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<p>Dear Elaine,</p>
<p><br>
</p>
<p>thanks for that fast and detailed answer. This looks doable, I hope I can make it work (:</p>
<p><br>
</p>
<p>Would it also be possible to color the residues in Chimera and save it in a way that I can open it with Chimera X?</p>
<p><br>
</p>
<p>Many thanks.<br>
</p>
<p><br>
</p>
<p>Best,</p>
<p>Claudia<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> Elaine Meng <meng@cgl.ucsf.edu><br>
<b>Sent:</b> 24 March 2020 23:35:37<br>
<b>To:</b> Bohg, Claudia<br>
<b>Cc:</b> chimerax-users@cgl.ucsf.edu<br>
<b>Subject:</b> Re: [chimerax-users] NMR CSPs</font>
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<div class="PlainText">Hi Claudia,<br>
ChimeraX doesn't yet have reading an attribute assignment file.<br>
<br>
However, you can create and assign custom attributes using the "setattr" command. You could reformat your chemical shift data into a ChimeraX command file (a text file of ChimeraX commands, with filename something.cxc) where each value is assigned in a "setattr"
command, and then simply open that file in ChimeraX to execute all the commands.<br>
<br>
<<a href="http://rbvi.ucsf.edu/chimerax/docs/user/commands/setattr.html">http://rbvi.ucsf.edu/chimerax/docs/user/commands/setattr.html</a>><br>
<<a href="http://rbvi.ucsf.edu/chimerax/docs/user/commands/usageconventions.html#cxc-files">http://rbvi.ucsf.edu/chimerax/docs/user/commands/usageconventions.html#cxc-files</a>><br>
<br>
Here is an example .cxc file that creates/assigns an attribute named "kdh" with values assigned per amino acid residue type:<br>
<<a href="http://rbvi.ucsf.edu/chimerax/docs/user/kyte-doolittle_hydrophobicity.cxc">http://rbvi.ucsf.edu/chimerax/docs/user/kyte-doolittle_hydrophobicity.cxc</a>><br>
<br>
... for example, one command in that file is<br>
<br>
setattr :asp res kdh -3.5 create t<br>
<br>
Instead of specifying residues by name like :asp you could specify by residue number, optionally including chain if you have more than one chain, e.g.
<br>
<br>
setattr /A:201 res csp 0.022 create t<br>
<br>
... repeating for all the residues to which you want to assign values. ( I assumed this is a residue attribute. You could alternatively create a per-atom attribute, see setattr manual page.)<br>
<br>
Then you can use ChimeraX command "color byattribute" to do the coloring. <br>
<<a href="http://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#byattribute">http://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#byattribute</a>><br>
<br>
However, ChimeraX does not yet have a color key. You could get fancy by making a color key in Chimera and then combining it with the image from ChimeraX as discussed in this previous post.<br>
<<a href="http://www.rbvi.ucsf.edu/pipermail/chimerax-users/2019-March/000452.html">http://www.rbvi.ucsf.edu/pipermail/chimerax-users/2019-March/000452.html</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>
> On Mar 24, 2020, at 1:12 PM, Bohg, Claudia <Bohg@fmp-berlin.de> wrote:<br>
> <br>
> Hey, <br>
> is it somehow possible to use this attribute in Chimera X?<br>
> <br>
> <a href="http://www.cgl.ucsf.edu/chimera/data/nmrcolor-nov2017/nmrcolor.html">http://www.cgl.ucsf.edu/chimera/data/nmrcolor-nov2017/nmrcolor.html</a><br>
> <br>
> Best,<br>
> Claudia<br>
<br>
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