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Hi Tristan Croll,</div>
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I presume that you meant "match #2/H to #1/D" and "match #2/L to #1/C" instead?<br>
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See <a href="https://i.imgur.com/dXCzuIP.png" id="LPlnkOWALinkPreview">https://i.imgur.com/dXCzuIP.png</a> and
<a href="https://i.imgur.com/VbKhKCd.png" id="LPlnkOWALinkPreview_1">https://i.imgur.com/VbKhKCd.png</a><br>
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Regards,</div>
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Phung Cheng Fei<br>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Tristan Croll <tcroll@altoslabs.com><br>
<b>Sent:</b> Monday, March 27, 2023 1:10 AM<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 dir="ltr">... huh. Looking at it again, it seems to me that AlphaFold has predicted the antibody heavy chain in the light chain conformation and vice versa. If you force it to align (predicted heavy) to (experimental light) with "match #2/D to #1/H" then
all four antibody domains align reasonably well. Seems like a failure on AlphaFold's part (and one I haven't seen before).</div>
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<div dir="ltr" class="x_gmail_attr">On Sun, Mar 26, 2023 at 1:37 PM Cheng Fei Phung via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu">chimerax-users@cgl.ucsf.edu</a>> wrote:<br>
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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" id="x_m_478550025460363679LPlnk329365" target="_blank">
http://ix.io/4rRO</a> ) and <a href="https://www.rcsb.org/structure/7CR5" id="x_m_478550025460363679LPNoLPOWALinkPreview" target="_blank">
https://www.rcsb.org/structure/7CR5</a></div>
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However, as seen in <a href="https://i.imgur.com/gHL8to3.png" id="x_m_478550025460363679LPlnkOWALinkPreview_1" target="_blank">
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" id="x_m_478550025460363679LPlnkOWALinkPreview_1" target="_blank">
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" id="x_m_478550025460363679LPlnkOWALinkPreview" target="_blank">
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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