Measure angle and effect length
Hi, What is the correct way to measure the angle between the EGF and Lectin domain of L-selectin: 3CFW and also the effective length of those domains? What is the difference between Helical correction and mass weighting? When should I use Helical correction and mass weighting? How is the length of the axis is determined? Is there a way to pick the length of the axis to be the effective length of the domain? Thanks
Hi, There is no single “correct way,” which is why the options are options. You have to decide for yourself because it all depends how you want to define those measurements based on your scientific judgment. Lengths (distances) could be measured between 2 atoms, and angles between 3 atoms, or you could calculate axes or planes from the two domains and then get the angle between them. However, if you calculate axes or planes, you have to decide which atoms to use to define each of those things. Distances, angles, axes, planes, etc. are all described here in the “Structure Measurements” page: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#structuremeas> The meaning of mass weighting and helical correction for axis calculation are also described in that same page (which you would see if you just clicked “Help” on the dialog). You cannot control axis length, it just extends as far as the farthest atoms used to calculate it, so for length measurements you might as well just pick two atoms and measure the distance between them. Personally, I always use helical correction. You can try both ways, it might not make much difference except for short helices. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 21, 2019, at 12:08 PM, Shishir Adhikari <sra42@case.edu> wrote:
Hi, What is the correct way to measure the angle between the EGF and Lectin domain of L-selectin: 3CFW and also the effective length of those domains? What is the difference between Helical correction and mass weighting? When should I use Helical correction and mass weighting? How is the length of the axis is determined? Is there a way to pick the length of the axis to be the effective length of the domain? Thanks
Another possibility is to use the command “measure inertia” to report principal axes in the Reply Log, but again you would have to decide/specify which atoms to use in the calculation. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#inertia> Elaine
On Feb 21, 2019, at 3:48 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi, There is no single “correct way,” which is why the options are options. You have to decide for yourself because it all depends how you want to define those measurements based on your scientific judgment. Lengths (distances) could be measured between 2 atoms, and angles between 3 atoms, or you could calculate axes or planes from the two domains and then get the angle between them. However, if you calculate axes or planes, you have to decide which atoms to use to define each of those things. Distances, angles, axes, planes, etc. are all described here in the “Structure Measurements” page: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#structuremeas>
The meaning of mass weighting and helical correction for axis calculation are also described in that same page (which you would see if you just clicked “Help” on the dialog). You cannot control axis length, it just extends as far as the farthest atoms used to calculate it, so for length measurements you might as well just pick two atoms and measure the distance between them.
Personally, I always use helical correction. You can try both ways, it might not make much difference except for short helices. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 21, 2019, at 12:08 PM, Shishir Adhikari <sra42@case.edu> wrote:
Hi, What is the correct way to measure the angle between the EGF and Lectin domain of L-selectin: 3CFW and also the effective length of those domains? What is the difference between Helical correction and mass weighting? When should I use Helical correction and mass weighting? How is the length of the axis is determined? Is there a way to pick the length of the axis to be the effective length of the domain? Thanks
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participants (2)
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Elaine Meng -
Shishir Adhikari