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Hi Rudy Richardson,</div>
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I loaded your "3d_align.pdb" file on Yasara which I just installed today <br>
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How do you see "RMSD of 1.094 A over 111 aligned residues with 100.0% similarity" from
<a href="https://i.imgur.com/GI0rmEc.png" id="LPlnkOWALinkPreview">https://i.imgur.com/GI0rmEc.png</a> ?<br>
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Regards,</div>
<div style="font-family: Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);" class="elementToProof">
Phung Cheng Fei<br>
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<div id="divRplyFwdMsg" dir="ltr"><font style="font-size:11pt" face="Calibri, sans-serif" color="#000000"><b>From:</b> Rudy Richardson <rjrich@umich.edu><br>
<b>Sent:</b> Sunday, March 26, 2023 9:20 PM<br>
<b>To:</b> Cheng Fei Phung <feiphung@hotmail.com><br>
<b>Cc:</b> chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu><br>
<b>Subject:</b> Re: [chimerax-users] AlphaFold best_model.pdb could not visually overlap the input sequence using matchmaker</font>
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<div class="x_gmail_default" style="font-family:arial,sans-serif">It seems that the problem could be with trying to align each of the entire complexes. Predictive models of structures with multiple protein chains can have a difficult time with finding the correct
interactions between chains.</div>
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Have you tried the 3D alignment with each of the corresponding 3 chains? I took the A-chain of 7cr5 and did a 3D alignment with the B chain of 4rR0 using Sheba in Yasara and got a Calpha RMSD of 1.094 A over 111 aligned residues with 100.0% similarity. I have
attached a PDB file of the aligned structures.</div>
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<div class="x_gmail_default" style="font-family:arial,sans-serif">Best regards,</div>
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<div class="x_gmail_default" style="font-family:arial,sans-serif">R.J. Richardson</div>
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<div dir="ltr" class="x_gmail_attr">On Sun, Mar 26, 2023 at 8:38 AM Cheng Fei Phung via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" data-auth="NotApplicable">chimerax-users@cgl.ucsf.edu</a>> wrote:<br>
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<div class="x_msg-545654020409776840">
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Hi,</div>
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I am trying do "matchmaker #2 to #1" between colab output ( best_model.pdb which is pasted here at
<a href="http://ix.io/4rRO" data-auth="NotApplicable" id="x_m_-545654020409776840LPlnk329365">
http://ix.io/4rRO</a> ) and <a href="https://www.rcsb.org/structure/7CR5" data-auth="NotApplicable" id="x_m_-545654020409776840LPNoLPOWALinkPreview">
https://www.rcsb.org/structure/7CR5</a></div>
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However, as seen in <a href="https://i.imgur.com/gHL8to3.png" data-auth="NotApplicable" id="x_m_-545654020409776840LPlnkOWALinkPreview_1">
https://i.imgur.com/gHL8to3.png</a> , there is not really much visual overlapping since the structures are not rotated properly to match each other.<br>
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The log for doing matchmaker command is available here at <a href="https://i.imgur.com/78h5CLq.png" data-auth="NotApplicable" id="x_m_-545654020409776840LPlnkOWALinkPreview_1">
https://i.imgur.com/78h5CLq.png</a><br>
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The colab notebook is also saved as a screenshot here at <a href="https://i.imgur.com/LSTdyZe.png" data-auth="NotApplicable" id="x_m_-545654020409776840LPlnkOWALinkPreview">
https://i.imgur.com/LSTdyZe.png</a></div>
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Manually doing "turn z 1 270 model #1 center #1" or similar rotations commands also do not help.<br>
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Please advise.<br>
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Regards,</div>
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Phung Cheng Fei<br>
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