<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 Jan,<div class=""><br class=""></div><div class=""> Those are good suggestions. I plan to have the PAE plot show you the residue numbers when you hover the mouse. But I agree that making a drag box on the plot do a selection of residues could be useful. I made it do coloring like the AlphaFold database web pages which show these plots because I think it was visually clearer. When it does the coloring, it replaces the entire coloring, including the residues outside the box you dragged. Maybe I can add an option to the plot to select instead of color. I find the plot button that colors domains does a nice job of showing the different regions where AlphaFold is confident. Gerard Kleywegt suggested also showing those same colors in the plot itself so the correspondence and interactions between the domains on the plot could easily be seen. I've made feature requests for these ideas.</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span><a href="https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/6724" class="">https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/6724</a></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span><a href="https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/6725" class="">https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/6725</a></div><div class=""><br class=""></div><div class=""> There are lot of other PAE improvements I am looking into, like putting in dividing lines on the plot between proteins for multimer predictions, zooming the plots, or coloring by confidence relative to residues chosen on the structure.</div><div class=""><br class=""></div><div class=""> Having a linear plot of pLDDT (predicted local distance difference test) per-residue scores could be nice. But I am a bit unclear on how it would be used. You already see the pLDDT coloring on the structure which makes those red unstructured regions stand out. In the ChimeraX AlphaFold tool (menu Tools / Structure Prediction / AlphaFold) there is a Coloring button that shows a panel where you can select all residues below a given pLDDT (confidence) score. So you can then delete them, or change their style, or do whatever you want with those selected residues.</div><div class=""><br class=""></div><div class=""> Here's a bit of info on the current ChimeraX PAE capabilities</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span><a href="https://www.rbvi.ucsf.edu/chimerax/data/pae-apr2022/pae.html" class="">https://www.rbvi.ucsf.edu/chimerax/data/pae-apr2022/pae.html</a></div><div class=""><br class=""></div><div class=""> Tom</div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Apr 27, 2022, at 3:08 AM, mailman-bounces--- 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 http-equiv="Content-Type" content="text/html; charset=utf-8" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="caret-color: rgb(0, 0, 0); font-family: "Segoe UI"; font-size: 16px; font-style: normal; font-variant-caps: normal; font-weight: normal; 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; margin: 0px;" class=""><span style="font-family: -webkit-system-font, "Helvetica Neue", Helvetica, sans-serif; color: rgb(127, 127, 127);" class=""><b class="">From:<span class="Apple-converted-space"> </span></b></span><span style="font-family: -webkit-system-font, "Helvetica Neue", Helvetica, sans-serif;" class="">"Jan Gebauer" <<a href="mailto:jan.gebauer@uni-koeln.de" class="">jan.gebauer@uni-koeln.de</a>><br class=""></span></div><div style="caret-color: rgb(0, 0, 0); font-family: "Segoe UI"; font-size: 16px; font-style: normal; font-variant-caps: normal; font-weight: normal; 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; margin: 0px;" class=""><span style="font-family: -webkit-system-font, "Helvetica Neue", Helvetica, sans-serif; color: rgb(127, 127, 127);" class=""><b class="">Subject:<span class="Apple-converted-space"> </span></b></span><span style="font-family: -webkit-system-font, "Helvetica Neue", Helvetica, sans-serif;" class=""><b class="">Identifying residues based on PAE plot?</b><br class=""></span></div><div style="caret-color: rgb(0, 0, 0); font-family: "Segoe UI"; font-size: 16px; font-style: normal; font-variant-caps: normal; font-weight: normal; 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; margin: 0px;" class=""><span style="font-family: -webkit-system-font, "Helvetica Neue", Helvetica, sans-serif; color: rgb(127, 127, 127);" class=""><b class="">Date:<span class="Apple-converted-space"> </span></b></span><span style="font-family: -webkit-system-font, "Helvetica Neue", Helvetica, sans-serif;" class="">April 27, 2022 at 3:04:30 AM PDT<br class=""></span></div><div style="caret-color: rgb(0, 0, 0); font-family: "Segoe UI"; font-size: 16px; font-style: normal; font-variant-caps: normal; font-weight: normal; 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; margin: 0px;" class=""><span style="font-family: -webkit-system-font, "Helvetica Neue", Helvetica, sans-serif; color: rgb(127, 127, 127);" class=""><b class="">To:<span class="Apple-converted-space"> </span></b></span><span style="font-family: -webkit-system-font, "Helvetica Neue", Helvetica, sans-serif;" class="">ChimeraX-users <<a href="mailto:chimerax-users-bounces@cgl.ucsf.edu" class="">chimerax-users-bounces@cgl.ucsf.edu</a>><br class=""></span></div><div style="caret-color: rgb(0, 0, 0); font-family: "Segoe UI"; font-size: 16px; font-style: normal; font-variant-caps: normal; font-weight: normal; 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; margin: 0px;" class=""><span style="font-family: -webkit-system-font, "Helvetica Neue", Helvetica, sans-serif; color: rgb(127, 127, 127);" class=""><b class="">Reply-To:<span class="Apple-converted-space"> </span></b></span><span style="font-family: -webkit-system-font, "Helvetica Neue", Helvetica, sans-serif;" class="">"Jan Gebauer" <<a href="mailto:jan.gebauer@uni-koeln.de" class="">jan.gebauer@uni-koeln.de</a>><br class=""></span></div><br