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FEATURE-Plugin

This is a plugin for PyMol 2.x under windows to find ion sites (Calcium) in a protein 3D structure using the ‘Feature’ program (https://simtk.org/projects/feature/) and to show the results in PyMol. It uses 'DSSP' and an 'R' script under windows but 'Feature' in a linux distribution.

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How to install ?

Ther are two plugins, one to run with a cygwin compilation of FEATURE, the other with its compilation in a wsl2 (ubuntu) environment. For the second version install the wsl2 environnement according to the well documented procedure : https://docs.microsoft.com/fr-fr/windows/wsl/install

Hints:

You have to execute the command line interface in the admin mode, else the error "the requested operation requires elevation" appears. You can directly choose which linux distribution to install. I took :> wsl -- install -d Ubuntu-18.04

D'ont forget to change the subsystem from wsl to wsl2 : >wsl --set-default-version 2

If you use an open source version of PyMol from Christophe Gohlkes site, you have to installe Python (3.8 and 3.9 will work fine) and PySide2 (https://pypi.org/project/PySide2/) under Windows according to your Python version. I installed the shiboken2-5.12.2 and PySide2-5.12.2 .whl files for my Python version manually with pip.

You also need to install 'R' for windows that you find at : https://cran.r-project.org/bin/windows/base/R-4.1.3-win.exe and (the old version of) dssp for windows : https://swift.cmbi.umcn.nl/gv/dssp/HTML/DSSPCMBI.EXE

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This is a plugin for PyMol 2.x under Windows to find and show Ca-ion sites in a protein structure in pdb format using the Feature program.

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