<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 dir="auto" style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi Linda,<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Chimera and ChimeraX treat alt locs differently. Chimera treated them as entirely separate atoms, which meant they naturally all showed at the same time (but which made some chemistry computations much more complicated). In ChimeraX they are treated as different positions of the same atom, so only the “current” setting/position of the alt loc is shown. There is no way to show them simultaneously and no easy way to switch between them. We intend to add some easy interface for switching between them, but we intend to add easy interfaces for many things :-) so it probably will be awhile before that happens.</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Nonetheless, there is a slightly awkward way to switch between alt locs by using the “setattr” command. For instance, in the 1a0m PDB entry, this would switch the CB in residue 4 of chain A to the ‘B’ alt loc:</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span><i class="">setattr /a:4@cb a alt_loc B</i></div><div class=""><span style="font-style: normal;" class=""><br class=""></span></div><div class="">which sets the atom-level attribute ‘alt_loc’ for that atom to ‘B’. That actually changes not only that atom’s alt loc, but possibly also connected atoms in order to make the set of alt locs consistent.</div><div class=""><br class=""></div><div class="">—Eric<br class=""><div class="">
<div style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; 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;" class=""><span class="Apple-tab-span" style="white-space: pre;"><br class="Apple-interchange-newline"> </span>Eric Pettersen</div><div style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; 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;" class=""><span class="Apple-tab-span" style="white-space: pre;"> </span>UCSF Computer Graphics Lab</div><div style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; 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;" class=""><br class=""></div></div><div><blockquote type="cite" class=""><div class="">On Dec 12, 2019, at 7:16 AM, Linda Schulte <<a href="mailto:schulte@nmr.uni-frankfurt.de" class="">schulte@nmr.uni-frankfurt.de</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="">Hi everyone,<br class=""><br class="">I have two conformation in a single PDB chain, see example below:<br class=""><br class="">ATOM 90444 N APHE z 9 253.604 183.844 259.994 0.50 47.28 N<br class="">ATOM 90455 N BPHE z 9 253.778 183.499 258.715 0.50 47.28 N<br class=""><br class="">Chimera can read in this two conformations of the chain, while chimerax shows only the A atoms of the chain.<br class="">How can I read in also the B atoms?<br class=""><br class="">Thanks a lot for your help.<br class="">Best,<br class="">Linda<br class=""><br class=""><br class=""><br class="">-- <br class="">Linda Schulte<br class="">Goethe-Universität Frankfurt am Main<br class="">Institut für Organische Chemie und Chemische Biologie, AK Schwalbe<br class=""><br class="">Max-von-Laue-Straße 7<br class="">D-60438 Frankfurt am Main<br class="">N160/300<br class=""><br class="">+49 (0)69 / 798-29956<br class=""><a href="mailto:schulte@nmr.uni-frankfurt.de" class="">schulte@nmr.uni-frankfurt.de</a><br class=""><br class=""><br class="">_______________________________________________<br class="">ChimeraX-users mailing list<br class="">ChimeraX-users@cgl.ucsf.edu<br class="">Manage subscription:<br class="">http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users<br class=""><br class=""></div></div></blockquote></div><br class=""></div></div></body></html>