<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi Brandon,<div class=""><br class=""></div><div class=""> Yes, the latest EBI AlphaFold database release changed the format of the PAE json files on July 28 to reduce their size so the last ChimeraX release (1.4) which came out before that change in June does not know how to read them. But the ChimeraX daily build since July 29 reads them correctly. So get the daily build on the ChimeraX download page.</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Tom</div><div class=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Sep 20, 2022, at 12:47 PM, Brandon Payliss via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><meta charset="UTF-8" class=""><div class="WordSection1" style="page: WordSection1; caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><div style="margin: 0cm; font-size: 12pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 11pt;" class="">Hi there,<o:p class=""></o:p></span></div><div style="margin: 0cm; font-size: 12pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 11pt;" class=""><o:p class=""> </o:p></span></div><div style="margin: 0cm; font-size: 12pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 11pt;" class="">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 class=""></o:p></span></div><div style="margin: 0cm; font-size: 12pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 11pt;" class=""><o:p class=""> </o:p></span></div><div style="margin: 0cm; font-size: 12pt; font-family: Calibri, sans-serif;" class=""><i class=""><span style="font-size: 11pt;" class="">JSON file "./predicted_aligned_error.json" is not AlphaFold predicted aligned error data, expected a dictionary with keys "residue1", "residue2" and "distance"<o:p class=""></o:p></span></i></div><div style="margin: 0cm; font-size: 12pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 11pt;" class=""><o:p class=""> </o:p></span></div><div style="margin: 0cm; font-size: 12pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 11pt;" class="">It appears that AlphaFold reduced their JSON file size by 4X on July 28<sup class="">th</sup><span class="Apple-converted-space"> </span>2022 (<a href="https://alphafold.ebi.ac.uk/faq" style="color: rgb(5, 99, 193); text-decoration: underline;" class="">https://alphafold.ebi.ac.uk/faq</a>) and it no longer uses “distances”, “residue 1” and “residue 2” keys.<o:p class=""></o:p></span></div><div style="margin: 0cm; font-size: 12pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 11pt;" class=""><o:p class=""> </o:p></span></div><div style="margin: 0cm; font-size: 12pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 11pt;" class="">Just curious, will there be an update coming to ChimeraX to support the new JSON file format from AlphaFold?<o:p class=""></o:p></span></div><div style="margin: 0cm; font-size: 12pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 11pt;" class=""><o:p class=""> </o:p></span></div><div style="margin: 0cm; font-size: 12pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 11pt;" class="">Thanks for your time!<o:p class=""></o:p></span></div><div style="margin: 0cm; font-size: 12pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 11pt;" class=""><o:p class=""> </o:p></span></div><div style="margin: 0cm; font-size: 12pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 11pt;" class="">Best,<o:p class=""></o:p></span></div><div style="margin: 0cm; font-size: 12pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 11pt;" class="">Brandon<o:p class=""></o:p></span></div><div style="margin: 0cm; font-size: 12pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 11pt;" class=""><o:p class=""> </o:p></span></div><div style="margin: 0cm; font-size: 12pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div></div><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">_______________________________________________</span><br style="caret-color: rgb(0, 0, 0); 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