I try to print the hydrophobicity patch area. But I can't find the program to do that. I remember the rosetta 3.3 has an option to use hpatch_score.txt to design the protein. Could anyone tell me where is program? Thank you very much~
If you don't want to do design, use -repack_only with fixbb, or port the flags from fixbb to score_jd2.
I try score_jd2.linuxgccrelease -score:weights design_hpatch.wts -database rosetta_database/ -s 1xnz.pdb and get the output file score.sc.
I don't know which one is the hydrophobicity patch area.....
SCORE: -231.405 -1101.607 253.294 555.737 2.655 11.728 -24.622 -55.576 -81.327 -24.066 -15.080 0.000 0.000 0.000 0.000 -4.568 3.227 297.150 -24.352 -26.046 0.000 0.000 2.048 2.000 1xnz_0001
OH, I think I got it. But I want the hydrophobic surface area but not the hpatch score...
Ron says, "I think it might be in the log file somewhere, but I'm not sure that's the surface area she wants. [You] really should just get NACCESS which is the program I used for calculating surface areas (hydrophobic and otherwise)."
OK. Thank you! So rosetta don't have code to calculate the surface? Instead, you use NACCESS? But I remember in the paper which descipts the hydrophobiciy patch term they also calculate the surface residues area.
Rosetta definitely has the ability to calculate surface areas. It can calculate total, hydrophobic and/or polar surface area, and you can get this information for just one atom, one residue, or a whole protein. But there aren't any apps/executables that I'm aware of that you can just run to get this information. You would have to write your own application that uses the functions in core/scoring/sasa.cc to get these values. The hpatch score does use surface area as part of scoring, but it uses expanded polar atom radii when it makes these area calculations. (The exact atom radii used for the surface area calculations are in one of the tables in the supplementary material of the hpatch score paper. During hydrophobic patch detection, however, the polar atom radii are expanded by 1.4 Angstroms. This is described in the methods section "Implementation of the hpatch scores..." in the paper.) Therefore, if you are looking for the total or hydrophobic surface area of some structure, I wouldn't use the fixbb executable to get this information. You would either have to write your own application that calls the SASA calculators, or download another program which was written specifically to calculate surface areas (such as NACCESS). There may be another app/executable in Rosetta that reports various SASA values, but I'm not aware of one.
Thank you very much!