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Tangram PLIP-GUI

An UCSF Chimera wrapper and GUI for PLIP.

Known issues

PLIP, the backend for this extension, relies on openbabel as a dependency. However, using pychimera, openbabel and rdkit (used by other extensions in Tangram) is not possible. So, if you want to use PLIP-GUI, you have to uninstall rdkit (and stop using Tangram SubAlign, amongst others) and install openbabel:

# From the activated conda environment
conda remove rdkit
conda install -c openbabel openbabel

Standalone installation on Ubuntu

sudo apt install python2.7-openbabel
pip install plip
pip install https://github.com/insilichem/libtangram/archive/v0.0.2.zip
pip install https://github.com/insilichem/tangram_plipgui/archive/v0.0.2.zip

Then, open UCSF Chimera and add ~/.local/lib/python2.7/site-packages in the Favorites> Add to Favorites/Toolbar> Third-party plugin locations dialog. If everything has worked so far, a new InsiliChem entry must appear in the Chimera Tools menu.

Standalone installation

If you want to install PLIP-GUI outside the Tangram Suite, follow these instructions:

Download this repo and install these packages as dependencies:

  • plip itself
  • openbabel & pybel
cd /your/chimera/extensions/directory
pip install -t . https://github.com/ssalentin/plip/archive/v1.3.3.zip --no-deps
# read http://openbabel.org/wiki/Category:Installation for openbabel

You can also use pychimera and conda to manage dependencies:

conda install -c openbabel openbabel
pychimera --gui  # to start patched UCSF Chimera