "blah" using dodger blue for 0.2, red for 1.0, and gold for 4.0:<br>
<br>
color byattr blah palette 0.2,dodgerblue:1.0,red:4.0,gold<br>
<br>
<<a href="https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#byattribute">https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#byattribute</a>><br>
<<a href="https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#palette-options">https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#palette-options</a>><br>
<br>
There are lots of named colors, although you could use hex codes instead if the named ones aren't quite what you want.<br>
<<a href="https://rbvi.ucsf.edu/chimerax/docs/user/commands/colornames.html">https://rbvi.ucsf.edu/chimerax/docs/user/commands/colornames.html</a>><br>
<br>
ChimeraX does not yet have a color-by-attribute GUI although that is something we would like to have eventually. The Color Key tool is just for drawing a color key to explain the coloring, but does not itself affect the structure coloring.<br>
<br>
By the way, you may be interested in the chimerax-users@cgl.ucsf.edu mailing list (CC'd on this reply) for questions/discussion specifically about ChimeraX.<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>
> On Apr 11, 2022, at 5:07 PM, Zimanyi, Marcell via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:<br>
> <br>
> Hello Chimera Community,<br>
> <br>
> I have a .defattr file where I have assigned a value to a few residues on my protein. I'd like to set the range to be 0.2, 1, and 4 so that values with 1.0 will be the middle color. I currently don't see a way to set the middle value for the range. In Chimera,
I could set the middle range value in the define attribute GUI. In Chimera X, I'm using color byattribute range 0.2,4 because the range argument will only accept two values. I see that I can bring up the color key gui, but when I change the color key I don't
see a way to update the coloring on the residues themselves.<br>
> <br>
> Could you please help me figure out how to set attribute range with 3 values as in Chimera?<br>
> <br>
> Thanks,<br>
> Marcell<br>
<br>
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