PyMol plugin for hydrogen bond and water wire analysis of crystal structures and MD simulations.
This implementation of the bridge analysis is deprecated and not maintained anymore. There is a new implementaion as a standalone Qt5 application under
https://github.com/maltesie/bridge2
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see https://www.gnu.org/licenses/.
Author: Malte Siemers, Freie Universität Berlin
If you use this software or anything it produces for work to be published, please cite:
Malte Siemers, Michalis Lazaratos, Konstantina Karathanou, Federico Guerra, Leonid Brown, and Ana-Nicoleta Bondar. Bridge: A graph-based algorithm to analyze dynamic H-bond networks in membrane proteins, Journal of Chemical Theory and Computation, 2019.
and
Federico Guerra, Malte Siemers, Christopher Mielack, and Ana-Nicoleta Bondar
Dynamics of Long-Distance Hydrogen-Bond Networks in Photosystem II
The Journal of Physical Chemistry B 2018 122 (17), 4625-4641
Bridge comes as a pymol plugin and depends on MDAnalysis (0.19.2+). To install pymol, we recommend using the miniconda python distribution for python 3 (https://docs.conda.io/en/latest/miniconda.html). If miniconda is set up correctly you can install pymol and MDAnalysis with:
conda install -c schrodinger pymol
conda install -c conda-forge mdanalysis
To open pymols plugin manager, click
Plugin->Plugin Manager
In the plugin manager, go to the 'Install New Plugin' tab and click 'Choose file ...'. Select the .zip file containing Bridge and restart pymol. Now start Bridge by clicking
Plugin->Bridge