I want an objective method to determine the diameter of a cylindrical
protein fiber made from multiple chains, e.g. a bacterial pilus assembly
such as *2hil.*
I have devised a script to select atoms on the surface by selecting
those close to an isosurface created for the mid-section (avoiding end
anomalies) of the filament model, using an isosurface with a specified
modest resolution (which is much better than the default for these large
structures), and a large probe radius (~5 Angstroms). (For 2hil, the mid
section is approximately atoms with z > -25 and z < 50.)
For the selected set of atoms, I want to generate an *array of distances
of each atom from the Z axis* (since the Z axis is the axis of the
helical filament model).
Then I want to determine the *average distance* of these surface atoms
from the Z axis. Twice that average distance (radius) would be the
diameter of the protein filament model, from centers of surface atoms. I
would add the diameter of a carbon atom (3.4 Angstroms) to get the full
diameter of the filament.
For each surface atom, its distance from the Z axis would be
*square root of (x**2 + y**2)**
*
Can someone please explain to me how to make the array of such
distances, one entry per selected surface atom? And how to report the
average of that array of values?
Thanks! Eric
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