<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi ChuHui,<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>The <span style="color: rgb(255, 0, 255);" class="">(-17.1389, 19.0272) </span>is how far the axis extends in each direction from the center <span style="color: rgb(103, 78, 167);" class="">(-2.10322, 14.8383, 52.9855) </span>along the orientation vector <span style="color: rgb(0, 0, 255);" class="">(-0.15332, 0.981517, -0.114532)</span>. The list of numbers are IDs for the atoms that were used to define the axis — arbitrary integers assigned by the overall session-saving mechanism.</div><div class=""><br class=""></div><div class="">—Eric</div><div class=""><br class=""></div><div class=""><div class="">
<div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div class=""><span class="Apple-tab-span" style="white-space: pre;"> </span>Eric Pettersen</div><div class=""><span class="Apple-tab-span" style="white-space: pre;"> </span>UCSF Computer Graphics Lab</div></div>
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<div><br class=""><blockquote type="cite" class=""><div class="">On Jun 7, 2018, at 9:56 AM, ChuHui Fu <<a href="mailto:cfu@haverford.edu" class="">cfu@haverford.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><div class="">Hi Elaine,</div><div class=""><br class=""></div><div class="">Thank you for getting back to me.<span class="Apple-converted-space"> </span><br class=""></div><div class=""><br class=""></div><div class="">I think I managed to add the third axis by changing the session file on python. I am slightly confused about what<span style="color: rgb(255, 0, 255);" class=""><span class="Apple-converted-space"> </span>(-17.1389, 19.0272)</span><span class="Apple-converted-space"> </span>refers to in the following lines in session file:<br class=""></div><div class=""><br class=""></div><div class="">"geomData = {'AxisManager': {(7, 1, 'z', 0, 0.1,<span class="Apple-converted-space"> </span><span style="color: rgb(56, 118, 29);" class="">(1, 0, 0, 1)</span>,<span class="Apple-converted-space"> </span><span style="color: rgb(255, 0, 255);" class="">(-17.1389, 19.0272)</span>,<span style="color: rgb(103, 78, 167);" class=""><span class="Apple-converted-space"> </span>(-2.10322, 14.8383, 52.9855),</span><span class="Apple-converted-space"> </span><span style="color: rgb(0, 0, 255);" class="">(-0.15332, 0.981517, -0.114532)</span>, True): ([<span style="background-color: rgb(230, 145, 56);" class="">501, 500, 499, 603, 602, 498, 497, 606, 496, 598, 597, 494, 493, 605, 492, 593, 491, 490, 509, 489, 608, 488, 487, 486, 585, 485, 484, 483, 482, 481, 480, 479, 577, 576, 575, 621, 574, 573, 601, 572, 571, 570, 569, 568, 567, 600, 521, 565, 564, 542, 563, 562, 599, 561, 518, 559, 517, 504, 516, 495, 515, 557, 514, 541, 556, 566, 555, 554, 512, 629, 553, 552, 551, 550, 596, 625, 548, 623, 547, 520, 546, 595, 545, 544, 543, 508, 607, 507, 540, 620, 539, 506, 538, 519, 505, 594, 536, 619, 534, 618, 532, 531, 530, 616, 529, 528, 537, 613, 560, 527, 592, 526, 525, 524, 523, 522, 510, 591, 535, 590, 589, 533, 558, 604, 617, 587, 503, 586, 624, 584, 615, 614, 513, 583, 582, 612, 581, 588, 580, 628, 579, 611, 627, 578, 610, 626, 622, 502, 609, 511, 478, 549</span>], [], None), ...."<br class=""></div><div class=""><br class=""></div><div class="">Does it have to do with length? And is 0 defined as where the axis meets the centroid?<span class="Apple-converted-space"> </span><br class=""></div><div class="">I understand that the<span class="Apple-converted-space"> </span><span style="color: rgb(56, 118, 29);" class="">(1,0,0,1)<span class="Apple-converted-space"> </span></span>has to do with color,<span class="Apple-converted-space"> </span><span style="color: rgb(103, 78, 167);" class="">(-2.10322, 14.8383, 52.9855)</span><span class="Apple-converted-space"> </span>has to do with centroid, and<span style="color: rgb(0, 0, 255);" class=""><span class="Apple-converted-space"> </span>(-0.15332, 0.981517, -0.114532)<span class="Apple-converted-space"> </span><font class="">has to do with vector orientation.</font></span></div><div class=""><span style="color: rgb(0, 0, 255);" class=""><font class=""><br class=""></font></span></div><div class=""><span style="color: rgb(0, 0, 255);" class=""><font class="">I am also slightly confused about the long list of<span class="Apple-converted-space"> </span><span style="background-color: rgb(230, 145, 56);" class="">numbers</span><span class="Apple-converted-space"> </span>enclosed by the [ ]. I assume they have to do with amino acid residues? What does their order signify?