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Re: [modeller_usage] wrong column range?



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
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