<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="">Dear Francesco,<div class="">Probably you just need to use "vop cover" as described in these previous posts:</div><div class=""><br class=""></div><div class=""><<a href="https://www.cgl.ucsf.edu/pipermail/chimera-users/2013-September/009142.html" class="">https://www.cgl.ucsf.edu/pipermail/chimera-users/2013-September/009142.html</a>></div><div class=""><<a href="https://www.cgl.ucsf.edu/pipermail/chimera-users/2020-July/017021.html" class="">https://www.cgl.ucsf.edu/pipermail/chimera-users/2020-July/017021.html</a>></div><div class=""><br class=""></div><div class="">Details on the "vop cover" command:</div><div class=""><<a href="https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#cover" class="">https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#cover</a>></div><div class=""><br class=""></div><div class=""><div class="">For future: the recommended address for questions is <a href="mailto:chimera-users@cgl.ucsf.edu" class="">chimera-users@cgl.ucsf.edu</a> (CC'd on this message) ... since I'm not the expert in everything (or might be sick or away from work), it's helpful if more people see the question! </div></div><div class=""><br class=""></div><div class="">I hope this helps,</div><div class="">Elaine</div><div class="">
<span class="Apple-style-span" style="border-collapse: separate; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; line-height: normal; border-spacing: 0px; -webkit-text-decorations-in-effect: none;"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div class="">-----</div><div class="">Elaine C. Meng, Ph.D. </div><div class="">UCSF Chimera(X) team</div><div class="">Department of Pharmaceutical Chemistry</div><div class="">University of California, San Francisco</div><div class=""><br class=""></div></div></span></div><div><blockquote type="cite" class=""><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;" class=""><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif; color:rgba(0, 0, 0, 1.0);" class=""><b class="">From: </b></span><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class="">Francesco Papi <<a href="mailto:Francesco.Papi@iit.it" class="">Francesco.Papi@iit.it</a>><br class=""></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;" class=""><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif; color:rgba(0, 0, 0, 1.0);" class=""><b class="">Subject: </b></span><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class=""><b class="">Chimera: Problem with electron density</b><br class=""></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;" class=""><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif; color:rgba(0, 0, 0, 1.0);" class=""><b class="">Date: </b></span><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class="">January 14, 2021 at 3:03:55 AM PST<br class=""></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;" class=""><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif; color:rgba(0, 0, 0, 1.0);" class=""><b class="">To: </b></span><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class="">"<a href="mailto:meng@cgl.ucsf.edu" class="">meng@cgl.ucsf.edu</a>" <<a href="mailto:meng@cgl.ucsf.edu" class="">meng@cgl.ucsf.edu</a>><br class=""></span></div><br class=""><div class=""><div class="WordSection1" style="page: WordSection1; caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 13px; 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 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Dear Elaine,</div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">I am using Chimera to get a picture of a small molecule (cif file) in an electron density map (xplor file). My issue deals with the position of some atoms of the molecule in an adjacent unit cell (see attached image) which prevents me to see some atoms within the map. I thought to simply expand the map beyond the cell boundaries and eventually crop the map, but it didn’t work. I have checked different tutorials and the chimera mailing list for troubleshooting but I haven’t found a solution to this problem. Is there something you can think of?<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Thank you.</div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Regards,<span style="font-size: 11pt;" class=""> </span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Francesco Papi<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><br class=""></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><b class="">Francesco Papi, PhD<o:p class=""></o:p></b></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">PostDoc<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Center for Nanotechnology Innovation@NEST<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span lang="IT" class="">Istituto Italiano di Tecnologia<o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span lang="IT" class="">Piazza San Silvestro, 12<o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span lang="IT" class="">56127 Pisa, Italy<o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span lang="IT" class="">Phone: +39 050 509 495<o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span lang="IT" class="">E-mail:<span class="Apple-converted-space"> </span></span><a href="mailto:francesco.papi@iit.it" style="color: rgb(149, 79, 114); text-decoration: underline;" class=""><span lang="IT" class="">francesco.papi@iit.it</span></a><span lang="IT" class=""><o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Skype: francesco.papi.89<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div></div><img style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 13px; 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="" apple-inline="yes" id="DBE632E6-1411-4622-9B02-8DE3C71928F4" src="cid:A5276282-518A-45DD-B92B-2A9D711E4215@gateway.sonic.net"></div></blockquote></div><br class=""></body></html>