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<span style="font-size:12.0pt;mso-ascii-font-family:Calibri;mso-fareast-font-family:"Times New Roman";mso-hansi-font-family:Calibri;mso-bidi-font-family:Calibri;color:black">Good morning,<o:p> </o:p></span></p>
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<span style="font-size:12.0pt;mso-ascii-font-family:Calibri;mso-fareast-font-family:"Times New Roman";mso-hansi-font-family:Calibri;mso-bidi-font-family:Calibri;color:black"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin:0in 0in 8pt;font-size:11pt;font-family:Calibri, sans-serif;margin-bottom:0in">
<span style="font-size:12.0pt;mso-ascii-font-family:Calibri;mso-fareast-font-family:"Times New Roman";mso-hansi-font-family:Calibri;mso-bidi-font-family:Calibri;color:black">I am a student intern at the Richard Scheltema Laboratory, and I am going to be continuing
with the modification of the XMAS bundle submitted to ChimeraX recently.<o:p> </o:p></span></p>
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<span style="font-size:12.0pt;mso-ascii-font-family:Calibri;mso-fareast-font-family:"Times New Roman";mso-hansi-font-family:Calibri;mso-bidi-font-family:Calibri;color:black"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin:0in 0in 8pt;font-size:11pt;font-family:Calibri, sans-serif;margin-bottom:0in">
<span style="font-size:12.0pt;mso-ascii-font-family:Calibri;mso-fareast-font-family:"Times New Roman";mso-hansi-font-family:Calibri;mso-bidi-font-family:Calibri;color:black">Right now, we are trying to extend the bundle to be able to extract specific distances
between specific amino acids for two different proteins but for a molecular dynamics simulation. Either by loading a trajectory coordinates +
<span style="mso-spacerun:yes"> </span>topology files or by using the “morph” command and then “coordset slider”.
<o:p> </o:p></span></p>
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<span style="font-size:12.0pt;mso-ascii-font-family:Calibri;mso-fareast-font-family:"Times New Roman";mso-hansi-font-family:Calibri;mso-bidi-font-family:Calibri;color:black"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin:0in 0in 8pt;font-size:11pt;font-family:Calibri, sans-serif;margin-bottom:0in">
<span style="font-size:12.0pt;mso-ascii-font-family:Calibri;mso-fareast-font-family:"Times New Roman";mso-hansi-font-family:Calibri;mso-bidi-font-family:Calibri;color:black">So, the idea would be to extract the distances between the alpha carbons, of a set
of pre-selected amino acids, in each frame of the simulation. Do you have any suggestions about any modules or methods that I should look into to extract this information in each frame? I saw there is a CooordSets class but I do not know if this would be the
right way to go about it.<o:p> </o:p></span></p>
<p class="MsoNormal" style="margin:0in 0in 8pt;font-size:11pt;font-family:Calibri, sans-serif;margin-bottom:0in">
<span style="font-size:12.0pt;mso-ascii-font-family:Calibri;mso-fareast-font-family:"Times New Roman";mso-hansi-font-family:Calibri;mso-bidi-font-family:Calibri;color:black"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin:0in 0in 8pt;font-size:11pt;font-family:Calibri, sans-serif;margin-bottom:0in">
<span style="font-size:12.0pt;mso-ascii-font-family:Calibri;mso-fareast-font-family:"Times New Roman";mso-hansi-font-family:Calibri;mso-bidi-font-family:Calibri;color:black">Kind regards,<o:p> </o:p></span></p>
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<span style="font-size:12.0pt;mso-ascii-font-family:Calibri;mso-fareast-font-family:"Times New Roman";mso-hansi-font-family:Calibri;mso-bidi-font-family:Calibri;color:black"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin:0in 0in 8pt;font-size:11pt;font-family:Calibri, sans-serif;margin-bottom:0in">
<span style="font-size:12.0pt;mso-ascii-font-family:Calibri;mso-fareast-font-family:"Times New Roman";mso-hansi-font-family:Calibri;mso-bidi-font-family:Calibri;color:black">Isabel de Moya Clark<o:p> </o:p></span></p>
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