<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div>Hi Francesco,</div><div><br></div><div>On Apr 19, 2010, at 12:29 AM, Francesco Pietra wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><span class="Apple-style-span" style="font-family: monospace; ">If at all, I did not understand if a continuous trace of the centroid<br>(instead of a series of balls) can be obtained in the context of the<br>protein. That would improve the presentation further. Otherwise, the<br>series of balls for the centroid, with appropriate choice of radius<br>and step size, shows the pathway of the ligand through the protein<br>adequately.<br></span></span></blockquote><div><br></div>Nothing simple comes to mind. One way that's a bit of work would be to save the centroid information to a file (the 'Save' button on the Axes/Planes/Centroids interface) and the use a text editor to create a BILD file (<a href="http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/bild.html">BILD format</a>) showing lines/cylinders connecting the centroid centers.</div><div><br><blockquote type="cite"><span class="Apple-style-span" style="font-family: monospace; ">As a minor point, I was unable to render helices transparent.<br>Transparency would help to to see the centroid trajectory in between<br>helices.<br></span></blockquote><br></div><div>Should be possible unless there's something wrong with your graphics cards. Try this:</div><div><br></div><div>Select->Structure->secondary structure->helix</div><div>Actions->Color->from editor</div><div><br></div><div>This will bring up a color editor. Try making a transparent red. For me, the editor looks like this when I do that:</div><div><br></div><div><img height="264" width="252" apple-width="yes" apple-height="yes" src="cid:52FDF9A2-BF89-40E7-98CC-08E9FE297150@cgl.ucsf.edu"></div><div>(note the "Opacity" box is checked)</div><div><br></div><div>and the structure looks like this:</div><div><br></div><div><img height="668" width="747" apple-width="yes" apple-height="yes" src="cid:94ED56EE-2434-40E2-ADE3-0DC608484C3A@cgl.ucsf.edu"></div><div><br></div><div>--Eric</div><div><br></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><br class="Apple-interchange-newline"></div></span> </div><br></body></html>