<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Unfortunately another issue is that neon knows nothing about metal-coordination pseudobonds and will not depict them. So you would have to put distance monitors wherever you want dashed lines... <div><br></div><div>--Eric</div><div><br><div apple-content-edited="true"> <span class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 16px; 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="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; "><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>Eric Pettersen</font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>UCSF Computer Graphics Lab</font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> </span><a href="http://www.cgl.ucsf.edu">http://www.cgl.ucsf.edu</a></font></p></div></span> </div><br><div><div>On Dec 23, 2009, at 10:03 AM, Elaine Meng wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Hi Thomas,<br>If you are on a non-Windows system, you could try the "neon" command -- this generates a static, shadowed image in which any dashed lines are shown as a series of short cylinders (actually more like medicine capsules since they have rounded ends).<br><br>The "neon" command is actually built on top of the "conic" command. Both make static images (not interactively rotatable) and share a large number of command-line options, but conic was meant to show CPK or spacefill, while neon extends it to showing tubes and sticks.<br><br><<a href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/neon.html">http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/neon.html</a>><br><<a href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/neon1.html">http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/neon1.html</a>><br><<a href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/conic.html">http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/conic.html</a>><br><<a href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/conic1.html">http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/conic1.html</a>><br><br>There are several potential caveats besides the unavailability of neon on Windows:<br><br>- the distance value is not shown<br>- dashed line style (dot-dash, spacing etc.), background color, lighting directions etc. are not taken directly from the Chimera settings but specified separately...<br>- there are many many options for both conic and neon, and neon reads a "neon.dat" control file<br><br>I guess the latter is really a double-edged sword, in that it is nice to have so many options, but potentially time-consuming to figure out how to deploy them. As a first stab you could just try the defaults, not specifying any options. I attach two images of a short peptide with distance measurement: image saved the normal way in Chimera and the result of using the command (on Mac):<br><br>neon -f tiff -o ~/Desktop/junk.tiff -s<br><br>Or, if you are on Windows it is all moot (sorry!) but perhaps other users would be interested.<br>Elaine<br>-----<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><br><span><image1.png></span><span><image.tiff></span><br><br><br>_______________________________________________<br>Chimera-users mailing list<br><a href="mailto:Chimera-users@cgl.ucsf.edu">Chimera-users@cgl.ucsf.edu</a><br>http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users<br></div></blockquote></div><br></div></body></html>