<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 Dmitry,<div class=""><br class=""></div><div class=""> Here's some example Python code to flip atom z coordinates in our newer program ChimeraX.</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span><a href="http://plato.cgl.ucsf.edu/trac/chimera/wiki/FlipZ" class="">http://plato.cgl.ucsf.edu/trac/chimera/wiki/FlipZ</a></div><div class=""><br class=""></div><div class=""> Tom</div><div class=""><br class=""><div><img apple-inline="yes" id="00C445BF-680D-43D7-9546-4F4E6DACAFDC" width="562" height="375" src="cid:4DA5F0D0-5177-49A6-9AD2-1644D6898FD0" class=""><br class=""><blockquote type="cite" class=""><div class="">On Sep 3, 2020, at 2:45 AM, Dmitry Semchonok <<a href="mailto:semchonok@gmail.com" class="">semchonok@gmail.com</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: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span lang="EN-US" class="">Dear Elaine,<o:p class=""></o:p></span></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span lang="EN-US" class=""><o:p class=""> </o:p></span></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span lang="EN-US" class="">By ‘model’ I mean coordinate file that is build up by coot/phenix for fitting into the volume map.<o:p class=""></o:p></span></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span lang="EN-US" class="">The ‘vop zflip’ works for the volume maps</span></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span lang="EN-US" class="">Any options how to flip the coordinate map?</span></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span lang="EN-US" class="">Thank you!</span></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span lang="EN-US" class="">Sincerely,</span></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span lang="EN-US" class="">Dmitry</span></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="border-style: solid none none; border-top-width: 1pt; border-top-color: rgb(225, 225, 225); padding: 3pt 0cm 0cm;" class=""><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif; border: none; padding: 0cm;" class=""><b class="">От:<span class="Apple-converted-space"> </span></b><a href="mailto:meng@cgl.ucsf.edu" style="color: blue; text-decoration: underline;" class="">Elaine Meng</a><br class=""><b class="">Отправлено:<span class="Apple-converted-space"> </span></b>2 сентября 2020 г. в 19:07<br class=""><b class="">Кому:<span class="Apple-converted-space"> </span></b><a href="mailto:semchonok@gmail.com" style="color: blue; text-decoration: underline;" class="">Dmitry Semchonok</a><br class=""><b class="">Копия:<span class="Apple-converted-space"> </span></b><a href="mailto:chimera-users@cgl.ucsf.edu" style="color: blue; text-decoration: underline;" class="">Chimera</a><br class=""><b class="">Тема:<span class="Apple-converted-space"> </span></b>Re: [Chimera-users] flipping model in chimera</div></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Hi Dmitry,</div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">It depends what you mean by "model" but for maps in Chimera there is a "vop zflip" command for flipping about the Z axis only:</div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><<a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#zFlip" style="color: blue; text-decoration: underline;" class="">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#zFlip</a>></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">There is no option to do this for other types of models.</div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">ChimeraX map flipping ("volume flip") can use other axes, not just Z:</div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><<a href="http://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#flip" style="color: blue; text-decoration: underline;" class="">http://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#flip</a>></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">I hope this helps,</div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Elaine</div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">-----</div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Elaine C. Meng, Ph.D. <span class="Apple-converted-space"> </span></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">UCSF Chimera(X) team</div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Department of Pharmaceutical Chemistry</div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">University of California, San Francisco</div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">> On Sep 2, 2020, at 8:40 AM, Dmitry Semchonok <<a href="mailto:semchonok@gmail.com" style="color: blue; text-decoration: underline;" class="">semchonok@gmail.com</a>> wrote:</div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">><span class="Apple-converted-space"> </span></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">> Dear colleagues,</div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">> <span class="Apple-converted-space"> </span></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">> How to flip the model in chimera?</div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">> <span class="Apple-converted-space"> </span></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">> Thank you!</div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">> <span class="Apple-converted-space"> </span></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">> Sincerely.</div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">> Dmitry</div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">> <span class="Apple-converted-space"> </span></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">> <span class="Apple-converted-space"> </span></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">> Отправлено из приложения "Почта" для Windows 10</div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">> <span class="Apple-converted-space"> </span></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">> _______________________________________________</div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">> Chimera-users mailing list: <a href="mailto:Chimera-users@cgl.ucsf.edu" class="">Chimera-users@cgl.ucsf.edu</a></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">> Manage subscription: <a href="https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" class="">https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0cm; 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); 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="">Chimera-users mailing list:<span class="Apple-converted-space"> </span></span><a href="mailto:Chimera-users@cgl.ucsf.edu" style="color: blue; text-decoration: underline; 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;" class="">Chimera-users@cgl.ucsf.edu</a><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="">Manage subscription:<span class="Apple-converted-space"> </span></span><a href="https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" style="color: blue; text-decoration: underline; 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;" class="">https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a></div></blockquote></div><br class=""></div></body></html>