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<div class="elementToProof"><span style="color: rgb(0, 0, 0); font-family: monospace;">Dear ChimeraX developers, </span></div>
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<div class="elementToProof"><span style="color: rgb(0, 0, 0); font-family: monospace;">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="elementToProof"><span style="color: rgb(0, 0, 0); font-family: monospace;">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" class="" id="LPNoLPOWALinkPreview_1">Showing
Sequence Conservation in Chimera (ucsf.edu)</a>). </span></div>
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<div class="elementToProof"><span style="color: rgb(0, 0, 0); font-family: monospace;">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>
<div class="elementToProof"><span style="color: rgb(0, 0, 0); font-family: monospace;">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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<div class="elementToProof"><span style="color: rgb(0, 0, 0); font-family: monospace;">The Tools > Structure Analysis > Define attribute mentioned </span><span style="color: rgb(0, 0, 0); font-family: monospace;">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>
<div class="elementToProof"><span style="color: rgb(0, 0, 0); font-family: monospace;">read it in using the command defattr instead. </span><span style="color: rgb(0, 0, 0); font-family: monospace;">The next step </span><span style="color: rgb(0, 0, 0); font-family: monospace;">would
be to use the tool Render by Attribute for coloring but I cannot find this option anymore. </span></div>
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<div class="elementToProof"><span style="color: rgb(0, 0, 0); font-family: monospace;">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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<div class="elementToProof"><span style="color: rgb(0, 0, 0); font-family: monospace;">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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<div class="elementToProof"><span style="color: rgb(0, 0, 0); font-family: monospace;">Thank you in advance for your help, </span></div>
<div class="elementToProof"><span style="color: rgb(0, 0, 0); font-family: monospace;">Andrea</span></div>
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<pre class="ContentPasted0 ContentPasted5"><div class="_Entity _EType_OWALinkPreview _EId_OWALinkPreview _EReadonly_1"><div id="LPBorder_GTaHR0cHM6Ly93d3cuY2dsLnVjc2YuZWR1L2NoaW1lcmEvZGF0YS90dXRvcmlhbHMvc3lzdGVtcy9vdXRsaW5lLmh0bWw." class="LPBorder554139" style="width: 100%; margin-top: 16px; margin-bottom: 16px; position: relative; max-width: 800px; min-width: 424px;"><table id="LPContainer554139" role="presentation" style="padding: 12px 36px 12px 12px; width: 100%; border-width: 1px; border-style: solid; border-color: rgb(200, 200, 200); border-radius: 2px;"><tbody><tr valign="top" style="border-spacing: 0px;"><td style="width: 100%;"><div id="LPTitle554139" style="font-size: 21px; font-weight: 300; margin-right: 8px; font-family: wf_segoe-ui_light, "Segoe UI Light", "Segoe WP Light", "Segoe UI", "Segoe WP", Tahoma, Arial, sans-serif; margin-bottom: 12px;"><a target="_blank" id="LPUrlAnchor554139" href="https://www.cgl.ucsf.edu/chimera/data/tutorials/systems/outline.html" style="text-decoration: none; color: var(--themePrimary);" data-loopstyle="link">Showing
Sequence Conservation in Chimera</a></div><div id="LPDescription554139" style="font-size: 14px; max-height: 100px; color: rgb(102, 102, 102); font-family: wf_segoe-ui_normal, "Segoe UI", "Segoe WP", Tahoma, Arial, sans-serif; margin-bottom: 12px; margin-right: 8px; overflow: hidden;">Example
2B Chimera session: ConSurf-1hd2-chimera19.py [show this last!] (result of submitting 1hd2 to the ConSurf server and choosing to show results in Chimera; alignment has 150 sequences including that of the query, 1hd2) . Given a protein structure, the ConSurf
server estimates the evolutionary conservation of amino acid positions based on the phylogenetic relations between homologous ...</div><div id="LPMetadata554139" style="font-size: 14px; font-weight: 400; color: rgb(166, 166, 166); font-family: wf_segoe-ui_normal, "Segoe UI", "Segoe WP", Tahoma, Arial, sans-serif;">www.cgl.ucsf.edu</div></td></tr></tbody></table></div></div><br><h2 style="font-family:"Times New Roman";text-align:-webkit-center" class="ContentPasted1"><br></h2></pre>
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