How to obtain size measures
Dear UCSF Chimera and ChimeraX developers, I would like to ask you if there's a method to obtain the size measures of a protein in order to compare with the heights and lengths obtained by AFM. Could you please suggest me how could I obtain such measurements? Thank you in advance for your help and support, Andrea
Hi Andrea, I guess you mean measuring the size of an atomic structure, such as from the Protein Databank. Given such a structure, you can do distance measurements between any two atoms. Or, with command "measure inertia" you can calculate an inertial ellipsoid for the protein, which reports the three axis lengths. See the "measurements" page and links therein for how to do many types of measurements in ChimeraX: <http://rbvi.ucsf.edu/chimerax/docs/user/measurements.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 4, 2020, at 7:23 AM, Andrea Dallapè <andrea.dallape@unitn.it> wrote:
Dear UCSF Chimera and ChimeraX developers, I would like to ask you if there's a method to obtain the size measures of a protein in order to compare with the heights and lengths obtained by AFM. Could you please suggest me how could I obtain such measurements? Thank you in advance for your help and support, Andrea
Hi Elaine, thank you, it was exactly what I was looking for! I'm enjoying ChimeraX a lot, you're really doing a wonderful job! Thank you for your attention and your help. Have a good weekend, Andrea Il giorno sab 4 lug 2020 alle ore 18:23 Elaine Meng <meng@cgl.ucsf.edu> ha scritto:
Hi Andrea, I guess you mean measuring the size of an atomic structure, such as from the Protein Databank. Given such a structure, you can do distance measurements between any two atoms. Or, with command "measure inertia" you can calculate an inertial ellipsoid for the protein, which reports the three axis lengths.
See the "measurements" page and links therein for how to do many types of measurements in ChimeraX: <http://rbvi.ucsf.edu/chimerax/docs/user/measurements.html>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 4, 2020, at 7:23 AM, Andrea Dallapè <andrea.dallape@unitn.it> wrote:
Dear UCSF Chimera and ChimeraX developers, I would like to ask you if there's a method to obtain the size measures of a protein in order to compare with the heights and lengths obtained by AFM. Could you please suggest me how could I obtain such measurements? Thank you in advance for your help and support, Andrea
participants (2)
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Andrea Dallapè -
Elaine Meng