[Chimera-users] defining planes and axes based on existing ones

[Eric Pettersen]

Hi ChuHui,
	The (-17.1389, 19.0272) is how far the axis extends in each direction from the center (-2.10322, 14.8383, 52.9855) along the orientation vector (-0.15332, 0.981517, -0.114532).  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.

—Eric

	Eric Pettersen
	UCSF Computer Graphics Lab

> On Jun 7, 2018, at 9:56 AM, ChuHui Fu <cfu at haverford.edu> wrote:
> 
> Hi Elaine,
> 
> Thank you for getting back to me. 
> 
> I think I managed to add the third axis by changing the session file on python. I am slightly confused about what (-17.1389, 19.0272) refers to in the following lines in session file:
> 
> "geomData = {'AxisManager': {(7, 1, 'z', 0, 0.1, (1, 0, 0, 1), (-17.1389, 19.0272), (-2.10322, 14.8383, 52.9855), (-0.15332, 0.981517, -0.114532), True): ([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], [], None), ...."
> 
> Does it have to do with length? And is 0 defined as where the axis meets the centroid? 
> I understand that the (1,0,0,1) has to do with color, (-2.10322, 14.8383, 52.9855) has to do with centroid, and (-0.15332, 0.981517, -0.114532) has to do with vector orientation.
> 
> I am also slightly confused about the long list of numbers enclosed by the [ ]. I assume they have to do with amino acid residues? What does their order signify? 
> 
> Thanks again! 
> 
> CHuHui
> 
> 
> On Thu, Jun 7, 2018 at 12:19 PM, Elaine Meng <meng at cgl.ucsf.edu <mailto:meng at cgl.ucsf.edu>> wrote:
> Hello ChuHui,
> There is an option in “Define axes…” to create “Plane normals,” that is, an axis orthogonal to a plane.
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#axes <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#axes>>
> 
> It can also be done with the “define axis” command:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/define.html#axis <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/define.html#axis>>
> 
> 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.
> 
> 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:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#inertia <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#inertia>>
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> > On Jun 7, 2018, at 7:47 AM, ChuHui Fu <cfu at haverford.edu <mailto:cfu at haverford.edu>> wrote:
> > 
> > Hello,
> > 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? 
> > Thanks!
> 
> 
> 
> 
> -- 
> ChuHui Fu 
> B.S.Candidate in Chemistry & Mathematics
> Haverford College, Class of 2019
> cfu at haverford.edu <mailto:cfu at haverford.edu>
> 
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