<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="">You can use Python in ChimeraX to find the shortest distance. Here is some example code closest.py to do that.<div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span><a href="https://rbvi.github.io/chimerax-recipes/closest/closest.html" class="">https://rbvi.github.io/chimerax-recipes/closest/closest.html</a></div><div class=""><br class=""></div><div class="">If you open that Python code in ChimeraX it registers a command "closest"</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>open 7LUP</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>closest /A to /B maxDist 100</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>> Minimum distance 2.27 between /A LYS 45 NZ and /B ASP 522 OD1</div><div class=""><div><br class=""></div><div> Tom</div><div><br class=""></div><div><br class=""><blockquote type="cite" class=""><div class="">On Sep 28, 2021, at 2:15 AM, Vorländer,Matthias Kopano 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: 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;"><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span lang="EN-US" style="font-size: 9pt;" class="">Dear all,<o:p class=""></o:p></span></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span lang="EN-US" style="font-size: 9pt;" class=""><o:p class=""> </o:p></span></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span lang="EN-US" style="font-size: 9pt;" class="">I am interested in measuring the shortest distance between two models (PDBs) without a priori knowledge of which atoms will be the closest ones. I am planning to do this for a large number of model pairs, therefore it would be great if this would be scriptable. Is this possible using ChimeraX?<o:p class=""></o:p></span></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span lang="EN-US" style="font-size: 9pt;" class="">Thanks a lot in advance,<o:p class=""></o:p></span></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span lang="EN-US" style="font-size: 9pt;" class=""><o:p class=""> </o:p></span></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span lang="EN-US" style="font-size: 9pt;" class="">Best,<o:p class=""></o:p></span></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span lang="EN-US" style="font-size: 9pt;" class="">Matthias<o:p class=""></o:p></span></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span lang="EN-US" style="font-size: 9pt;" class=""><o:p class=""> </o:p></span></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: 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; float: none; display: inline !important;" class="">_______________________________________________</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; 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=""><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; 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; float: none; display: inline !important;" class="">ChimeraX-users mailing list</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; 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=""><a href="mailto:ChimeraX-users@cgl.ucsf.edu" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">ChimeraX-users@cgl.ucsf.edu</a><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; 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=""><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; 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; float: none; display: inline !important;" class="">Manage subscription:</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; 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=""><a href="https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</a></div></blockquote></div><br class=""></div></body></html>