Hi Everyone, Hopefully this isn't a stupid question. I've used the define plane command for a few residues of slightly twisted beta-strand, trying to judge the distance and twist in relation to a helix across the binding groove at different conditions. It seems to work the way I would like it to, but I would like to know in more specific terms, how the plane is actually determined. When the structure measurements data is saved, the file returns the center coordinate, normal vector, and the radius. Could anyone tell me how these values are determined? For define axes, I can follow references from ksdssp, but there's really no similar definition for the define plane command in the user documentation. Thanks, Steve
Hi Steven, I wouldn't go by any information for "ksdssp," as that is completely separate from Axes/Planes/Centroids calculations. Axes/Planes/Centroids: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/struc...> "Each axis is anchored at the the centroid of the defining atomic coordinates and aligned with the principal component of the coordinates (prior to any helical correction)." There is also a choice of mass-weighting or not. If you choose the each-helix option, it is only using the backbone atoms N,CA,C. The plane is the best-fit plane to the specified points (atoms). Maybe Eric can clarify if more details are needed, however. Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Mar 15, 2013, at 10:53 AM, Steven Waldauer wrote:
Hi Everyone,
Hopefully this isn't a stupid question.
I've used the define plane command for a few residues of slightly twisted beta-strand, trying to judge the distance and twist in relation to a helix across the binding groove at different conditions. It seems to work the way I would like it to, but I would like to know in more specific terms, how the plane is actually determined. When the structure measurements data is saved, the file returns the center coordinate, normal vector, and the radius. Could anyone tell me how these values are determined?
For define axes, I can follow references from ksdssp, but there's really no similar definition for the define plane command in the user documentation.
Thanks,
Steve
Forgot to mention the plane center and radius. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/define.html#plane> "The disk center is the non-mass-weighted centroid of the atoms; disk radius can be set to a fixed value as described below or set automatically to enclose the projections of the atoms (default). An extra margin (padding, default 0.0 Å) can be added to the automatically determined radius, but is ignored if a fixed radius is supplied." On Mar 15, 2013, at 11:25 AM, Elaine Meng wrote:
Hi Steven, I wouldn't go by any information for "ksdssp," as that is completely separate from Axes/Planes/Centroids calculations.
Axes/Planes/Centroids: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/struc...>
"Each axis is anchored at the the centroid of the defining atomic coordinates and aligned with the principal component of the coordinates (prior to any helical correction)." There is also a choice of mass-weighting or not. If you choose the each-helix option, it is only using the backbone atoms N,CA,C.
The plane is the best-fit plane to the specified points (atoms).
On Mar 15, 2013, at 11:32 AM, Elaine Meng wrote:
Forgot to mention the plane center and radius.
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/define.html#plane>
"The disk center is the non-mass-weighted centroid of the atoms; disk radius can be set to a fixed value as described below or set automatically to enclose the projections of the atoms (default). An extra margin (padding, default 0.0 Å) can be added to the automatically determined radius, but is ignored if a fixed radius is supplied."
On Mar 15, 2013, at 11:25 AM, Elaine Meng wrote:
Hi Steven, I wouldn't go by any information for "ksdssp," as that is completely separate from Axes/Planes/Centroids calculations.
Axes/Planes/Centroids: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/struc...>
"Each axis is anchored at the the centroid of the defining atomic coordinates and aligned with the principal component of the coordinates (prior to any helical correction)." There is also a choice of mass-weighting or not. If you choose the each-helix option, it is only using the backbone atoms N,CA,C.
The plane is the best-fit plane to the specified points (atoms).
To expand on the last bolded part: the centroid is subtracted from the atoms and then eigenvectors/values are computed. The eigenvector with the smallest eigenvalue is consider to be the normal to the plane (i.e. the two largest-valued eigenvectors define the plane). A point (centroid) and a normal defines a plane. The radius is as described in the first bolded section above. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
On Mar 15, 2013, at 10:42 PM, Eric Pettersen wrote:
To expand on the last bolded part: the centroid is subtracted from the atoms and then eigenvectors/values are computed. The eigenvector with the smallest eigenvalue is consider to be the normal to the plane (i.e. the two largest-valued eigenvectors define the plane). A point (centroid) and a normal defines a plane. The radius is as described in the first bolded section above.
Thanks for the quick responses. I think I got it, but just to clarify, let me know if this is correct: The atoms in the selected residues are taken into consideration, and their coordinates are converted into a non-mass weighted centroid system. Then the principal axes are determined with the smallest vector considered normal to the plane defined by the other two axes. If this is correct, my only other question is: Which atoms are used in the calculation? Is it just N,CA,C like for helices? Thanks again for all the help. ****** Steven Andrew Waldauer Ph.D. Postdoctoral Fellow, Hamm Group Universität Zürich Physikalisch-Chemisches Institut Winterthurerstr. 190, CH-8057 Zürich Tel: +41 (0)44 635 44 66 Fax: +41 (0)44 635 68 38 E-Mail: waldauer@pci.uzh.ch
Hi Steven, The "all helices" (protein) option is the only case where certain atoms are automatically used. All other axis, plane, centroid calculations use whichever atoms you have specified in the define command (or if using GUI, whichever atoms are in the current selection). I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Mar 16, 2013, at 7:42 AM, Steven Waldauer wrote:
On Mar 15, 2013, at 10:42 PM, Eric Pettersen wrote:
To expand on the last bolded part: the centroid is subtracted from the atoms and then eigenvectors/values are computed. The eigenvector with the smallest eigenvalue is consider to be the normal to the plane (i.e. the two largest-valued eigenvectors define the plane). A point (centroid) and a normal defines a plane. The radius is as described in the first bolded section above.
Thanks for the quick responses. I think I got it, but just to clarify, let me know if this is correct:
The atoms in the selected residues are taken into consideration, and their coordinates are converted into a non-mass weighted centroid system. Then the principal axes are determined with the smallest vector considered normal to the plane defined by the other two axes.
If this is correct, my only other question is: Which atoms are used in the calculation? Is it just N,CA,C like for helices?
Thanks again for all the help.
****** Steven Andrew Waldauer Ph.D. Postdoctoral Fellow, Hamm Group
participants (3)
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Elaine Meng -
Eric Pettersen -
Steven Waldauer