<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 André,<div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Feb 16, 2023, at 2:50 PM, André Graça 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: 11pt; font-family: Calibri, sans-serif;" class="">Hi everyone!<br class=""><br class="">Does ChimeraX have a tool to calculate distance maps in the same fashion as Chimera does with RRDistMaps?<br class=""></div></div></div></blockquote><div><br class=""></div>No, though we have a feature-request ticket open in our bug-tracking database for this. I have added you to the recipient list for that ticket.</div><div><br class=""><blockquote type="cite" class=""><div 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: 11pt; font-family: Calibri, sans-serif;" class="">I believe Chimera's RRDistMaps only calculates intermodal distances between C-alpha atoms. Does anyone know a tool or have a script that could calculate all atom distances from two sequence identical models?</div></div></div></blockquote><br class=""></div></div><div>Assuming those models are the only structures open, the below would save the distances to a file named "distances.txt" in your home directory:</div><div><br class=""></div><div>from chimera.atomic import all_atomic_structures</div><div>s1, s2 = all_atomic_structures(session)</div><div>from chimera.geometry import distance</div><div>import os.path</div><div>with open(os.path.expanduser("~/distances.txt"), 'w') as f:</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>for a1, a2 in zip(s1.atoms, s2.atoms):</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>print(a1, a2, distance(a1, a2), file=f)</div><div><br class=""></div><div>You could put the above in a file with a '.py' suffix and open it in ChimeraX to run it.</div><div><br class=""></div><div><div>--Eric</div><div><br class=""></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>Eric Pettersen</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>UCSF Computer Graphics Lab</div><div><br class=""></div></div></body></html>