<html><head><meta http-equiv="Content-Type" content="text/html charset=windows-1252"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">So I enhanced the "define axis" command so that if your atom spec is just a single plane identifier, it will create an axis normal to the plane. You have no control over the length of the axis, but I hope I've picked a reasonable default (1/2 the plane radius) and since you really want it for measurement purposes hopefully it doesn't really matter too much. Available in tonight's daily build.<div><br></div><div>It will be awhile before I add the corresponding capability to the graphical interface.</div><div><br></div><div>--Eric</div><div><br><div><div>On Apr 7, 2015, at 11:32 AM, Oliver Clarke <<a href="mailto:olibclarke@gmail.com">olibclarke@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><meta http-equiv="Content-Type" content="text/html charset=windows-1252"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Thanks Elaine, that’s very helpful indeed. The other way I figured out was to define two centroids using a single atom from each subunit in the channel from two sets of residues in different planes (which would otherwise define two parallel planes) and define an axis from the two resultant centroids. Your way looks more general though - I will see if I can figure out a way to put it into an alias so I can call it with a single command.<div class=""><br class=""></div><div class="">Best,</div><div class="">Oliver.</div><div class=""><br class=""></div><div class=""><br class=""><div class=""><div><blockquote type="cite" class=""><div class="">On Apr 7, 2015, at 1:09 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=""><meta http-equiv="Content-Type" content="text/html charset=windows-1252" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; " class="">Hi Oliver,<div class=""><div class="">If you have a plane defined in Axes/Planes/Centroids, you can write out its information including the normal (Save button on that tool), then place atoms at either end allowing you to define the axis. There are a few steps...</div><div class=""><br class=""></div><div class="">In my little test, the plane output information included:</div><div class=""><br class=""></div><div class=""><div class="">Planes</div><div class="">plane name, ID, center, normal, radius</div><div class="">plane: p1 ( 19.023, 17.733, 7.080) (-0.380, 0.757, 0.531) 24.199</div><div class=""><br class=""></div><div class="">Then I used Tools… Build Structure, Start Structure, add atom at specific coordinates to add two atoms, one at the center of that plane and one to show the normal. The latter's coordinates are (center + normal) coordinates, and you can multiply the normal coordinates by some constant to make the axis longer. For example, I multiplied the normal coordinates by 10 before adding them to the center coordinates to give the position of the second atom as:</div><div class=""><br class=""></div><div class="">x 15.223 y 25.303 z 12.390</div><div class=""><br class=""></div><div class="">Then I selected the two new atoms and used them to define an axis in Axes/Planes/Centroids, see attached image.</div><div class="">I hope this helps,</div><div class="">Elaine</div><div apple-content-edited="true" class="">
<span class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px; "><div class="">----------</div><div class="">Elaine C. Meng, Ph.D. </div><div class="">UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab</div><div class="">Department of Pharmaceutical Chemistry</div><div class="">University of California, San Francisco</div><div class=""><br class=""></div><div class=""><span id="cid:45F66EEC-1474-44FB-9BE7-09E43209660E@compbio.ucsf.edu"><junk.png></span></div></span><br class="Apple-interchange-newline">
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<div class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; " class=""><div class=""><div class="">On Apr 6, 2015, at 5:01 PM, Oliver Clarke <<a href="mailto:olibclarke@gmail.com" class="">olibclarke@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite" class="">Alternatively, would it be possible (or is there some way already) to define a separate axis that is the normal of a plane? In this case I’m working with an ion channel, so I’m looking for a consistent way to represent the change in orientation of particular extramembrane domains with respect to the channel axis. If I could define an axis for the membrane plane normal, I could at least measure the absolute orientation of the principal axes of particular domains or individual helices with respect to the channel axis. It seems like the plane normal is computed already (because there is an option in axes/planes/centroids) to align screen x/y/z to it, but I can’t see a way to generate it as a separate axis that I can use for measuring angles etc.<br class=""><br class="">Thanks for all your help as always!<br class=""><br class="">Oliver.<br class=""></blockquote></div><br class=""></div></div><br class=""></div></div></div></div></blockquote></div><br class=""></div></div></div>_______________________________________________<br>Chimera-users mailing list<br><a href="mailto:Chimera-users@cgl.ucsf.edu">Chimera-users@cgl.ucsf.edu</a><br>http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users<br></blockquote></div><br></div></body></html>