<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
<style type="text/css" style="display:none;"> P {margin-top:0;margin-bottom:0;} </style>
</head>
<body dir="ltr">
<div style="font-family: Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);" class="elementToProof">
Hi Rudy Richardson,</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">
<br>
</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 ContentPasted1">
See <a href="http://ix.io/4rWg" id="LPlnk983933">http://ix.io/4rWg</a> PDB file for the alignment between ChimeraX colabFold output and the reference 7cr5 pdb from rcsb.</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 ContentPasted1">
<br>
</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 ContentPasted0">
As seen at the bottom right of <a href="https://i.imgur.com/sraWQY4.png" id="LPlnkOWALinkPreview">
https://i.imgur.com/sraWQY4.png</a> , there is still quite a structure mismatch which I had highlighted in gold color.</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 ContentPasted0">
<br>
</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 ContentPasted0">
Note: I have already tried MUSTANG, MMLIGNER, Smith&Waterman, and Needleman&Wunsch alignment methods.<br>
</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">
<br>
</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">
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>
</div>
<div id="appendonsend"></div>
<hr style="display:inline-block;width:98%" tabindex="-1">
<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Rudy Richardson <rjrich@umich.edu><br>
<b>Sent:</b> Monday, March 27, 2023 12:32 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>
<div> </div>
</div>
<div>
<div dir="ltr">
<div class="x_gmail_default" style="font-family:arial,sans-serif">PS: I forgot to mention -- if you already have a 3D alignment, you can go to Analyze > RMSD of, and choose Objects, Molecules, Residues, or Atoms to get corresponding RMSD values. You could also
run Analyze > Global distance test of, and choose one of the same list of structures. The YASARA documentation has explanations of these procedures.</div>
<div class="x_gmail_default" style="font-family:arial,sans-serif"><br>
</div>
<div class="x_gmail_default" style="font-family:arial,sans-serif">-- RJR</div>
</div>
<br>
<div class="x_gmail_quote">
<div dir="ltr" class="x_gmail_attr">On Sun, Mar 26, 2023 at 12:26 PM Rudy Richardson <<a href="mailto:rjrich@umich.edu">rjrich@umich.edu</a>> wrote:<br>
</div>
<blockquote class="x_gmail_quote" style="margin:0px 0px 0px 0.8ex; border-left:1px solid rgb(204,204,204); padding-left:1ex">
<div dir="ltr">
<div class="x_gmail_default" style="font-family:arial,sans-serif">Which version of YASARA do you have? If it is the free viewer, I am not sure which features are included. I have purchased a license for YASARA-Structure along with WHATIF and the NMR module.
In my version at least, when I load two structures, I can go to the Analyze > Align menu and choose from several 3D alignment programs, e.g., MUSTANG, MM Ligner, or Sheba. When the alignment is finished, the data are shown in the console.</div>
<div class="x_gmail_default" style="font-family:arial,sans-serif"><br>
</div>
<div class="x_gmail_default" style="font-family:arial,sans-serif">-- Rudy</div>
<div class="x_gmail_default" style="font-family:arial,sans-serif"><br>
</div>
</div>
<br>
<div class="x_gmail_quote">
<div dir="ltr" class="x_gmail_attr">On Sun, Mar 26, 2023 at 12:16 PM Cheng Fei Phung <<a href="mailto:feiphung@hotmail.com" target="_blank">feiphung@hotmail.com</a>> wrote:<br>
</div>
<blockquote class="x_gmail_quote" style="margin:0px 0px 0px 0.8ex; border-left:1px solid rgb(204,204,204); padding-left:1ex">
<div>
<div dir="ltr">
<div style="font-family:Calibri,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0); background-color:rgb(255,255,255)">
Hi Rudy Richardson,</div>
<div style="font-family:Calibri,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0); background-color:rgb(255,255,255)">
<br>
</div>
<div style="font-family:Calibri,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0); background-color:rgb(255,255,255)">
I loaded your "3d_align.pdb" file on Yasara which I just installed today <br>
</div>
<div style="font-family:Calibri,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0); background-color:rgb(255,255,255)">
<br>
</div>
<div style="font-family:Calibri,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0); background-color:rgb(255,255,255)">
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="x_m_-8763334932954396071m_-8018013152704150119LPlnkOWALinkPreview" target="_blank">
https://i.imgur.com/GI0rmEc.png</a> ?<br>
</div>
<div style="font-family:Calibri,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0); background-color:rgb(255,255,255)">
<br>
</div>
<div style="font-family:Calibri,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0); background-color:rgb(255,255,255)">
Regards,</div>
<div style="font-family:Calibri,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0); background-color:rgb(255,255,255)">
Phung Cheng Fei<br>
</div>
<div id="x_m_-8763334932954396071m_-8018013152704150119appendonsend"></div>
<div style="font-family:Calibri,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)">
<br>
</div>
<hr style="display:inline-block; width:98%">
