Cannot Install POVME2

[edleon123]

I am trying to install version 2.2.2 with:
git clone https://github.com/durrantlab/POVME
cd POVME
git checkout v2.2.2

I am using my conda enviroment with its own version of pip to overcome:
error: externally-managed-environment

after:
pip install .

I get this:
error: directory '.' is not installable. neither 'setup.py' nor 'pyproject.toml' found.

I also tried to install vmd plugin:
set auto_path "$auto_path $::env(POVME_PATH)/POVME/vmdplugin"
menu main on
vmd_install_extension povme2 povme2_tk_cb "Analysis/POVME2"
set ::povme2::povme2_directory "$::env(POVME_PATH)/POVME/POVME3.py"

but then i get this:
ERROR) Creation of window for 'povme2' failed (invalid command name "povme2_tk_cb").

So i tried doing something more manual:

Load POVME2 plugin

if {[llength [info commands ::povme2::povme2_mainwin]] == 0} {
source /usr/local/lib/vmd/plugins/noarch/tcl/povme3.0/Povme2.tcl
}

Set paths

set ::povme2::povme2_directory /home/lalo/miniconda2/bin/POVME3.py
set ::povme2::python_executable /home/lalo/miniconda2/bin/python

Create a short alias command

proc povme {} {
::povme2::povme2_mainwin
}

but it is using povme3 so im guessing that is why it gave this:
Generating the pocket-encompassing point field

Saving the point field as a PDB and NPY file
Point field saved to ./frameInfo/inclusion.pdb to permit visualization
Point field saved to ./frameInfo/inclusion.npy to optionally load for the volume calculation

Traceback (most recent call last):
File "/home/lalo/miniconda2/bin/POVME3.py", line 2205, in
if name == "main": dorun = runit(sys.argv)
File "/home/lalo/miniconda2/bin/POVME3.py", line 1964, in init
raise Exception("ConvexHullExlusion keyword not recognized. '%s' is not one of ['none','max','first','each']" %(parameters[ConvexHullExclusion].lower()))
Exception: ConvexHullExlusion keyword not recognized. 'true' is not one of ['none','max','first','each']
Alert: POVME2 failed to load volumetric density file. The file was not located where expected: ./volumetric_density.dx.
Alert: POVME2 failed to load hbondAcceptor colored density files. The files were not located where expected.
Alert: POVME2 failed to load hbondDonor colored density files. The files were not located where expected.
Alert: POVME2 failed to load aromatic colored density files. The files were not located where expected.
Alert: POVME2 failed to load hydrophobic colored density files. The files were not located where expected.
Alert: POVME2 failed to load hydrophilic colored density files. The files were not located where expected.
Alert: POVME2 failed to load adjacency colored density files. The files were not located where expected.
Alert: POVME2 failed to load occupancy colored density files. The files were not located where expected.
Alert: POVME2 failed to load tabbed volume file. The file was not located where expected. Unable to plot volume data. Location: ./volumes.tabbed.txt
id: 0
which_mol: 0
exists: 1

I'm pretty sure i could use povme3 but i really wanted to be able to use the vmd plugin which im not sure if that is possible with that version

[MayarMAhmed]

Hi @edleon123

There are a few separate things going on here, so I'll address each one.

1. Installing v2.2.2

The pip install . error is expected — the v2.2.2 tag predates any Python packaging (setup.py / pyproject.toml), so pip has nothing to install. That version is a standalone script meant to be run directly. After checking out the tag, set up a conda environment with the required dependencies and run the script:

git clone https://github.com/durrantlab/POVME
cd POVME
git checkout v2.2.2

conda create -n povme python=3.11 numpy=1.23 scipy=1.10
conda activate povme

python3 POVME2.py your_input.init

You can verify the installation with:

python3 POVME2.py --test

We are working on updating the README to document this more clearly.

2. VMD plugin

The VMD plugin (.vmdrc setup, povme2_tk_cb, POVME3.py) is part of POVME3, which is a separate package maintained under a different repository. That project inherited the earlier POVME2 codebase and added the VMD Tk plugin on top of it. The ConvexHullExclusion error you're hitting is also a POVME3 issue — that version expects one of 'none', 'max', 'first', or 'each' rather than 'true'. I'd recommend opening an issue on their repository for help with the plugin and that specific error.

3. What we recommend

If your goal is pocket detection and volume measurement, the latest version of this repository (durrantlab/POVME) handles both without needing a VMD plugin or manual region definition. It automatically detects binding pockets from a PDB structure:

povme detect -c config.yaml -i structure.pdb -o output/
povme volume -c config.yaml -i structure.pdb -o output/

You can then visualize the results directly in VMD by loading the output PDB files. POVME writes pocket-occupying points as PDB files and optionally produces volumetric density maps in DX format — both of which VMD handles natively

For full details, see our documentation at https://durrantlab.github.io/POVME/.