<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div>On Mar 9, 2010, at 2:17 PM, Francesco Pietra wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Hello Eric:<br>I have seen your later correction mail.<br><br>I had a bad day, that is little time for chimera and with little<br>success. Please try to guess were I was faulty.<br><br>francesco@tya64:~$ chimera --version<br>chimera alpha version 1.5 (build 30193) 2010-03-06 09:27:34 GMT<br>francesco@tya64:~$<br>This is amd64, at the moment I have no 32bit computer.<br><br><select ligand> selects too much.<br><br><select :residue.number><br><select :residue.name><br>do select exactly what I want (which is a small ligand of HEME ligand<br>of the protein.<br><br>The problem was with <define> command<br><br>MD-movie...Per-Frame "define centroid :residue.number" ... Apply<br><br>then activating the movie gave the same view as not going through the<br>Per_Frame, i.e., the small ligand does not leave any sphere on the<br>path. I did not investigate if the sphere are too small to be seen at<br>the magnification I used, ore have the same color as the background<br>(black). Very likely, I did some other major mistake.<br></div></blockquote></div><br><div>Not sure what to say. Works for me. I've appended an image of centroids tracing the motion of a small ligand in an RNA binding site. I used a step size of 10 and this 'define' command:</div><div><br></div><div>define centroid raiseTool false radius 1.0 color goldenrod sel</div><div><br></div><div>"raiseTool false" prevents 'define' from trying to bring up the Axes/Planes/Centroids tool (and update that tool's table) for every centroid created. The other options control the size and color of the centroid. I had the small ligand selected so 'sel' is my atom spec. I tried it a second time with ":35" (which also selects the small ligand) and that worked too.</div><div><br></div><div>FYI, "~define" will get rid of all the centroids.</div><div><br></div><div>I hope this helps somehow. Are you sure you had the "Interpret script as" part of the per-frame dialog set to "Chimera commands"? I can't imagine that you didn't, since you would have gotten some kind of error if it had been interpreted as Python.</div><div><br></div><div>--Eric</div><br><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><img height="763" width="618" apple-width="yes" apple-height="yes" src="cid:A6888701-DD99-4804-8281-A0EE8FADC23A@cgl.ucsf.edu"></body></html>