<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 Diego,<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Sorry, but that command was supposed to return the distance value but wasn't in all cases. In tomorrow's daily build it will.</div><div class=""><br class=""></div><div class="">--Eric<br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Sep 8, 2021, at 2:22 AM, Diego Amaya <<a href="mailto:diaamayaram@unal.edu.co" class="">diaamayaram@unal.edu.co</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" 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=""><div class="">Hi again Eric.</div><div class=""><br class=""></div><div class="">sorry, just one more question. How could I catch the value from<span class="Apple-converted-space"> </span><i class=""><span style="font-family: arial, sans-serif;" class="">rc(session,</span>'<span style="white-space: pre-wrap;" class=""></span>dist ##name=AA1 ##name=AA2')</i><span class="Apple-converted-space"> </span>in a python variable ?</div><div class=""><br class=""></div><div class="">Thanks in advance.<br class=""></div><div class=""><br class=""></div></div><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=""><div class="gmail_quote" 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;"><div dir="ltr" class="gmail_attr">El mié, 8 sept 2021 a las 11:07, Diego Amaya (<<a href="mailto:diaamayaram@unal.edu.co" class="">diaamayaram@unal.edu.co</a>>) escribió:<br class=""></div><blockquote class="gmail_quote" style="margin: 0px 0px 0px 0.8ex; border-left-width: 1px; border-left-style: solid; border-left-color: rgb(204, 204, 204); padding-left: 1ex;"><div dir="ltr" class=""><div class="">Hi Eric,</div><div class=""><br class=""></div><div class="">thank you so much. Your suggestion works like a charm.</div><div class=""><br class=""></div><div class="">Best regards,<br class=""></div></div><br class=""><div class="gmail_quote"><div dir="ltr" class="gmail_attr">El mar, 7 sept 2021 a las 20:20, Eric Pettersen (<<a href="mailto:pett@cgl.ucsf.edu" target="_blank" class="">pett@cgl.ucsf.edu</a>>) escribió:<br class=""></div><blockquote class="gmail_quote" style="margin: 0px 0px 0px 0.8ex; border-left-width: 1px; border-left-style: solid; border-left-color: rgb(204, 204, 204); padding-left: 1ex;"><div class="">Hi Diego,<div class=""><span style="white-space: pre-wrap;" class=""> </span>Centroids are created as 'markers' and therefore are referred to in commands in the same way as atoms are. So specifically, your first 'define' command creates a structure named AA1, with one residue named 'centroid', with one atom named 'cent'. Therefore this command will create the distance:</div><div class=""><br class=""></div><div class=""><span style="white-space: pre-wrap;" class=""> </span>dist ##name=AA1 ##name=AA2</div><div class=""><br class=""></div><div class="">If you have exactly two of these centroids open, then this command will also do it:</div><div class=""><br class=""></div><div class=""><span style="white-space: pre-wrap;" class=""> </span>dist :centroid</div><div class=""><br class=""></div><div class="">Therefore, it might be easiest to not even give these centroids names but instead use two 'define' commands followed by 'dist :centroid' and then 'close :centroid'.</div><div class=""><br class=""></div><div class=""><div class="">--Eric</div><div class=""><br class=""></div><div class=""><span style="white-space: pre-wrap;" class=""> </span>Eric Pettersen</div><div class=""><span style="white-space: pre-wrap;" class=""> </span>UCSF Computer Graphics Lab</div></div><div class=""><br class=""><div class=""><br class=""><blockquote type="cite" class=""><div class="">On Sep 6, 2021, at 10:14 AM, Diego Amaya via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" target="_blank" class="">chimerax-users@cgl.ucsf.edu</a>> wrote:</div><br class=""><div class=""><div dir="ltr" class=""><div class="">Hello,</div><div class=""><br class=""></div><div class="">I'm trying to compute the distance between the centers of mass of two residues using the python API. I tried two different ways :</div><div class=""><br class=""></div><div class="">1.<span class="Apple-converted-space"> </span><br class=""></div><div class=""><i class="">rc(session, 'define centroid :43 massWeighting true name AA1')<br class="">rc(session, 'define centroid :35 massWeighting true name AA2')<br class="">rc(session, 'distance AA1 AA2')<span class="Apple-converted-space"> </span></i></div><div class=""><br class=""></div><div class="">2.</div><div class=""><i class=""><span style="font-family: arial, sans-serif;" class="">rc(session, ' measure center :43 mark true name AA1')<br class="">rc(session, 'measure center :35 mark true name AA2')<br class="">rc(session, 'distance AA1 AA2')</span></i></div><div class=""><br class=""></div><div class="">But I get this error in the third line in both cases :<span class="Apple-converted-space"> </span><br class=""></div><div class=""><i class="">chimerax.core.errors.UserError: Missing or invalid "objects" argument: invalid objects specifier<span class="Apple-converted-space"> </span><br class=""></i></div><div class=""><i class=""><br class=""></i></div><div class="">What is wrong ?<br class=""></div><div class=""><br class=""></div><div class="">Thanks in advance.