<div id="x_m_-8763334932954396071m_-8018013152704150119divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> Rudy Richardson <<a href="mailto:rjrich@umich.edu" target="_blank">rjrich@umich.edu</a>><br>
<b>Sent:</b> Sunday, March 26, 2023 9:20 PM<br>
<b>To:</b> Cheng Fei Phung <<a href="mailto:feiphung@hotmail.com" target="_blank">feiphung@hotmail.com</a>><br>
<b>Cc:</b> <a href="mailto:chimerax-users@cgl.ucsf.edu" target="_blank">chimerax-users@cgl.ucsf.edu</a> <<a href="mailto:chimerax-users@cgl.ucsf.edu" target="_blank">chimerax-users@cgl.ucsf.edu</a>><br>
<b>Subject:</b> Re: [chimerax-users] AlphaFold best_model.pdb could not visually overlap the input sequence using matchmaker</font>
<div> </div>
</div>
<div>
<div dir="ltr">
<div 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>
<div style="font-family:arial,sans-serif"><br>
</div>
<div style="font-family:arial,sans-serif">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>
<div style="font-family:arial,sans-serif"><br>
</div>
<div style="font-family:arial,sans-serif">Best regards,</div>
<div style="font-family:arial,sans-serif"><br>
</div>
<div style="font-family:arial,sans-serif">R.J. Richardson</div>
<div style="font-family:arial,sans-serif"><br>
</div>
</div>
<br>
<div>
<div dir="ltr">On Sun, Mar 26, 2023 at 8:38 AM Cheng Fei Phung via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" target="_blank">chimerax-users@cgl.ucsf.edu</a>> wrote:<br>
</div>
<blockquote style="margin:0px 0px 0px 0.8ex; border-left:1px solid rgb(204,204,204); padding-left:1ex">
<div>
<div dir="ltr">
<div style="font-family:Calibri,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0); background-color:rgb(255,255,255)">
Hi,</div>
<div style="font-family:Calibri,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0); background-color:rgb(255,255,255)">
<br>
</div>
<div style="font-family:Calibri,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0); background-color:rgb(255,255,255)">
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_-8763334932954396071m_-8018013152704150119x_m_-545654020409776840LPlnk329365" target="_blank">
http://ix.io/4rRO</a> ) and <a href="https://www.rcsb.org/structure/7CR5" id="x_m_-8763334932954396071m_-8018013152704150119x_m_-545654020409776840LPNoLPOWALinkPreview" target="_blank">
https://www.rcsb.org/structure/7CR5</a></div>
<div style="font-family:Calibri,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0); background-color:rgb(255,255,255)">
<br>
</div>
<div></div>
<div style="font-family:Calibri,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0); background-color:rgb(255,255,255)">
However, as seen in <a href="https://i.imgur.com/gHL8to3.png" id="x_m_-8763334932954396071m_-8018013152704150119x_m_-545654020409776840LPlnkOWALinkPreview_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>
</div>
<div style="font-family:Calibri,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0); background-color:rgb(255,255,255)">
<br>
</div>
<div style="font-family:Calibri,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0); background-color:rgb(255,255,255)">
The log for doing matchmaker command is available here at <a href="https://i.imgur.com/78h5CLq.png" id="x_m_-8763334932954396071m_-8018013152704150119x_m_-545654020409776840LPlnkOWALinkPreview_1" target="_blank">
https://i.imgur.com/78h5CLq.png</a><br>
</div>
<div style="font-family:Calibri,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0); background-color:rgb(255,255,255)">
<br>
</div>
<div style="font-family:Calibri,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0); background-color:rgb(255,255,255)">
The colab notebook is also saved as a screenshot here at <a href="https://i.imgur.com/LSTdyZe.png" id="x_m_-8763334932954396071m_-8018013152704150119x_m_-545654020409776840LPlnkOWALinkPreview" target="_blank">
https://i.imgur.com/LSTdyZe.png</a></div>
<div style="font-family:Calibri,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0); background-color:rgb(255,255,255)">
<br>
</div>
<div style="font-family:Calibri,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0); background-color:rgb(255,255,255)">
Manually doing "turn z 1 270 model #1 center #1" or similar rotations commands also do not help.<br>
</div>
<div style="font-family:Calibri,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0); background-color:rgb(255,255,255)">
Please advise.<br>
</div>
<div style="font-family:Calibri,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0); background-color:rgb(255,255,255)">
<br>
</div>
<div style="font-family:Calibri,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0); background-color:rgb(255,255,255)">
Regards,</div>
<div style="font-family:Calibri,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0); background-color:rgb(255,255,255)">
Phung Cheng Fei<br>
</div>
</div>
_______________________________________________<br>
ChimeraX-users mailing list<br>
<a href="mailto:ChimeraX-users@cgl.ucsf.edu" target="_blank">ChimeraX-users@cgl.ucsf.edu</a><br>
Manage subscription:<br>
<a href="https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users" target="_blank">https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</a><br>
</div>
</blockquote>
</div>
</div>
</div>
</div>
</blockquote>
</div>
</blockquote>
</div>
</div>
</body>
</html>