<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Looking at Tom's "plans" page (<a href="http://www.cgl.ucsf.edu/chimera/plans.html)">http://www.cgl.ucsf.edu/chimera/plans.html)</a>, I see this feature listed there (#57). According to the blurb for #57, Karin Gross and Christoph Best have written an extension called TomoPlane for doing this: <a href="http://tigertiger.de/cb/TomoPlane/index.html">Christoph Best: TomoPlane</a><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><br class="Apple-interchange-newline"></div></span> </div><br><div><div>On Aug 7, 2008, at 10:59 AM, Jeff Triffo wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>yes,<br><br>that would work but seems tedious for frequent use, and assumes the <br>desired orientation is known. There is a capability in IMOD to do this <br>"live" through their 3dmod Slicer viewer - which I have been assuming <br>just does on-the-fly interpolation of the data, because it is a live <br>update. It's an incredibly useful function to have access to because the <br>user is often "hunting" for the right orientation for a slice, and I <br>often find myself wanting it in Chimera. So I find myself doing quite a <br>bit of pre-work modeling in 3dmod prior to being able to jump to Chimera.<br><br>but, for now, I could just find desired orientations in IMOD, and try to <br>reproduce that using a resampling of the entire volume in Chimera. In my <br>case, that would require knowing the relationships between the Euler <br>convention in 3dmod and Chimera, along with where each program defines <br>the center of rotation (which I have looked into many times for various <br>reasons - such as using IMOD models superimposed with volume displays in <br>Chimera - but always forget soon after).<br><br>-Jeff<br><br><br>Elaine Meng wrote:<br><blockquote type="cite">Hi Jeff,<br></blockquote><blockquote type="cite">That's definitely a Tom Goddard question, but he is away on vacation <br></blockquote><blockquote type="cite">this week.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Pending a definitive answer, I am guessing it is not in the plans. <br></blockquote><blockquote type="cite">However, I believe you can do what you want by resampling the data on <br></blockquote><blockquote type="cite">a differently oriented grid, and then using the "Planes" feature on <br></blockquote><blockquote type="cite">that second, resampled set of data. You would generate the resampled <br></blockquote><blockquote type="cite">data using the "Subregion selection" feature of Volume Viewer, by <br></blockquote><blockquote type="cite">turning on "Select subregions..." with the mouse, and after drawing <br></blockquote><blockquote type="cite">the selection box, turning on "Rotate selection box" and change the <br></blockquote><blockquote type="cite">orientation as desired, then clicking the Resample button. This does <br></blockquote><blockquote type="cite">not mess up your original data, just creates an additional, resampled <br></blockquote><blockquote type="cite">data set.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Downsides are that it may take some coordination or a couple of tries <br></blockquote><blockquote type="cite">to rotate the box as desired, and resampling causes some loss of <br></blockquote><blockquote type="cite">resolution. It may be that resampling is necessary for showing <br></blockquote><blockquote type="cite">arbitrarily oriented planes, however, even if such an option were <br></blockquote><blockquote type="cite">added to the GUI.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">I hope this helps,<br></blockquote><blockquote type="cite">Elaine<br></blockquote><blockquote type="cite">-----<br></blockquote><blockquote type="cite">Elaine C. Meng, Ph.D. <a href="mailto:meng@cgl.ucsf.edu">meng@cgl.ucsf.edu</a><br></blockquote><blockquote type="cite">UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab<br></blockquote><blockquote type="cite">Department of Pharmaceutical Chemistry<br></blockquote><blockquote type="cite">University of California, San Francisco<br></blockquote><blockquote type="cite"> <a href="http://www.cgl.ucsf.edu/home/meng/index.html">http://www.cgl.ucsf.edu/home/meng/index.html</a><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">On Aug 7, 2008, at 10:07 AM, Jeff Triffo wrote:<br></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">anyone know if the volume plane tool will support arbitrary orientation<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">of the plane any time soon?<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">-Jeff<br></blockquote></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><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>