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<p class="MsoNormal"><span style="font-size:11.0pt">Hi there,<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">I’m having some issues loading the PAE JSON file from a recent AlphaFold multimer prediction into ChimeraX, generated using a Colab notebook. The warning message is as follows:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><i><span style="font-size:11.0pt">JSON file "./predicted_aligned_error.json" is not AlphaFold predicted aligned error data, expected a dictionary with keys "residue1", "residue2" and "distance"<o:p></o:p></span></i></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">It appears that AlphaFold reduced their JSON file size by 4X on July 28<sup>th</sup> 2022 (<a href="https://alphafold.ebi.ac.uk/faq">https://alphafold.ebi.ac.uk/faq</a>) and it no longer uses “distances”,
“residue 1” and “residue 2” keys.<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">Just curious, will there be an update coming to ChimeraX to support the new JSON file format from AlphaFold?<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">Thanks for your time!<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,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Brandon<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
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