mittinatten
commented
2 years ago Hi, FreeSASA ignores hydrogens by default, could that be an explanation? You can include hydrogens, but the atomic radii are calibrated for the hydrogens being excluded, so then you might want to use another set of radii.
Simon
On Fri, 18 Mar 2022 at 17:58, maxsw2 @.***> wrote:
Hi, So I was using FreeSASA to calculate the SASA of my polymer system that has voids. So on PDB it says, I have 32998 atoms. However, on FreeSASA output, I get a much lower total of atoms. I have attached my PDB file below, and here is my output for FreeSASA.
PARAMETERS algorithm : Shrake & Rupley probe-radius : 1.400 threads : 2 testpoints : 100
INPUT source : traj.pdb chains : A model : 0 atoms : 13710
traj.txt https://github.com/mittinatten/freesasa/files/8306381/traj.txt
RESULTS (A^2) Total : 84985.85 Apolar : 0.00 Polar : 0.00 Unknown : 84985.85 CHAIN A : [84985.85]
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Hi, So I was using FreeSASA to calculate the SASA of my polymer system that has voids. So on PDB it says, I have 32998 atoms. However, on FreeSASA output, I get a much lower total of atoms. I have attached my PDB file below, and here is my output for FreeSASA.
PARAMETERS algorithm : Shrake & Rupley probe-radius : 1.400 threads : 2 testpoints : 100
INPUT source : traj.pdb chains : A model : 0 atoms : 13710
traj.txt
RESULTS (A^2) Total : 84985.85 Apolar : 0.00 Polar : 0.00 Unknown : 84985.85 CHAIN A : [84985.85]