B-factor and error in distance measurements
I have two structures of a protein solved to different resolutions, one pretty good and the second not so good, and I want to compare distances between congruent atoms in the structures. It occurred to me that I have no idea if the differences in the distances are within the positional error of the atoms or not. Therefore, is there a way to propagate the positional uncertainty in the B-factors into a linear distance uncertainty? Sincerely, Charles
Googling for how is b-factor related to atom positional uncertainty says "The B-factor is mathematically related to the mean squared displacement of an atom from its average position. Specifically, B = 8π²〈u²〉, where 〈u²〉 is the mean squared displacement. " Tom
On Aug 15, 2025, at 7:31 AM, Charles Midgett via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
I have two structures of a protein solved to different resolutions, one pretty good and the second not so good, and I want to compare distances between congruent atoms in the structures. It occurred to me that I have no idea if the differences in the distances are within the positional error of the atoms or not.
Therefore, is there a way to propagate the positional uncertainty in the B-factors into a linear distance uncertainty?
Sincerely, Charles _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Hi Charles, With Render by Attribute GUI (or command "size byattribute") you can map atomic B-factor values to the radii of atoms shown as spheres. That might help give a more intuitive sense of their uncertainty. In the Render by Attribute tool (menu under Tools... Depiction or Structure Analysis), use atom attribute "bfactor" shown with "Radii" <https://rbvi.ucsf.edu/chimerax/docs/user/tools/render.html> Using that will generate the corresponding "size byattribute" command and show it in the Log, so you would have examples of how to use the command if you choose to use that in the future instead of the GUI. Command docs here: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/size.html#byattribute> Or, instead of (or in addition to) atom sphere sizes, you can show the bfactor values with atom colors, using the Render by Attribute tool, or with command "color by attribute" <https://rbvi.ucsf.edu/chimerax/docs/user/tools/render.html#colors> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#byattribute> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 18, 2025, at 12:24 PM, Tom Goddard via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Googling for
how is b-factor related to atom positional uncertainty
says
"The B-factor is mathematically related to the mean squared displacement of an atom from its average position. Specifically, B = 8π²〈u²〉, where 〈u²〉 is the mean squared displacement. "
Tom
On Aug 15, 2025, at 7:31 AM, Charles Midgett via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
I have two structures of a protein solved to different resolutions, one pretty good and the second not so good, and I want to compare distances between congruent atoms in the structures. It occurred to me that I have no idea if the differences in the distances are within the positional error of the atoms or not.
Therefore, is there a way to propagate the positional uncertainty in the B-factors into a linear distance uncertainty?
Sincerely, Charles
participants (3)
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Charles Midgett -
Elaine Meng -
Tom Goddard