<span class="Apple-converted-space"> </span><br class=""></font></span></div><div class=""><span style="color: rgb(0, 0, 255);" class=""><font class=""><br class=""></font></span></div><div class=""><span style="color: rgb(0, 0, 255);" class=""><font class="">Thanks again!<span class="Apple-converted-space"> </span><br class=""></font></span></div><div class=""><span style="color: rgb(0, 0, 255);" class=""><font class=""><br class=""></font></span></div><div class=""><span style="color: rgb(0, 0, 255);" class=""><font class="">CHuHui<br class=""></font></span></div><div class=""><br class=""></div></div><div class="gmail_extra" style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><br class=""><div class="gmail_quote">On Thu, Jun 7, 2018 at 12:19 PM, Elaine Meng<span class="Apple-converted-space"> </span><span dir="ltr" class=""><<a href="mailto:meng@cgl.ucsf.edu" target="_blank" class="">meng@cgl.ucsf.edu</a>></span><span class="Apple-converted-space"> </span>wrote:<br class=""><blockquote class="gmail_quote" style="margin: 0px 0px 0px 0.8ex; border-left-width: 1px; border-left-style: solid; border-left-color: rgb(204, 204, 204); padding-left: 1ex;">Hello ChuHui,<br class="">There is an option in “Define axes…” to create “Plane normals,” that is, an axis orthogonal to a plane.<br class=""><<a href="http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#axes" rel="noreferrer" target="_blank" class="">http://www.rbvi.ucsf.edu/<wbr class="">chimera/docs/<wbr class="">ContributedSoftware/<wbr class="">structuremeas/structuremeas.<wbr class="">html#axes</a>><br class=""><br class="">It can also be done with the “define axis” command:<br class=""><<a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/define.html#axis" rel="noreferrer" target="_blank" class="">http://www.rbvi.ucsf.edu/<wbr class="">chimera/docs/UsersGuide/midas/<wbr class="">define.html#axis</a>><br class=""><br class="">However, there is no option to define a plane from another object (plane, axis, or centroid), sorry. Planes can only be defined from sets of atoms or markers.<br class=""><br class="">Maybe interesting: you can show the inertia ellipsoid for a set of atoms using command “measure inertia”… the ellipsoid shows the principal axes in 3D:<br class=""><<a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#inertia" rel="noreferrer" target="_blank" class="">http://www.rbvi.ucsf.edu/<wbr class="">chimera/docs/UsersGuide/midas/<wbr class="">measure.html#inertia</a>><br class="">-----<br class="">Elaine C. Meng, Ph.D.<br class="">UCSF Chimera(X) team<br class="">Department of Pharmaceutical Chemistry<br class="">University of California, San Francisco<br class=""><div class="HOEnZb"><div class="h5"><br class="">> On Jun 7, 2018, at 7:47 AM, ChuHui Fu <<a href="mailto:cfu@haverford.edu" class="">cfu@haverford.edu</a>> wrote:<br class="">><span class="Apple-converted-space"> </span><br class="">> Hello,<br class="">> I am trying to define planes and axes that are orthogonal to the planes and axes that I have previously defined. I have an alpha helix, and I only managed to define one plane and two orthogonal axes around the helix. Is it possible to define the rest of the axes and planes?<span class="Apple-converted-space"> </span><br class="">> Thanks!<br class=""><br class=""></div></div></blockquote></div><br class=""><br clear="all" class=""><br class="">--<span class="Apple-converted-space"> </span><br class=""><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class="">ChuHui Fu </div><div class="">B.S.Candidate in Chemistry & Mathematics</div><div class=""><span style="font-size: 12.8px;" class="">Haverford College, Class of 2019</span><br class=""></div><div class=""><a href="mailto:cfu@haverford.edu" target="_blank" class="">cfu@haverford.edu</a></div><div class=""><br class=""></div></div></div></div></div></div></div></div></div></div></div></div><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">_______________________________________________</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">Chimera-users mailing list:<span class="Apple-converted-space"> </span></span><a href="mailto:Chimera-users@cgl.ucsf.edu" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">Chimera-users@cgl.ucsf.edu</a><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">Manage subscription:<span class="Apple-converted-space"> </span></span><a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a></div></blockquote></div><br class=""></div></body></html>