<i class=""><br class=""></i></div><div class="">--<span class="Apple-converted-space"> </span><br class=""><div dir="ltr" class=""><div dir="ltr" class="">Diego A. Amaya Ramírez</div></div></div></div><br class=""><b style="color: rgb(34, 34, 34); font-family: Calibri, sans-serif; font-size: 14.6667px; font-style: normal; letter-spacing: normal; text-align: justify; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; background-color: rgb(255, 255, 255);" class=""><span style="font-size: 6.5pt; line-height: 9.96667px; font-family: "Ancizar Sans", sans-serif;" class="">Aviso legal:</span></b><span style="font-style: normal; font-weight: 400; letter-spacing: normal; text-align: justify; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; background-color: rgb(255, 255, 255); font-size: 6.5pt; line-height: 9.96667px; font-family: "Ancizar Sans", sans-serif;" class=""> El contenido de este mensaje y los archivos adjuntos son confidenciales y de uso exclusivo de la Universidad Nacional de Colombia. Se encuentran dirigidos sólo para el uso del destinatario al cual van enviados. 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Los Datos Personales serán tratados conforme a la Ley 1581 de 2012 y a nuestra Política de Datos Personales que podrá consultar en la página web </span><span style="color: rgb(34, 34, 34); font-family: Calibri, sans-serif; font-style: normal; font-weight: 400; letter-spacing: normal; text-align: justify; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; background-color: rgb(255, 255, 255); font-size: 6.5pt; line-height: 9.96667px;" class=""><a href="http://www.unal.edu.co/" target="_blank" style="color: blue;" class=""><span style="font-family: "Ancizar Sans", sans-serif;" class="">www.unal.edu.co</span></a></span><span style="font-style: normal; font-weight: 400; letter-spacing: normal; text-align: justify; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; background-color: rgb(255, 255, 255); font-size: 6.5pt; line-height: 9.96667px; font-family: "Ancizar Sans", sans-serif;" class="">.<u class=""><span class=""> </span></u>Las opiniones, informaciones, conclusiones y cualquier otro tipo de dato contenido en este correo electrónico, no relacionados con la actividad de la Universidad Nacional de Colombia, se entenderá como personales y de ninguna manera son avaladas por la Universidad.</span><br class=""><span style="color: rgb(245, 132, 111); font-family: ClearSans-Regular, Arial, Verdana, Helvetica, sans-serif; font-size: 14px; font-style: normal; font-weight: 400; letter-spacing: normal; text-align: left; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; background-color: rgb(255, 255, 255); display: inline; float: none;" class=""><span class=""></span></span><span style="color: rgb(245, 132, 111); font-family: ClearSans-Regular, Arial, Verdana, Helvetica, sans-serif; font-size: 14px; font-style: normal; font-weight: 400; letter-spacing: normal; text-align: left; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; background-color: rgb(255, 255, 255); display: inline; float: none;" class=""><span class=""></span></span>_______________________________________________<br class="">ChimeraX-users mailing list<br class=""><a href="mailto:ChimeraX-users@cgl.ucsf.edu" target="_blank" class="">ChimeraX-users@cgl.ucsf.edu</a><br class="">Manage subscription:<br class=""><a href="https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users" target="_blank" class="">https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</a><br class=""></div></blockquote></div><br class=""></div></div></blockquote></div><br clear="all" class=""><br class="">--<span class="Apple-converted-space"> </span><br class=""><div dir="ltr" class=""><div dir="ltr" class="">Diego A. Amaya Ramírez</div></div></blockquote></div><br clear="all" 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=""><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="">--<span class="Apple-converted-space"> </span></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=""><div dir="ltr" class="gmail_signature" 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;"><div dir="ltr" class="">Diego A. Amaya Ramírez</div></div><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=""><b style="font-style: normal; font-variant-caps: normal; letter-spacing: normal; orphans: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; text-decoration: none; color: rgb(34, 34, 34); font-family: Calibri, sans-serif; font-size: 14.6667px; text-align: justify; background-color: rgb(255, 255, 255);" class=""><span style="font-size: 6.5pt; line-height: 9.96667px; font-family: "Ancizar Sans", sans-serif;" class="">Aviso legal:</span></b><span style="font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; text-align: justify; background-color: rgb(255, 255, 255); font-size: 6.5pt; line-height: 9.96667px; font-family: "Ancizar Sans", sans-serif;" class=""> El contenido de este mensaje y los archivos adjuntos son confidenciales y de uso exclusivo de la Universidad Nacional de Colombia. 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Los Datos Personales serán tratados conforme a la Ley 1581 de 2012 y a nuestra Política de Datos Personales que podrá consultar en la página web </span><span style="font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; orphans: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; text-decoration: none; color: rgb(34, 34, 34); font-family: Calibri, sans-serif; text-align: justify; background-color: rgb(255, 255, 255); font-size: 6.5pt; line-height: 9.96667px;" class=""><a href="http://www.unal.edu.co/" target="_blank" style="color: blue;" class=""><span style="font-family: "Ancizar Sans", sans-serif;" class="">www.unal.edu.co</span></a></span><span style="font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; text-align: justify; background-color: rgb(255, 255, 255); font-size: 6.5pt; line-height: 9.96667px; font-family: "Ancizar Sans", sans-serif;" class="">.<u class=""><span class=""> </span></u>Las opiniones, informaciones, conclusiones y cualquier otro tipo de dato contenido en este correo electrónico, no relacionados con la actividad de la Universidad Nacional de Colombia, se entenderá como personales y de ninguna manera son avaladas por la Universidad.</span></div></blockquote></div><br class=""></div></body></html>