<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,<div class=""><br class=""></div><div class="">Sorry, Raster3D is what I meant. I know about the Volume Viewer and I have used it to produce some very nice ED figures. </div><div class=""><br class=""></div><div class="">The COOT save/RasMol import does not require all the fiddling with the Volume Viewer settings it is essentially what you see in COOT is what you get in pyMol but with better defination.</div><div class=""><br class=""></div><div class="">Thanks,</div><div class=""><br class=""></div><div class="">John</div><div class=""><br class=""></div><div class=""><br class=""><div class="">
<span class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; " class="">John Rose Ph.D.</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; " class="">Associate Professor</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; " class="">B204B, The Fred C. Davison Life Sciences Complex</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; " class="">120 Green Street</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; " class="">Department of Biochemistry and Molecular Biology</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; " class="">University of Georgia</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; " class="">Athens, GA 30602-7229</div><div class="">=========================================</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; " class="">Phone: <span class="Apple-converted-tab"> </span>706-542-1750</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; " class="">Fax:<span class="Apple-converted-tab"> </span>706-542-3077</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; " class=""><br class="khtml-block-placeholder"></div><br class="Apple-interchange-newline"></span>
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<br class=""><div><blockquote type="cite" class=""><div class="">On Feb 29, 2016, at 6:22 PM, Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" class="">meng@cgl.ucsf.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hi John,<div class="">I don’t know anything about Rasmol format from Coot, but I see it can write a Raster3D file. Chimera does not read rasmol or raster3D files, but it can certainly read density maps in many formats:</div><div class=""><<a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#volume" class="">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#volume</a>></div><div class=""><br class=""></div><div class="">…and has many options for density map display. Just open the density map with File… Open and then adjust the contour level interactively in the Volume Viewer, which will automatically appear when you open the map. You can show isosurfaces as mesh or transparent surfaces, color them however you like, control mesh linewidth, show only the density near some selected atoms, etc. </div><div class=""><div class=""><br class=""></div><div class="">Example images, tutorial:</div><div class=""><<a href="http://www.rbvi.ucsf.edu/chimera/features.html#density" class="">http://www.rbvi.ucsf.edu/chimera/features.html#density</a>></div><div class=""><<a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/density.html" class="">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/density.html</a>></div><div class=""><br class=""></div><div class="">Further, you can change the background color and turn on shadows, for example, commands:</div><div class="">set bgColor white</div><div class="">set shadows</div><div class=""><br class=""></div><div class="">If you want the mesh to look like solid sticks, try command “meshmol”</div><div class=""><<a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/meshmol.html" class="">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/meshmol.html</a>></div><div class=""><br class=""></div><div class="">Those are just a few options of many. I attached an example of meshmol with shadows below. I didn’t spend time optimizing appearance, but it gives you a rough idea.</div><div class="">I hope this helps,</div><div class="">Elaine<br class=""><div class="">----------<br class="">Elaine C. Meng, Ph.D. <br class="">UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab<br class="">Department of Pharmaceutical Chemistry<br class="">University of California, San Francisco<br class=""><br class=""></div><div class=""><span id="cid:20419ED3-81F3-4E3E-81E0-80DF42E1FDDF@compbio.ucsf.edu"><image2.png></span></div><div class=""><br class=""></div><br class=""><blockquote type="cite" class="">On Feb 29, 2016, at 7:22 AM, John Rose <<a href="mailto:rose@bcl4.bmb.uga.edu" class="">rose@bcl4.bmb.uga.edu</a>> wrote:<br class=""><br class="">Hi,<br class="">I colleague of mine just showed me that pyMOL can display great looking ED images from COOT which were saved in RASMOL format. Is there a way for CHIMERA to do this.<br class="">John Rose<br class=""> <br class=""></blockquote><br class=""></div></div></div></div></blockquote></div><br class=""></div></body></html>