<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hi Sushree,<div class=""><br class=""></div><div class=""> Why does your "vop boxes” command use model #0 for both the map and the markers? That can’t be right. If your marker(s) are in model #1 you would need “vop boxes #0 #1 size 36”. What are you trying to do?</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span><a href="http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/vop.html#boxes" class="">http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/vop.html#boxes</a></div><div class=""><br class=""></div><div class=""> Tom</div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Apr 15, 2015, at 1:03 PM, Sushree Tripathy wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><span style="font-size:12.8000001907349px" class="">Hi,</span><div style="font-size:12.8000001907349px" class=""><br class=""></div><div style="font-size:12.8000001907349px" class="">I went through the chimera user's guide and as per the syntax used <font color="#ff0000" class="">"vop boxes #0 #0 useMarkerSize true" or "vop boxes #0 #0 size 36" </font>(the simplest case) to create a cubic box from my density map (54, 36, 51). It is neither giving me any error nor giving me the output map.</div><div style="font-size:12.8000001907349px" class=""><br class=""></div><div style="font-size:12.8000001907349px" class="">Please help.</div><div style="font-size:12.8000001907349px" class="">Thanks</div><div style="font-size:12.8000001907349px" class="">Sushree.</div><div style="font-size:12.8000001907349px" class=""><div class=""><div id=":363" class="" tabindex="0"><img class="" src="https://ssl.gstatic.com/ui/v1/icons/mail/images/cleardot.gif"></div><div id=":363" class="" tabindex="0"><br class=""></div></div></div><div class=""><div class="gmail_signature"><div dir="ltr" class="">Sushree Tripathy<div class="">Graduate Student</div><div class="">Department of Physics</div><div class="">University at Buffalo</div></div></div></div>
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