style="caret-color: rgb(0, 0, 0); font-family: "Segoe UI"; font-size: 16px; font-style: normal; font-variant-caps: normal; font-weight: normal; 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;" class=""><br style="caret-color: rgb(0, 0, 0); font-family: "Segoe UI"; font-size: 16px; font-style: normal; font-variant-caps: normal; font-weight: normal; 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;" class=""><div style="caret-color: rgb(0, 0, 0); font-family: "Segoe UI"; font-size: 16px; font-style: normal; font-variant-caps: normal; font-weight: normal; 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;" class="">Hi everyone,</div><div style="caret-color: rgb(0, 0, 0); font-family: "Segoe UI"; font-size: 16px; font-style: normal; font-variant-caps: normal; font-weight: normal; 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;" class=""><br class=""></div><div style="caret-color: rgb(0, 0, 0); font-family: "Segoe UI"; font-size: 16px; font-style: normal; font-variant-caps: normal; font-weight: normal; 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;" class="">love the "new" work in the dailys for ChimeraX and visualising the PAE and pLDTT scores. As I calculate my AF structures on my own, this helps a lot to analyses the structures.</div><div style="caret-color: rgb(0, 0, 0); font-family: "Segoe UI"; font-size: 16px; font-style: normal; font-variant-caps: normal; font-weight: normal; 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;" class=""><br class=""></div><div style="caret-color: rgb(0, 0, 0); font-family: "Segoe UI"; font-size: 16px; font-style: normal; font-variant-caps: normal; font-weight: normal; 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;" class="">I have one question/suggestion however: If I select a region in the PAE plot, it gets coloured in the the "3D-view", however, I found no way to actually get the residues number or a proper selection for the coloured residues. Is there a way? I'd like to colour multiple selections differently...</div><div style="caret-color: rgb(0, 0, 0); font-family: "Segoe UI"; font-size: 16px; font-style: normal; font-variant-caps: normal; font-weight: normal; 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;" class="">Another nice feature would be a pLDTT plot, as this enables easier detection of unordered stretches...</div><div style="caret-color: rgb(0, 0, 0); font-family: "Segoe UI"; font-size: 16px; font-style: normal; font-variant-caps: normal; font-weight: normal; 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;" class=""><br class=""></div><div style="caret-color: rgb(0, 0, 0); font-family: "Segoe UI"; font-size: 16px; font-style: normal; font-variant-caps: normal; font-weight: normal; 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;" class="">As always: Many thanks for all the good work!</div><div style="caret-color: rgb(0, 0, 0); font-family: "Segoe UI"; font-size: 16px; font-style: normal; font-variant-caps: normal; font-weight: normal; 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;" class=""><br class=""></div><div style="caret-color: rgb(0, 0, 0); font-family: "Segoe UI"; font-size: 16px; font-style: normal; font-variant-caps: normal; font-weight: normal; 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;" class="">Best</div><div style="caret-color: rgb(0, 0, 0); font-family: "Segoe UI"; font-size: 16px; font-style: normal; font-variant-caps: normal; font-weight: normal; 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;" class="">Jan</div><div style="caret-color: rgb(0, 0, 0); font-family: "Segoe UI"; font-size: 16px; font-style: normal; font-variant-caps: normal; font-weight: normal; 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;" class=""><br class=""></div><div id="signature_old" style="caret-color: rgb(0, 0, 0); font-family: "Segoe UI"; font-size: 16px; font-style: normal; font-variant-caps: normal; font-weight: normal; 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;" class=""><div id="xb7454239a230424" class=""><pre class="moz-signature" cols="72"><div id="xcae1d71cca764e2b8f46e025f75da513" class=""><div class="plain_line">--</div><div class="plain_line"><font face="Bahnschrift Light" class="">Dr. Jan Gebauer <span style="background-color: rgba(0, 0, 0, 0); font-size: 12pt;" class="">|</span><span style="font-size: 12pt;" class=""> π Head of C2<i class="">f</i> </span><span style="background-color: rgba(0, 0, 0, 0); font-size: 12pt;" class="">|</span><span style="font-size: 12pt;" class="">π¬ Member of AG Prof. Baumann
</span></font></div><div class="plain_line"><font face="Bahnschrift Light" class="">Institut fΓΌr Biochemie | University of Cologne</font></div><div class="plain_line"><font face="Bahnschrift Light" class="">Zuelpicher Str. 47 | 50674 Cologne | Germany</font></div><div class="plain_line"><font face="Bahnschrift Light" class="">π +49 (221) 470 3212 π Fax: +49 (221 470 5066)</font></div><div class="plain_line"><font face="Bahnschrift Light" class="">π§ <a href="mailto:jan.gebauer@uni-koeln.de" class="">jan.gebauer@uni-koeln.de</a> π<a href="http://px.uni-koeln.de/" class="">http://px.uni-koeln.de/</a> </font></div><div class="plain_line"><span style="background-color: rgba(0, 0, 0, 0); font-family: "Bahnschrift Light";" class="">πVisit the Cologne Crystallisation facility (C2f) !</span><span style="background-color: rgba(0, 0, 0, 0); font-size: 12pt; font-family: "Bahnschrift Light";" class="">π</span><a href="http://c2f.uni-koeln.de/" style="background-color: rgba(0, 0, 0, 0); font-size: 12pt; font-family: "Bahnschrift Light";" class="">http://c2f.uni-koeln.de/</a></div></div></pre></div></div></div>_______________________________________________<br class="">ChimeraX-users mailing list<br class=""><a href="mailto:ChimeraX-users@cgl.ucsf.edu" class="">ChimeraX-users@cgl.ucsf.edu</a><br class="">Manage subscription:<br class="">https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users<br class=""></div></blockquote></div><br class=""></div></body></html>