The Geo Measures Plugin can carry out geometric analysis on protein structures.In addition, it makes other trajectory analyzes such as Probability Density Function (PDF), Root Mean Square Deviation (RMSD), Radius of Gyration (RG), Free Energy Landscape (FEL), Principal Component Analysis (PCA), Ramachandran map, Root Mean Square Fluctuation (RMSF), Define Secondary Structure of Proteins (DSSP), and Modevectors. Altogether there are 14 tools, which can be easily used by the graphical interface.
https://pymolwiki.org/index.php/Geo_Measures_Plugin
PyMOL version higher than 2.0.
It is highly recommended to install PyMOL using the Ananconda3 package.
You need to install python packages.
To do this use the command:
pip install pandas matplotlib scipy mdtraj sklearn
Install geo_measures_pymol-master.zip using the PyMOL Plugin Manager
Author(s): Luciano Porto Kagami, Gustavo Machado das Neves, Rafael Andrade Cáceres, Vera Lucia Eifler-Lima and Luís Fernando Saraiva Macedo Timmers
Please cite us: Kagami LP, das Neves GM, Timmers LFSM, Caceres RA,Eifler-Lima VL, Geo-Measures: A PyMOL plugin for protein structure ensembles analysis,Computational Biology and Chemistry(2020) doi.org/10.1016/j.compbiolchem.2020.107322