Attila Gulyas-Kovacs wrote: > 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.

Ben Webb, Modeller Caretaker