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<div class="elementToProof"><span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);"><span class="x_elementToProof" style="font-size:15px;font-family:"Segoe UI", "Segoe UI Web (West European)", "Segoe UI", -apple-system, BlinkMacSystemFont, Roboto, "Helvetica Neue", sans-serif;margin:0px;color:rgb(36, 36, 36);background-color:rgb(255, 255, 255)"><span style="font-family:monospace;margin:0px;color:rgb(0, 0, 0)" class="ContentPasted0">Dear
ChimeraX developers, </span></span>
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<span style="font-family:monospace;margin:0px;color:rgb(0, 0, 0)" class="ContentPasted0">I am trying to map sequence conservation onto a protein structure. I am using ChimeraX version (version 1.4 (2022-06-03). </span></div>
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<div class="x_elementToProof" style="font-size:15px;font-family:"Segoe UI", "Segoe UI Web (West European)", "Segoe UI", -apple-system, BlinkMacSystemFont, Roboto, "Helvetica Neue", sans-serif;margin:0px;color:rgb(36, 36, 36);background-color:rgb(255, 255, 255)">
<span style="font-family:monospace;margin:0px;color:rgb(0, 0, 0)" class="ContentPasted0">For this purpose, I was trying to use a tutorial from 2014 for Chimera for Mapping Sequence Conservation onto Structures (<a href="https://www.cgl.ucsf.edu/chimera/data/tutorials/systems/outline.html" target="_blank" rel="noopener noreferrer" data-auth="NotApplicable" class="ContentPasted0" data-safelink="true" data-linkindex="0" style="margin:0px" data-loopstyle="link">Showing
Sequence Conservation in Chimera (ucsf.edu)</a>). </span></div>
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</span></div>
<div class="x_elementToProof" style="font-size:15px;font-family:"Segoe UI", "Segoe UI Web (West European)", "Segoe UI", -apple-system, BlinkMacSystemFont, Roboto, "Helvetica Neue", sans-serif;margin:0px;color:rgb(36, 36, 36);background-color:rgb(255, 255, 255)">
<span style="font-family:monospace;margin:0px;color:rgb(0, 0, 0)" class="ContentPasted0">It seems that some the tools mentioned in this tutorial are no longer available, or maybe work differently. Specifically, the tutorial's "Case 4" (calculating values outside
of </span></div>
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<span style="font-family:monospace;margin:0px;color:rgb(0, 0, 0)" class="ContentPasted0">Chimera but showing them in Chimera) has you set an attribute, and then render/color the structure based on the attribute. </span></div>
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<span style="font-family:monospace;margin:0px;color:rgb(0, 0, 0)" class="ContentPasted0">The Tools > Structure Analysis > Define attribute mentioned </span><span style="font-family:monospace;margin:0px;color:rgb(0, 0, 0)" class="ContentPasted0">in the tutorial
is no longer available. I was as able to assign values directly to structure residues in a text file and </span></div>
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<span style="font-family:monospace;margin:0px;color:rgb(0, 0, 0)" class="ContentPasted0">read it in using the command defattr instead. </span><span style="font-family:monospace;margin:0px;color:rgb(0, 0, 0)" class="ContentPasted0">The next step </span><span style="font-family:monospace;margin:0px;color:rgb(0, 0, 0)" class="ContentPasted0">would
be to use the tool Render by Attribute for coloring but I cannot find this option anymore. </span></div>
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</span></div>
<div class="x_elementToProof" style="font-size:15px;font-family:"Segoe UI", "Segoe UI Web (West European)", "Segoe UI", -apple-system, BlinkMacSystemFont, Roboto, "Helvetica Neue", sans-serif;margin:0px;color:rgb(36, 36, 36);background-color:rgb(255, 255, 255)">
<span style="font-family:monospace;margin:0px;color:rgb(0, 0, 0)" class="ContentPasted0">Is there a different command I can use for this step, or a new functionality built into ChimeraX I could use for my purpose of mapping sequence conservation onto the structure? </span></div>
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<span style="font-family:monospace;margin:0px;color:rgb(0, 0, 0)" class="ContentPasted0">One relevant point is that I already have my sequence identify values calculated from another program, and I want to import those values. </span></div>
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<span style="font-family:monospace;margin:0px;color:rgb(0, 0, 0)" class="ContentPasted0">Thank you in advance for your help, </span></div>
<span class="x_elementToProof" style="font-size:15px;font-family:"Segoe UI", "Segoe UI Web (West European)", "Segoe UI", -apple-system, BlinkMacSystemFont, Roboto, "Helvetica Neue", sans-serif;margin:0px;color:rgb(36, 36, 36);background-color:rgb(255, 255, 255)"><span style="font-family:monospace;margin:0px;color:rgb(0, 0, 0)" class="ContentPasted0">Andrea</span></span><br class="Apple-interchange-newline ContentPasted0">
<br>
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