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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">Dear Eric,<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 had a question regarding Pseudobonds in ChimeraX. I was wondering if there is a way
to add an attribute to pseudobond. Let’s say you have a group of pseudobonds for a model, how can I add an attribute to each individual pseudobond (for example the likelihood of each pseudobond)? Also, how can I do it in a way that this attribute stays saved
in the session?<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>
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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">I hope you are having a good day,<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>
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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">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>
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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">Isabel de Moya Clark<o:p> </o:p></span></p>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Moya Clark, I.O. de (Isabel) <i.o.demoyaclark@students.uu.nl><br>
<b>Sent:</b> Tuesday, April 26, 2022 10:23<br>
<b>To:</b> ChimeraX Users Help <chimerax-users@cgl.ucsf.edu><br>
<b>Subject:</b> Re: [chimerax-users] ChimeraX - XMAS pluggin modification questions</font>
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Good morning Eric,</div>
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Thank you very much for the information. I'll take a look at it and see if I can make it work.</div>
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I hope you have a good week,</div>
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Kind regards,</div>
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<br>
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Isabel de Moya Clark</div>
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<div id="x_divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> Eric Pettersen <pett@cgl.ucsf.edu><br>
<b>Sent:</b> Monday, April 25, 2022 18:23<br>
<b>To:</b> Moya Clark, I.O. de (Isabel) <i.o.demoyaclark@students.uu.nl><br>
<b>Cc:</b> chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu><br>
<b>Subject:</b> Re: [chimerax-users] ChimeraX - XMAS pluggin modification questions</font>
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<div>Hi Isabel,
<div class=""><span class="x_x_Apple-tab-span" style="white-space:pre"></span>Yes, CoordSets are the way to go. Assuming you want to extract these distances without necessarily playing through the trajectory/morph, the plan would be:</div>
<div class=""><br class="">
</div>
<div class="">(1) Get the coordinate set IDs from the structure</div>
<div class="">(2) Loop through IDs to get coordinate sets</div>
<div class="">(3) For each set, compute the distance</div>
<div class=""><br class="">
</div>
<div class="">If your structure was in a variable named 's' and the atoms you wanted to measure the distance between were 'a1' and 'a2' then the code would be:</div>
<div class=""><br class="">
</div>
<div class="">a1_index = a1.coord_index</div>
<div class="">a2_index = a2.coord_index</div>
<div class="">from chimerax.geometry import distance</div>
<div class="">for cid in s.coordset_ids:</div>
<div class=""><span class="x_x_Apple-tab-span" style="white-space:pre"></span>cs = s.coordset(cid)</div>
<div class=""><span class="x_x_Apple-tab-span" style="white-space:pre"></span>d = distance(cs[a1_index], cs[a2_index])</div>
<div class=""><span class="x_x_Apple-tab-span" style="white-space:pre"></span><i class="">do something with the 'd' you just computed</i></div>
<div class=""><span class="" style="font-style:normal"><br class="">
</span></div>
<div class="">Glad to hear you are going to continue improving the already excellent XMAS bundle!</div>
<div class=""><br class="">
</div>
<div class="">
<div class="">--Eric</div>
<div class=""><br class="">
</div>
<div class=""><span class="x_x_Apple-tab-span" style="white-space:pre"></span>Eric Pettersen</div>
<div class=""><span class="x_x_Apple-tab-span" style="white-space:pre"></span>UCSF Computer Graphics Lab</div>
</div>
<div class=""><br class="">
<div><br class="">
<blockquote type="cite" class="">
<div class="">On Apr 25, 2022, at 3:12 AM, Moya Clark, I.O. de (Isabel) via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a>> wrote:</div>
<br class="x_x_Apple-interchange-newline">
<div class="">
<div class="x_x_elementToProof" style="font-style:normal; font-variant-caps:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none; font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt">
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<span class="" style="font-size:12pt">Good morning, </span></div>
<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
<span class="" style="font-size:12pt"> </span></div>
<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
<span class="" style="font-size:12pt">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. </span></div>
<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
<span class="" style="font-size:12pt"> </span></div>
<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
<span class="" style="font-size:12pt">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 class=""> </span>topology files or by using the “morph” command and then “coordset slider”. </span></div>
<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
<span class="" style="font-size:12pt"> </span></div>
<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
<span class="" style="font-size:12pt">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. </span></div>
<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
<span class="" style="font-size:12pt"> </span></div>
<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
<span class="" style="font-size:12pt">Kind regards, </span></div>
<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
<span class="" style="font-size:12pt"> </span></div>
<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
<span class="" style="font-size:12pt">Isabel de Moya Clark </span></div>
<br class="">
</div>
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<a href="https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users" class="" style="font-family:Helvetica; font-size:12px; font-style:normal; font-variant-caps:normal; font-weight:normal; letter-spacing:normal; orphans:auto; text-align:start; text-indent:0px; text-transform:none; white-space:normal; widows:auto; word-spacing:0px">https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</a></div>
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