length of a curved alpha helix
Dear All I was wondering as how can I measure the length of "curved" alpha helix. Thanks Andy Dr. Anindito Sen (Ph.D) Research Associate , Dept. of Biochemistry and Molecular Genetics University of Virginia Box 800733 Charlottesville, VA 22908
Hi Andy, The question becomes philosophical: what really is the length of a curved helix? I suspect you are thinking a curved tube could represent its axis, and the length would be the distance from end to end of the straightened tube. I can't think of any way in Chimera to measure that. Some possibilities that are not quite the same thing: (A) measure a series of backbone atom-atom distances and add them up. This would be a zigzag distance that would be an upper bound on the actual helix length. Of course, you could measure a single distance from an atom on one end to an atom on the other end, but I assume that is not really what you want. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/struc...
(B) decide to model the curved helix as several straight segments. For example, residues 1-9 as one segment, 10-19 as another, etc. For each segment, select the residues and use Axes to create an axis. The length of the axis is reported. Add them together. Again this will be a series of straight lines and probably an upper bound to what you had in mind. Or, you could draw one Axis for the whole helix, but again it would be straight. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/struc...
(C) you could do something really crazy like put a tape measure up to the screen and curve it along the helix. You could calibrate by comparing to a linear distance measurement also on the screen. You'd probably want to use "orthographic" projection to avoid artifacts from the "perspective" projection (see Tools... Viewing Controls... Camera). This would be really crude and approximate, however. Tom G gets credit for this idea. 8-) I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Dec 10, 2008, at 11:26 AM, Anindito Sen wrote:
Dear All I was wondering as how can I measure the length of "curved" alpha helix. Thanks Andy
Dr. Anindito Sen (Ph.D) Research Associate , Dept. of Biochemistry and Molecular Genetics University of Virginia Box 800733 Charlottesville, VA 22908
Hi Andy, I was credited with the idea of using a tape measure. But now I have some sensible ideas. The length of the curved alpha helix is probably going to differ by a miniscule amount from the length measured directly between its two end points. For example, a 20 degree circular arc is only half a percent longer (1.005 times as long) as the straight segment between its end points. So I'd suggest a more meaningful quantification of a curved half helix is "how many degrees does it curve". You can think about how to define that -- we don't have any predefined notion in Chimera of how many degrees a helix curves. Probably a sensible meaning of that since the curve is not a circular segment is to instead think about how far the middle of the bent helix deviates off the straight line connecting its end points. Tom Elaine Meng wrote:
Hi Andy, The question becomes philosophical: what really is the length of a curved helix? I suspect you are thinking a curved tube could represent its axis, and the length would be the distance from end to end of the straightened tube. I can't think of any way in Chimera to measure that.
Some possibilities that are not quite the same thing:
(A) measure a series of backbone atom-atom distances and add them up. This would be a zigzag distance that would be an upper bound on the actual helix length. Of course, you could measure a single distance from an atom on one end to an atom on the other end, but I assume that is not really what you want. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/struc...
(B) decide to model the curved helix as several straight segments. For example, residues 1-9 as one segment, 10-19 as another, etc. For each segment, select the residues and use Axes to create an axis. The length of the axis is reported. Add them together. Again this will be a series of straight lines and probably an upper bound to what you had in mind. Or, you could draw one Axis for the whole helix, but again it would be straight. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/struc...
(C) you could do something really crazy like put a tape measure up to the screen and curve it along the helix. You could calibrate by comparing to a linear distance measurement also on the screen. You'd probably want to use "orthographic" projection to avoid artifacts from the "perspective" projection (see Tools... Viewing Controls... Camera). This would be really crude and approximate, however. Tom G gets credit for this idea. 8-)
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html
On Dec 10, 2008, at 11:26 AM, Anindito Sen wrote:
Dear All I was wondering as how can I measure the length of "curved" alpha helix. Thanks Andy
Dr. Anindito Sen (Ph.D) Research Associate , Dept. of Biochemistry and Molecular Genetics University of Virginia Box 800733 Charlottesville, VA 22908
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (3)
-
Anindito Sen -
Elaine Meng -
Tom Goddard