This is a PyMol Plugin for the original WaterDock and the new and improved WaterDock 2.0 specific for holo structures.
Written by Akshay Sridhar with updates from Patrick McCubbin and Phil Biggin.
There are 3 Files: init.py, addwater.py and dockcheck.py
Download all three and place in a folder and follow steps below.
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Open PyMol
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Plugin --> Plugin Manager --> Install New Plugin --> Install From Local File
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Choose the init.py file when prompted
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DONE!!
Next time PyMol is restarted, Under Plugin, 2 Options will be available
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Apo Waterdock -- The originial WaterDock
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Holo Waterdock -- The new pipeline specific to holo structures
Dependencies
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PyMol ofcourse
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MDAnalysis -- (version > 0.13)
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numpy and Scipy (usually done as part of your MDanalysis install)
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Autodock Vina
Things to Note
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The script runs AutoDock Vina through system calls of the command 'vina'. The system checks if the command 'vina' is callable and alerts if it is not. Ensure 'vina' in the system refers to AutoDock Vina.
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For the Holo-Dock, Please ensure the ligand has Hydrogens added to the structure. And inspect the correct protonation states of relevant atoms.
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The output file of both WaterDock options is written as 'predictedwaters.pdb'. If 'predictedwaters.pdb' already exists in the folder, it is renamed to 'predictedwaters1.pdb' and the new file is written as 'predictedwaters.pdb'.
Newer versions of MDAnalysis now support Apple Silicon (ie. M1 and M2 chips). However, you will have to most likely compile vina from source (see below). If you have vina working and installed and you already compiled pymol on your mac you can add then necessary packages thus (I write the packages as explicit separate lines here):
>>> import pip
>>> pip.main(['install','numpy'])
>>> pip.main(['install','scipy'])
>>> pip.main(['install','MDAnalysis'])
then follow the above installation WaterDock_Pymol
At the time of writing (Oct 2023) there was no pip installable version of vina for Apple Silicon. Therefore, we have to compile ourselves
The instructions are here:-
https://autodock-vina.readthedocs.io/en/latest/installation.html
But there are two things to note:
- You will need to use homebrew to install certain libraries (boost and swig)
- The Makefile will need changing to something like:-
BASE=/opt/homebrew
BOOST_VERSION=
BOOST_INCLUDE = $(BASE)/include
C_PLATFORM=-pthread
CXXFLAGS= DBOOST_TIMER_ENABLE_DEPRECATED
GPP=/usr/bin/clang++
C_OPTIONS= -O3 -DNDEBUG -std=c++11 -DBOOST_TIMER_ENABLE_DEPRECATED
BOOST_LIB_VERSION=
include ../../makefile_common
Good luck!
Best installation route is via conda with python 3.5 --> 3.8 (we had trouble with python 3.9).
you can either compile pymol from source or the simplest route is pure conda with the schrondinger incentive verison of pymol as in the following example:-
conda create --name pymol-env python=3.7
conda activate pymol-env
conda config --add channels conda-forge
conda install -c schrodinger pymol-bundle
conda install mdanalysis
conda install -c bioconda autodock-vina
conda install -c anaconda pyqt
Then fire up Pymol and install the plugin as per the instructions above.
- Ensure that you have the correct version of python active
sudo port select --list python
This should return something like:-
Available versions for python: none (active) python26-apple python27 python27-apple
You need to make the python27-apple active:-
sudo port select python python27-apple
You can check it is by doing the list option again, but it should be fine, then fire up MacPymol and do the install and the plugin should work (assuming you have vina in your path as well)..
- After Installation, copy the two additional files addwater.py and dockcheck.py into the folder you instructed pymol to install the plugin.
Please use the separate windows-specific refactored branch.
Please don't hesitate to report issues or email [email protected]