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<p class="MsoNormal"><span style="font-size:11.0pt">Hi Camille,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">The coordinate files from the PDB are independent of each other and each has its own reference frame; unless a single structure contains a complex of the two proteins, any overlap or contact between them is
just a coincidence. You can use existing mutational, biophysical, genomic data, etc., to begin to make a testable prediction of the interaction, but ChimeraX is not aware of any of this.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Best wishes<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Kevin<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><b><span style="font-size:12.0pt;color:black">From:
</span></b><span style="font-size:12.0pt;color:black">Chimera-users <chimera-users-bounces@cgl.ucsf.edu> on behalf of Lake, Camille (NIH/NIAID) [C] via Chimera-users <chimera-users@cgl.ucsf.edu><br>
<b>Date: </b>Sunday, October 30, 2022 at 4:42 PM<br>
<b>To: </b>chimera-users@cgl.ucsf.edu <chimera-users@cgl.ucsf.edu><br>
<b>Subject: </b>[Chimera-users] Question regarding protein-protein interactions in ChimeraX<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:12.0pt;color:black">Hello, <o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:12.0pt;color:black">My name is Camille Lake and I have used ChimeraX to model proteins. I was wondering - if I load two completely separate proteins from PDB, what is the nature of their interaction
as shown by ChimeraX? The two proteins I'm interested in, TIM-3 (5f71) and CEACAM1 (5dzl), are predicted to interact in the literature, but if I load them separately into ChimeraX, is this predicted interaction what displays automatically? It seems that they
are, but I can't find anywhere on the web whether this is automatically done in ChimeraX. Other proteins I randomly add in generally keep far away from each other in space. <o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:12.0pt;color:black">Thank you, <o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:12.0pt;color:black">Camille<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="color:black">Camille Lake, PhD</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black">Emerging Leaders in Data Science (ORISE) Fellow</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black">National Institute of Allergy and Infectious Diseases (NIAID) - Office of Data Science and Emerging Technologies (ODSET)</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black">National Institutes of Health (NIH)</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black">5601 Fishers Lane, 6C5</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black">Rockville, MD 20871</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black">camille.lake@nih.gov</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black">301-761-7976</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black">----------------------------------------------</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:8.0pt;color:black;background:white">The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended
recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. The National Institute of Allergy and Infectious Diseases (NIAID) shall not accept liability for any statement made
that are the sender’s own and not expressly made on behalf of the NIAID by one of its representatives.</span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
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