<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=""><div><blockquote type="cite" class=""><div class="">Begin forwarded message:</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;" class=""><br class=""></div><div class=""><div style="caret-color: rgb(0, 0, 0); font-family: "Segoe UI"; font-size: 16px; 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; margin: 0px;" class=""><span style="font-family: -webkit-system-font, "Helvetica Neue", Helvetica, sans-serif; color: rgb(127, 127, 127);" class=""><b class="">From:<span class="Apple-converted-space"> </span></b></span><span style="font-family: -webkit-system-font, "Helvetica Neue", Helvetica, sans-serif;" class="">"Jan Gebauer" <<a href="mailto:jan.gebauer@uni-koeln.de" class="">jan.gebauer@uni-koeln.de</a>><br class=""></span></div><div style="caret-color: rgb(0, 0, 0); font-family: "Segoe UI"; font-size: 16px; 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; margin: 0px;" class=""><span style="font-family: -webkit-system-font, "Helvetica Neue", Helvetica, sans-serif; color: rgb(127, 127, 127);" class=""><b class="">Subject:<span class="Apple-converted-space"> </span></b></span><span style="font-family: -webkit-system-font, "Helvetica Neue", Helvetica, sans-serif;" class=""><b class="">Analog command to reinit & create?</b><br class=""></span></div><div style="caret-color: rgb(0, 0, 0); font-family: "Segoe UI"; font-size: 16px; 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; margin: 0px;" class=""><span style="font-family: -webkit-system-font, "Helvetica Neue", Helvetica, sans-serif; color: rgb(127, 127, 127);" class=""><b class="">Date:<span class="Apple-converted-space"> </span></b></span><span style="font-family: -webkit-system-font, "Helvetica Neue", Helvetica, sans-serif;" class="">December 13, 2021 at 7:11:40 AM PST<br class=""></span></div><div style="caret-color: rgb(0, 0, 0); font-family: "Segoe UI"; font-size: 16px; 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; margin: 0px;" class=""><span style="font-family: -webkit-system-font, "Helvetica Neue", Helvetica, sans-serif; color: rgb(127, 127, 127);" class=""><b class="">To:<span class="Apple-converted-space"> </span></b></span><span style="font-family: -webkit-system-font, "Helvetica Neue", Helvetica, sans-serif;" class="">ChimeraX-users <<a href="mailto:chimerax-users-bounces@cgl.ucsf.edu" class="">chimerax-users-bounces@cgl.ucsf.edu</a>><br class=""></span></div><div style="caret-color: rgb(0, 0, 0); font-family: "Segoe UI"; font-size: 16px; 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; margin: 0px;" class=""><span style="font-family: -webkit-system-font, "Helvetica Neue", Helvetica, sans-serif; color: rgb(127, 127, 127);" class=""><b class="">Reply-To:<span class="Apple-converted-space"> </span></b></span><span style="font-family: -webkit-system-font, "Helvetica Neue", Helvetica, sans-serif;" class="">"Jan Gebauer" <<a href="mailto:jan.gebauer@uni-koeln.de" class="">jan.gebauer@uni-koeln.de</a>><br class=""></span></div><br style="caret-color: rgb(0, 0, 0); font-family: "Segoe UI"; font-size: 16px; 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: "Segoe UI"; font-size: 16px; 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 style="caret-color: rgb(0, 0, 0); font-family: "Segoe UI"; font-size: 16px; 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="">Hi everyone,</div><div style="caret-color: rgb(0, 0, 0); font-family: "Segoe UI"; font-size: 16px; 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 class=""></div><div style="caret-color: rgb(0, 0, 0); font-family: "Segoe UI"; font-size: 16px; 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="">I am currently teaching a crystallographic course and this year I am introducing ChimeraX for the first time (previous years we have used PyMol).</div><div style="caret-color: rgb(0, 0, 0); font-family: "Segoe UI"; font-size: 16px; 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="">I still am in the middle of my personal transiston from PyMol to ChimeraX and potentially I am still stuck too much in the "PyMol"-way to do it, but I still miss a couple of commands. Could anyone help with that?</div><div style="caret-color: rgb(0, 0, 0); font-family: "Segoe UI"; font-size: 16px; 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 class=""></div><div style="caret-color: rgb(0, 0, 0); font-family: "Segoe UI"; font-size: 16px; 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="">1) Analog to Reinit</div><div style="caret-color: rgb(0, 0, 0); font-family: "Segoe UI"; font-size: 16px; 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="">I generate all my publication figures with scripts (now cxc). The Reinit command in Pymol, always gave me a fresh enviroment, however the closest analog I found "Close" only closes the current model. All other settings (Lightning etc.) are kept and only reset after closing ChimeraX. Therefore, I do not get the same results from my script, if I run it multiple times...</div><div style="caret-color: rgb(0, 0, 0); font-family: "Segoe UI"; font-size: 16px; 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 class=""></div><div style="caret-color: rgb(0, 0, 0); font-family: "Segoe UI"; font-size: 16px; 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="">2) Create object </div><div style="caret-color: rgb(0, 0, 0); font-family: "Segoe UI"; font-size: 16px; 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="">Is there a way to copy a selection of atoms into a new molecule - for complicated visualisations?</div><div style="caret-color: rgb(0, 0, 0); font-family: "Segoe UI"; font-size: 16px; 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 class=""></div><div style="caret-color: rgb(0, 0, 0); font-family: "Segoe UI"; font-size: 16px; 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="">Thanks so far to the developers - I love more things on ChimeraX than I miss 👍</div><div style="caret-color: rgb(0, 0, 0); font-family: "Segoe UI"; font-size: 16px; 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="">Best,</div><div style="caret-color: rgb(0, 0, 0); font-family: "Segoe UI"; font-size: 16px; 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="">Jan</div><div style="caret-color: rgb(0, 0, 0); font-family: "Segoe UI"; font-size: 16px; 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 class=""></div><div id="signature_old" style="caret-color: rgb(0, 0, 0); font-family: "Segoe UI"; font-size: 16px; 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 id="xae68fcde9a1d41e" class=""><div id="xaf25931e944b429abac967a708fd04ae" style="font-family: "Segoe UI"; font-size: 12pt; background-color: rgb(255, 255, 255); margin-left: 0px; margin-right: 8px;" class=""><div style="zoom: 0.89;" class=""><div dir="auto" class=""><div id="aqm-signature" dir="auto" class=""><div dir="auto" style="margin: 0px;" class="">--<span class="Apple-converted-space"> </span></div><div dir="auto" style="margin: 0px;" class="">Dr. Jan Gebauer</div><div dir="auto" style="margin: 0px;" class="">AG Baumann / Biochemistry Cologne</div><div dir="auto" style="margin: 0px;" class="">Zülpicher Str. 47 / 50764 Köln</div><div dir="auto" style="margin: 0px;" class="">+49 - 221 - 470 - 3212</div></div></div></div></div></div></div></div></blockquote></div><br class=""></body></html>