<html><head><meta http-equiv="Content-Type" content="text/html charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Esther,<div><br></div><div> Here are example commands that open a map, show two contour levels 0.8 blue, and 1.0 yellow, and clip perpendicular to the z axis with a slab of thickness 10 Angstroms.<br><div><br></div><div>open emdbID:1080</div><div>volume #0 level .8 color blue level 1 color yellow</div><div>mclip #0 axis z coord local origin 0,0,0 slab true thickness 10</div><div><br></div><div>This doesn't look good though because the blue and yellow flat surfaces at the clip plane are exactly overlapped so the graphics shows one or the other based on floating point round-off errors and it looks like a scrambled set of triangles. So your "kludge" method is in fact better. Here's an example of that.</div><div><br></div><div>open emdbID:1080</div><div>vop scale #0</div><div>volume #0 level 0.8 color blue</div><div>volume #1 level 1.0 color yellow</div><div>mclip #0,1 axis z coord local origin 0,0,0 slab true thickness 10 stagger 0.5</div><div><br></div><div>The "vop scale #0" copies volume 0 (scales it by default factor = 1). The mclip command now has the extra "stagger 0.5" option to offset the clip planes of the different models by 0.5 Angstroms.</div><div><br></div><div> I've attached pictures of the results of these two methods.</div><div><br></div><div> When using the volume dialog you can add extra contour levels by ctrl-click on the histogram.</div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>Tom</div><div><br></div><div><br></div><div><img height="384" width="512" apple-width="yes" apple-height="yes" id="938b242e-d602-4460-8792-754a45338bd8" src="cid:3E19BBFF-0E92-4015-9560-997E92EB6217@cgl.ucsf.edu"><img height="384" width="512" apple-width="yes" apple-height="yes" id="82c627fc-c7bb-4b21-8a83-ca0fe3655296" src="cid:5D184462-BF0D-47C5-9AA2-367240ECD110@cgl.ucsf.edu"></div><div><div><div>On May 8, 2013, at 3:04 PM, Bullitt Esther wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">Hi,<br><br>Is it possible to choose n levels of gray for a volume map? I'd like to make a known-thickness slice using clip, and then see that slice as a defined number of colors.<br><br>I can kluge it by displaying the map 4 times at 4 contour levels, but is there a better way?<br><br>thanks,<br>Esther<br>---<br>Esther Bullitt, Ph.D.<br>Dept. of Physiology & Biophysics<br>Boston University School of Medicine<br>700 Albany Street, Room W302<br>Boston, MA 02118-2526<br><br>Email: <a href="mailto:bullitt@bu.edu">bullitt@bu.edu</a><br>Telephone: 617-638-5037<br>Facsimile: 617-638-4041<br><a href="http://www.bumc.bu.edu/phys-biophys/faculty/bullitt">http://www.bumc.bu.edu/phys-biophys/faculty/bullitt</a><br><br><br>_______________________________________________<br>Chimera-users mailing list<br>Chimera-users@cgl.ucsf.edu<br>http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users<br><br></blockquote></div><br></div></div></body></html>