<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="">I’d recommend converting your script to a ChimeraX command. </div><div class=""><br class=""></div><div class="">Put your script under a function, say “visualize_pairs(live_session, saved_session, pair_input, pairs)” and then, at the bottom of your script, include some boilerplate to register the command along the lines of this example:</div><div class=""><br class=""></div><div class=""><a href="https://rbvi.github.io/chimerax-recipes/copycolors/copycolors.html" class="">https://rbvi.github.io/chimerax-recipes/copycolors/copycolors.html</a></div><div class=""><br class=""></div><div class="">Then, when you launch ChimeraX you need only open your Python script to register the command. </div><div class=""><br class=""></div><div class="">Please look at the linked page and let me know if you have any questions for adapting your Python script into a ChimeraX command. </div><div class=""><br class=""></div><div class="">— Zach </div><div class=""><br class=""></div><div class=""><div><br class=""><blockquote type="cite" class=""><div class="">On May 22, 2022, at 22:51, 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=""><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: 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="">I have a python script that allows the user to visualize specific residue pairs.</div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Here is an overview of how the script functions:</div><ul type="disc" style="margin-bottom: 0in; margin-top: 0in;" class=""><li class="MsoListParagraph" style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;">Ask the user to input the path of a .cxs file (created previously) and a text file containing the pairs to be visualized</li><li class="MsoListParagraph" style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;">Print the names of the pairs along a uniquely assigned number</li><li class="MsoListParagraph" style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;">Ask the user to input a number in order to visualize the pair assigned to it</li></ul><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="">To run the script currently, I have to do the following: i)Open chimerax ii)Show the shell iii) Call the script from the shell</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="">Now, is it possible to include some codes in the script that would allow me to just open chimerax, click on File -> Open -> this script, and then the shell would show up and the execution would continue there?</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="">Right now, if I ran the script using File -> Open -> this script, I would get this error:</div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Traceback (most recent call last):<br class="">File "C:/Users/Shubham/Desktop/this_script.py", line 8, in<span class="Apple-converted-space"> </span><br class="">session_path = input('Enter file (.cxs) to be visualized with path: \n')<br class="">RuntimeError: input(): lost sys.stdin<span class="Apple-converted-space"> </span></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><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); 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); 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