<html><head><meta http-equiv="Content-Type" content="text/html charset=windows-1252"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">Hi Guizhen,<div><br></div><div> Here are a few more details. This is kind of tricky because Chimera focuses on 3d images, not 2d plots.</div><div><br></div><div> Use volume dialog menu Features / Planes to show one plane of your map, switch to surface style, use volume dialog menu Tools / Surface Color and color the plane by "volume data value”. Now we make the contour lines by making a copy of the map, volume dialog menu File / Duplicate, show the same plane, set style to Mesh, turn off the “Cap high values at box faces” option (Features / Surface and Mesh Options), add more contour levels using ctrl-click on the histogram, increase line thickness (Featues / Surface and Mesh Options), color all levels black (command "color black #1”). Since the planes are at exactly the same level the contour lines are probably hidden. To fix this move the contour plane slightly forward with command “move z 1 model #1 coord #1” (move map #1 by 1 Angstrom along the z direction of the coordinate system of map #1). I did this on a ryanodine receptor map, emdb 5014 (plane 89). Here’s the result.</div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>Tom</div><div><br></div><div><img height="480" width="480" apple-width="yes" apple-height="yes" apple-inline="yes" id="84DC7AA9-5ED5-499D-BF77-FBC4A508817C" src="cid:AA542426-475E-424A-A4AF-1A2B8F6CD933@cgl.ucsf.edu"></div><div><br></div><div><img height="331" width="640" apple-width="yes" apple-height="yes" apple-inline="yes" id="7B6FF218-1D3A-421D-BBAF-E81B63422C9B" src="cid:4DA3E6F7-7E56-4F07-A354-E450DA49142D@cgl.ucsf.edu"></div><div><br></div><div><br><div><div>On Nov 5, 2014, at 10:36 AM, Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu">meng@cgl.ucsf.edu</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">Hi Guizhen,<div>I don’t know of a way to make a figure exactly like yours, with colors between black lines. However, I know how to show a slice in which the contour lines themselves are colored, as in the attached image. To make that image, I used the “Planes” feature in Volume Viewer, with multiple contour levels and other specific settings as described in this previous post:</div><div><br></div><div><<a href="http://plato.cgl.ucsf.edu/pipermail/chimera-users/2010-August/005454.html">http://plato.cgl.ucsf.edu/pipermail/chimera-users/2010-August/005454.html</a>></div><div><br></div><div>I hope this helps,</div><div>Elaine</div><div>-----<br>Elaine C. Meng, Ph.D. <br>UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab<br>Department of Pharmaceutical Chemistry<br>University of California, San Francisco<br></div><div><br></div><div><span><contourlines.png></span><br>On Nov 5, 2014, at 7:41 AM, Fan, Guizhen <<a href="mailto:Guizhen.Fan@uth.tmc.edu">Guizhen.Fan@uth.tmc.edu</a>> wrote:<br><br><blockquote type="cite">Hi,<br>How can I get multi contour lines like attached figure?<br>Thank you.<br>Guizhen</blockquote></div><br><br></div>_______________________________________________<br>Chimera-users mailing list<br><a href="mailto:Chimera-users@cgl.ucsf.edu">Chimera-users@cgl.ucsf.edu</a><br>http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users<br></blockquote></div><br></div></body></html>