A script based on NanoShaper protein surface software returning the list of atoms and residues solvent exposed (or according to a user defined probe radius)
- Install NanoShaper https://gitlab.iit.it/SDecherchi/nanoshaper
- or directly use executable provided in the "NS" folder:
- To correctly link the libraries install patchelf (sudo apt get install patchelf or https://gist.github.com/ruario/80fefd174b3395d34c14) then run the "install_script"
Important:
- in the working folder the provided temp folder must be present with a working NanoShaper executable inside (run the install_script before, see above)
- The input file must be in PQR format
python3 expRes.py <structure_name> For help type python3 expRes.py -h
Default parameters: Probe_radius=1.4 (water), Thread_number=1 (for NanoShaper triangulation)
Note: The probe radius can be changed.
Hen Egg-White Lisozyme 1hew.pqr:
python3 expRes.py --savePQR --saveRES 1hew
--> 1hew_exposed.pqr file containing the subset of exposed atoms of the original PQR
--> 1hew_resList.txt file containing the list of exposed residues