<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 Shubham,<div class=""><br class=""></div><div class=""> This coordset command behavior is confusing so I changed it in tomorrow's ChimeraX daily build (not in 1.4) so that "coordset #1 5" will act immediately without waiting for a frame to be drawn. If you specify a range of frames "coordset #1 5,15" then they are still only drawn one at a time when the graphics is drawn -- that is for recording movies.</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Tom<br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On May 24, 2022, at 11:15 AM, Eric Pettersen 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="">Hi Shubham,<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Since the "coordset" command sets up playback of coordinate frames, it doesn't actually do anything until a frame is drawn, which is why in nogui mode nothing changes, and why you have to "create a delay" in GUI mode. You can force a frame to get drawn with the "wait 1" command, which will get your script working in both modes.</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Alternatively, if you have the structure model in a variable (i.e. from the list of models returned by the 'open' command, or culled from session.models), you can change the coordset directly, <i class="">e.g.</i><span style="font-style: normal;" class="">:</span></div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span># if the structure model is in the 's' variable</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>for cid in s.coordset_ids:</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>s.active_coordset_id = cid</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span># do whatever you need to do with this coordset</div><div class=""><br class=""></div><div class=""><div class="">--Eric</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Eric Pettersen</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>UCSF Computer Graphics Lab</div></div><div class=""><br class=""><div class=""><br class=""><blockquote type="cite" class=""><div class="">On May 24, 2022, at 1:22 AM, Shubham Devesh Ramgoolam 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=""><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: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Hi all,</div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class="">I hope you are doing well.</div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class="">I have a python script for measuring the distance between aromatic rings of specific residues for different frames of a trajectory.</div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class="">To measure the distance, I am first defining centroids at the center of aromatic rings and then use the command distance. This process is repeated for each frame to be analyzed.</div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class="">To navigate between frames, I am using the command ‘coordset #1 {desired frame}’.</div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class="">When executing the script in no gui mode, the centroids are always defined with respect to the residue’s location in frame 1 even though the command coordset has changed the frame.</div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class="">In gui mode, the script only works if a delay is created between changing the frame and defining the new centroids.</div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class="">I introduced that delay by asking for a dummy user input (I ran the script from python Shell):</div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif; text-indent: 0.5in;" class="">run(session, 'coordset #1 ' + {new_frame})</div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif; text-indent: 0.5in;" class="">y = input('dummy')</div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif; text-indent: 0.5in;" class="">run (session, 'define centroid /A:8 & aromatic-ring radius 0.3 color yellow mass false name d1’)</div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class="">My chimeraX version: 1.4rc202205060510 (2022-05-06)</div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Should I be using a different command for changing frames of trajectories when in nogui mode?</div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Regards,</div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Shubham</div><p class="MsoNormal" style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;"> <span class="Apple-converted-space"> </span></p><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Sent from<span class="Apple-converted-space"> </span><a href="https://go.microsoft.com/fwlink/?LinkId=550986" style="color: blue; text-decoration: underline;" class="">Mail</a><span class="Apple-converted-space"> </span>for Windows</div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div></div><span style="caret-color: rgb(0, 0, 0); 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