<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 <span style="font-family: -webkit-system-font, "Helvetica Neue", Helvetica, sans-serif;" class="">Michał,</span><div class=""><font face="-webkit-system-font, Helvetica Neue, Helvetica, sans-serif" class=""><br class=""></font></div><div class=""><font face="-webkit-system-font, Helvetica Neue, Helvetica, sans-serif" class=""> The values of a 3d image (volume) are considered to be intensities at a 3d grid of points. Each of these points is at the center of a small cube called a voxel, the size of a voxel is part of the image file and is sometimes referred to as the grid plane spacing. The outline box exactly includes all voxels in the grid. So for instance if your data is 2 by 2 by 2 grid points with voxel size 1.2 Angstroms along each axis, then the outline box with be 2.4 Angstroms on a side. The rendered graphics, either contour surface, or solid (volumetric) rendering only extends to the boundary grid points and does not cover boundary voxels. So the surface or solid leaves half a voxel padding around the boundary relative to the outline box. The reason for this is that surface and solid rendering uses linear interpolation of data values between grid points — since there is not grid point beyond the boundary it cannot interpolate beyond the center point of the edge voxels. That would require extrapolating or making some assumption like the values are zero outside the grid, and Chimera does not do that.</font></div><div class=""><font face="-webkit-system-font, Helvetica Neue, Helvetica, sans-serif" class=""><br class=""></font></div><div class=""><font face="-webkit-system-font, Helvetica Neue, Helvetica, sans-serif" class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Tom</font></div><div class=""><font face="-webkit-system-font, Helvetica Neue, Helvetica, sans-serif" class=""><br class=""></font><div><br class=""><blockquote type="cite" class=""><div class="">On Nov 21, 2017, at 8:40 AM, Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" class="">meng@cgl.ucsf.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><meta http-equiv="Content-Type" content="text/html charset=utf-8" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div class=""><blockquote type="cite" class=""><br class="Apple-interchange-newline"><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;" class=""><b class="">From: </b></span><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class="">Michał Kadlof <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;" class=""><b class="">Subject: </b></span><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class=""><b class="">Does volume outline is bigger than actual volume?</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;" class=""><b class="">Date: </b></span><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class="">November 21, 2017 at 6:00:17 AM PST</span></div><br class=""><div class=""><div dir="ltr" class=""><div class="gmail_default" style="font-family:monospace,monospace">Hello, <br class=""></div><div class="gmail_default" style="font-family:monospace,monospace"><br class=""></div><div class="gmail_default" style="font-family:monospace,monospace">I need to understand precisely what Chimera do. Please look at the attached screen shoot. The arrows are anchored in point (0,0,0), and they are point in direction [(1,0,0),(0,1,0),(0,0,1)] red, yellow and blue respectively.<br class=""></div><div class="gmail_default" style="font-family:monospace,monospace"><br class=""></div><div class="gmail_default" style="font-family:monospace,monospace">I set my volume to minimum (grey cube), I checked "Show outline box using color", and I noticed it does not cover the shape of my volume.</div><div class="gmail_default" style="font-family:monospace,monospace"><br class=""></div><div class="gmail_default" style="font-family:monospace,monospace">There are "margins" in the top, and the bottom visible in the image and much smaller on the sides.</div><div class="gmail_default" style="font-family:monospace,monospace"><br class=""></div><div class="gmail_default" style="font-family:monospace,monospace">Why they are there? What is its exact size? Where does volume actually begins in the (0,0,0), or slightly below that point?<br class=""></div><div class="gmail_default" style="font-family:monospace,monospace"><br clear="all" class=""></div><div class=""><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><span style="font-family:monospace,monospace" class="">--<br class=""><div style="font-family:monospace,monospace;display:inline" class="gmail_default">best wishes,</div><div style="font-family:monospace,monospace;display:inline" class="gmail_default"><span style="font-family:monospace,monospace" class=""><br class=""></span></div><div style="font-family:monospace,monospace;display:inline" class="gmail_default"><span style="font-family:monospace,monospace" class="">Michał Kadlof <<a href="mailto:m.kadlof@cent.uw.edu.pl" target="_blank" class="">m.kadlof@cent.uw.edu.pl</a>></span><br class=""></div></span></div></div></div></div></div></div>
</div>
</div></blockquote></div><br class=""></div>_______________________________________________<br class="">Chimera-users mailing list: <a href="mailto:Chimera-users@cgl.ucsf.edu" class="">Chimera-users@cgl.ucsf.edu</a><br class="">Manage subscription: <a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" class="">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br class=""></div></blockquote></div><br class=""></div></body></html>