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Apologies I attached the wrong file, </div>
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I've attached the correct file to this email. </div>
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Kind regards, </div>
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David </div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> David Leeming<br>
<b>Sent:</b> 04 May 2021 12:06<br>
<b>To:</b> chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu><br>
<b>Subject:</b> Saving name attribute</font>
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Hi, </div>
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I'm attempting to use a python script to save the names of each residue in a protein </div>
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The code I have is as follows: </div>
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<span><span style="color:#c586c0">import</span><span> chimerax, </span></span>sys</div>
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<span><span style="color:#c586c0">from</span><span> chimerax.core.commands </span><span style="color:#c586c0">import</span><span> run</span></span></div>
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<span><span>cwd = (</span><span style="color:#4ec9b0">str</span><span>(sys.argv[</span><span style="color:#b5cea8">0</span><span>][:-</span><span style="color:#b5cea8">17</span><span>]))</span></span></div>
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<span><span>prot = </span><span style="color:#ce9178">"/A"</span></span></div>
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<span><span>run(session, </span><span style="color:#ce9178">"open 3GDM"</span><span>)</span></span>
<div><span>run(session, </span><span style="color:#ce9178">"save "</span><span> + </span><span style="color:#4ec9b0">str</span><span>(cwd) + </span><span style="color:#ce9178">"/script_content/sasa/name.defattr "</span><span> + </span><span style="color:#4ec9b0">str</span><span>(prot) + </span><span style="color:#ce9178">" & protein attrName r:name format defattr"</span><span>)</span></div>
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The command being input into the command line of ChimeraX by the script is as follows: </div>
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"save [file path]/name.defattr /A & protein attrName r:name format defattr" </div>
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I've also tried using: </div>
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"<span style="background-color:rgb(255,255,255); display:inline!important">save [file path]/name.defattr attrName r:name format defattr models /A & protein" </span></div>
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However, both commands give me a file with all the residues and all the names contained within the model rather than just the chain I'm interested in. </div>
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Could you advise on how I can better use this command to save a file with the residue positions and corresponding amino acid for each residue from a single chain only? </div>
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I've attached the resultant file to this email. </div>
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Kind regards, </div>
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David </div>
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