choosing VDW, SAS or SES surfaces

[johnnytam100]

Hi @fwaibl ! I'm sorry for multiple questions but I'm almost getting to the point where I can use Pep-Patch in my figures.

I want to know if it is possible to choose VDW, SAS or SES surfaces to represent electric and hydrophobic potential?

Currently, I am getting different surfaces:

pep_patch_electrostatic 1510259A_1-201.pdb 1510259A_1-201.pdb --apbs_dir apbs --ply_out potential -o patches.csv

pep_patch_hydrophobic 1510259A_1-201.pdb 1510259A_1-201.pdb --scale crippen --ply_out hydrophobic_crippen.ply --potential

I want to standardize them.

[fwaibl]

Hello,

it seems that this is currently possible in the electrostatics script, but not in the hydrophobicity script:

  --surface_type {sas,ses,gauss}
                        Which type of molecular surface to produce. (default: sas)

For hydrophobicity, we decided to use a SES / Connolly surface to be consistent with the original definition of the "hydrophobic potential". It would be easy to allow other surfaces - let us know whether you need that! However, you might have to adjust also some other settings to get "good" results.

For electrostatics, we decided to go with a SAS because it intersects the first solvation shell, so it might be more representative of the protein-water interaction. But you can choose a different one as shown above.

Best,
Franz