<commit_before># POVME

[![CircleCI](https://circleci.com/gh/POVME/POVME.svg?style=svg)](https://circleci.com/gh/POVME/POVME)

We present a substantial update to the open-source POVME binding pocket analysis software. New capabilities of POVME 3.0 include a flexible chemical coloring scheme for feature identification, post-analysis tools for comparing large ensembles of pockets (e.g., from molecular dynamics simulations), and the introduction of scripts and methods that facilitate binding pocket comparison and analysis. We envision the use of this software for visualization of binding pocket dynamics, selection of representative structures for ensemble docking, and incorporation of molecular dynamics results into ligand design efforts.

A publication associated with this software is at https://doi.org/10.1021/acs.jctc.7b00500. It showcases several capabilities of POVME 3.0, and performs a simple benchmark of grid-based binding pocket similarity analysis.

This document is specific to POVME 3.0. Users interested in POVME 2.0 will find resources [here](http://rocce-vm0.ucsd.edu/data/sw/hosted/POVME/)

## Install

If POVME2 is installed on your system, we recommend making a separate python environment. We normally install POVME3.0 using [miniconda](https://conda.io/docs/install/quick.html):

```
wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh
bash Miniconda2-latest-Linux-x86_64.sh -b -p miniconda2
source miniconda2/bin/activate
pip install povme
```

Note that this method will create a separate python build. You will need to run ```source miniconda2/bin/activate``` in each terminal where you want to use POVME3.



# Examples Directory
<commit_msg>Update install instructions with conda.sh, add mac install instructions, point to new POVME2 link<commit_after># POVME

[![CircleCI](https://circleci.com/gh/POVME/POVME.svg?style=svg)](https://circleci.com/gh/POVME/POVME)

We present a substantial update to the open-source POVME binding pocket analysis software. New capabilities of POVME 3.0 include a flexible chemical coloring scheme for feature identification, post-analysis tools for comparing large ensembles of pockets (e.g., from molecular dynamics simulations), and the introduction of scripts and methods that facilitate binding pocket comparison and analysis. We envision the use of this software for visualization of binding pocket dynamics, selection of representative structures for ensemble docking, and incorporation of molecular dynamics results into ligand design efforts.

A publication associated with this software is at https://doi.org/10.1021/acs.jctc.7b00500. It showcases several capabilities of POVME 3.0, and performs a simple benchmark of grid-based binding pocket similarity analysis.

This document is specific to POVME 3.0. Users interested in POVME 2.0 will find resources [~here~](http://rocce-vm0.ucsd.edu/data/sw/hosted/POVME/)[here(more up to date)](https://git.durrantlab.pitt.edu/jdurrant/POVME)

## Install

If POVME2 is installed on your system, we recommend making a separate python environment. We normally install POVME3.0 using [miniconda](https://conda.io/docs/install/quick.html):

### Linux
```
wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh
bash Miniconda2-latest-Linux-x86_64.sh -b -p miniconda2
. miniconda2/etc/profile.d/conda.sh
conda activate base
pip install povme
```
### Mac
```
wget https://repo.continuum.io/miniconda/Miniconda2-latest-MacOSX-x86_64.sh
bash Miniconda2-latest-MacOSX-x86_64.sh -b -p miniconda2
. miniconda2/etc/profile.d/conda.sh
conda activate base
pip install povme
```


Note that this method will create a separate python build. You will need to run ```source miniconda2/bin/activate``` in each terminal where you want to use POVME3.



# Examples Directory

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