PyMol

Introduction

PyMOL is a user-sponsored molecular visualization system on an open-source foundation, maintained and distributed by Schrödinger.

There is an open-source version freely available. More details can be found at pymolwiki

Installation

Windows

Instructions available from pymolwiki

Create an installation directory in the root with the File Manager

c:\PyMOL_Installation

Download the necessary files in the installation directory

Python

Python download

Pre-compiled version of PyMOL and required software from Christoph Gohlke page
(open Gohlke page, in the page CTRL-F and use the search window to find the required software copying the strings below in the search window)

pymol‑2.3.0‑cp37‑cp37m‑win_amd64.whl
pymol_launcher‑2.1‑cp37‑cp37m‑win_amd64.whl
pip‑19.0.2‑py2.py3‑none‑any.whl
numpy‑1.16.2+mkl‑cp37‑cp37m‑win_amd64.whl
Pmw‑2.0.1‑py3‑none‑any.whl

Install Python (if necessary, before to begin the installation check if the software is present in your PC)

Choose the Customize option
Customize install location and change in C:\Python37
Disable path length limit as suggested by installation tool

Open a cmd window and change directory to the installation directory

cd c:\PyMOL_Installation

Install PyMOL and required software:

c:\PyMOL_Installation>c:\Python37\python pip-19.0.2-py2.py3-none-any.whl\pip install --no-index --find-links="%CD%" pymol_launcher

Where it is important the correct version of pip whereas pymol_launcher does not require any further specifications
Finally, the PyMol.exe program will be found inside the Python folder

Matteo's plugin

Copy the following lines in a file named psa_3d.py located in c:\PyMOL_Installation

from pymol import cmd
def psa3d (arg1=0.6, arg2=-0.6):
   obj_list = cmd.get_names('objects')
   for obj in obj_list:
       cmd.select('noh', '(pc.>'+str(arg1)+'|pc.<'+str(arg2)+'|(e. n OR e. o OR e. h AND(neighbor e. n OR e. o))) AND ' + obj)
        print("3DPSA_noh06 %12s %.3f" % (obj, cmd.get_area('noh')))
   return obj
cmd.extend("psa3d", psa3d)

Run PyMOL

Click on Plugin - Plugin Manager - Install New Plugin - Choose file

Choose psa_3d.py in the directory c:\PyMOL_Installation

Click Ok

If all is ok a messagge will be shown that inform you that the plugin has been installed

Check on the Plugin Manager that the plugin is installed and close it.

The plugin is ready.

Load a molecule and type psa3d in the PyMOL command window

It should be possible that it is necessary to exit and rerun PyMOL to activate the plugin

When the plugin works, the PSA (SA 3D PSA – NOH+0.6) could be calculated with the following instruction:

set solvent_radius=1.4; set dot_density=4; set dot_solvent=1; psa3d