I am using the model.write_data function with output='PSA' to calculate
the atomic solvent accessibility. The 'output.sol' pdb file has two new
columns on the right. I figured out that the rightmost column must be
the atomic solvent accessibility values. But what is the meaning of the
one to the left (the second rightmost column)?
That's the VDW radii of the atoms, scaled by radii_factor (which should
usually be 1.0).
Second question: these two new columns seem 'right shifted' as compared
to the Occupancy value (should have column range 55-60) and B-value
(expected between 61-66). This shift messes up with other applications
that use these arrays. Am I wrong about this shift? If now, can the
model.write_data function easily be corrected?
The .sol file looks similar to a PDB file, but it is not a PDB file. You
should not expect the columns line to up, or to be able to read it with
your PDB viewer.