<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=""> In Chimera “atoms” means an atomic model, for example from a PDB file, not a density map. If you want to reduce your map to a cube by cropping and it is size 54,36,51 use command<div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>volume #0 region 0,0,0,35,35,35</div><div class=""><br class=""></div><div class="">That gets the lower left corner. To get the center part</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>volume #0 region 9,0,7,44,35,42</div><div class=""><br class=""></div><div class="">The 6 numbers are imin,jmin,kmin,imax,jmax,kmax where i,j,k are indices along the 3 map axes. You can also do this with the Volume Viewer dialog menu entry Features / Region Bounds, or interactively with the mouse using Features / Subregion Selection. For more info about map manipulations</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/data/tutorials/volumetour/volumetour.html" class="">http://www.cgl.ucsf.edu/chimera/data/tutorials/volumetour/volumetour.html</a></div><div class=""><br class=""></div><div class=""> Tom</div><div class=""><br class=""></div><div class=""><br class=""><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Apr 15, 2015, at 1:17 PM, Sushree Tripathy wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">Hi,<div class=""><br class=""></div><div class="">Thanks for your prompt reply. What I am trying to do is I have a map which I have loaded in chimera as #0. Now I want to reduce it to cubic size. Since the syntax is "<a name="boxes" style="font-family: 'Times New Roman'; font-size: inherit;" class=""><b class="">vop boxes</b></a><span style="font-family: 'Times New Roman'; font-size: inherit;" class=""> </span><i style="font-family: 'Times New Roman'; font-size: inherit;" class="">volume-spec</i><span style="font-family: 'Times New Roman'; font-size: inherit;" class=""> </span><a href="https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html" target="_top" style="font-family: 'Times New Roman'; font-size: inherit;" class=""><i class="">atom-spec</i></a><span style="font-family: 'Times New Roman'; font-size: inherit;" class=""> </span><b style="font-family: 'Times New Roman'; font-size: inherit;" class="">size</b><span style="font-family: 'Times New Roman'; font-size: inherit;" class=""> </span><i style="font-family: 'Times New Roman'; font-size: inherit;" class="">d", </i><span style="font-family: 'Times New Roman'; font-size: inherit;" class="">so I am choosing #0 for my volume and all the atoms in that volume. so #0 again. Please correct me if I am wrong.</span></div><div class=""><span style="font-family: 'Times New Roman'; font-size: inherit;" class=""><br class=""></span></div><div class=""><span style="font-family: 'Times New Roman'; font-size: inherit;" class=""><br class=""></span></div><div class=""><span style="font-family: 'Times New Roman'; font-size: inherit;" class="">Thanks</span></div><div class=""><span style="font-family: 'Times New Roman'; font-size: inherit;" class="">Sushree.</span></div></div><div class="gmail_extra"><br clear="all" class=""><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>
<br class=""><div class="gmail_quote">On Wed, Apr 15, 2015 at 4:13 PM, Tom Goddard wrote:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word" 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 style="white-space:pre-wrap" class=""> </span><a href="http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/vop.html#boxes" target="_blank" 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 class=""><blockquote type="cite" class=""><div class=""><div class="h5"><div class="">On Apr 15, 2015, at 1:03 PM, Sushree Tripathy wrote:</div><br class=""></div></div><div class=""><div class=""><div class="h5"><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 class=""><img src="https://ssl.gstatic.com/ui/v1/icons/mail/images/cleardot.gif" class=""></div><div class=""><br class=""></div></div></div><div class=""><div class=""><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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