<div dir="ltr"><div>Hi Elaine,</div><div><br></div><div>Thank you for getting back to me. <br></div><div><br></div><div>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)"> (-17.1389, 19.0272)</span> refers to in the following lines in session file:<br></div><div><br></div><div>"geomData = {'AxisManager': {(7, 1, 'z', 0, 0.1, <span style="color:rgb(56,118,29)">(1, 0, 0, 1)</span>, <span style="color:rgb(255,0,255)">(-17.1389, 19.0272)</span>,<span style="color:rgb(103,78,167)"> (-2.10322, 14.8383, 52.9855),</span> <span style="color:rgb(0,0,255)">(-0.15332, 0.981517, -0.114532)</span>, True): ([<span style="background-color:rgb(230,145,56)">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></div><div><br></div><div>Does it have to do with length? And is 0 defined as where the axis meets the centroid? <br></div><div>I understand that the <span style="color:rgb(56,118,29)">(1,0,0,1) </span>has to do with color, <span style="color:rgb(103,78,167)">(-2.10322, 14.8383, 52.9855)</span> has to do with centroid, and<span style="color:rgb(0,0,255)"> (-0.15332, 0.981517, -0.114532) <font color="#000000">has to do with vector orientation.</font></span></div><div><span style="color:rgb(0,0,255)"><font color="#000000"><br></font></span></div><div><span style="color:rgb(0,0,255)"><font color="#000000">I am also slightly confused about the long list of <span style="background-color:rgb(230,145,56)">numbers</span> enclosed by the [ ]. I assume they have to do with amino acid residues? What does their order signify? <br></font></span></div><div><span style="color:rgb(0,0,255)"><font color="#000000"><br></font></span></div><div><span style="color:rgb(0,0,255)"><font color="#000000">Thanks again! <br></font></span></div><div><span style="color:rgb(0,0,255)"><font color="#000000"><br></font></span></div><div><span style="color:rgb(0,0,255)"><font color="#000000">CHuHui<br></font></span></div><div><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Thu, Jun 7, 2018 at 12:19 PM, Elaine Meng <span dir="ltr"><<a href="mailto:meng@cgl.ucsf.edu" target="_blank">meng@cgl.ucsf.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hello ChuHui,<br>
There is an option in “Define axes…” to create “Plane normals,” that is, an axis orthogonal to a plane.<br>
<<a href="http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#axes" rel="noreferrer" target="_blank">http://www.rbvi.ucsf.edu/<wbr>chimera/docs/<wbr>ContributedSoftware/<wbr>structuremeas/structuremeas.<wbr>html#axes</a>><br>
<br>
It can also be done with the “define axis” command:<br>
<<a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/define.html#axis" rel="noreferrer" target="_blank">http://www.rbvi.ucsf.edu/<wbr>chimera/docs/UsersGuide/midas/<wbr>define.html#axis</a>><br>
<br>
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>
<br>
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>
<<a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#inertia" rel="noreferrer" target="_blank">http://www.rbvi.ucsf.edu/<wbr>chimera/docs/UsersGuide/midas/<wbr>measure.html#inertia</a>><br>
-----<br>
Elaine C. Meng, Ph.D.<br>
UCSF Chimera(X) team<br>
Department of Pharmaceutical Chemistry<br>
University of California, San Francisco<br>
<div class="HOEnZb"><div class="h5"><br>
> On Jun 7, 2018, at 7:47 AM, ChuHui Fu <<a href="mailto:cfu@haverford.edu">cfu@haverford.edu</a>> wrote:<br>
> <br>
> Hello,<br>
> 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? <br>
> Thanks!<br>
<br>
</div></div></blockquote></div><br><br clear="all"><br>-- <br><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div>ChuHui Fu </div><div>B.S.Candidate in Chemistry & Mathematics</div><div><span style="font-size:12.8px">Haverford College, Class of 2019</span><br></div><div><a href="mailto:cfu@haverford.edu" target="_blank">cfu@haverford.edu</a></div><div><br></div></div></div></div></div></div></div></div></div></div></div>
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