[Chimera-users] [feature request] would it be possible to drive/launch PLIP from within chimera?

[Jaime Rodríguez-Guerra Pedregal]

Hi!

We have developed a Chimera extension for this (PLIPGUI), within our Tangram Project. It should be usable separate of the full suite, but the dependencies must be installed manually:

- PLIPGUI: The extension -> https://github.com/insilichem/tangram_plipgui
- libtangram: Some common code for Tangram extensions -> https://github.com/insilichem/libtangram
- PLIP: The code itself, with no dependencies
- Openbabel: Plip needs it.
- In some cases, I had to install lxml and future, as well.

I normally create a conda environment with Python 2.7 and install the dependencies there, but you can also use a normal directory and use pip install -t <location> <packages> to install them there. Then, make sure to point to that location in the Chimera> Favorites> Add to Favorites/Tools> Locations dialog. More information here: https://tangram-suite.readthedocs.io/en/latest/install.html#install-only-one-specific-extension. Make sure that PLIP does not install numpy, because it will be incompatible with Chimera's. To sum up:

1. Install Miniconda for Py2.7 if you haven't. https://conda.io/miniconda.html
2. Create a new environment: conda create -n plip -c openbabel python=2.7 lxml openbabel
3. Activate the environment: conda activate plip
4. Install PLIP with no deps: pip install pip install https://github.com/ssalentin/plip/archive/master.zip --no-deps  # so it does not try to install numpy and openbabel again
5. Install PLIPGUI: pip install future https://github.com/insilichem/libtangram/archive/master.zip https://github.com/insilichem/tangram_plipgui/archive/master.zip
6. Obtain extensions path: echo ${CONDA_PREFIX}/lib/python2.7/site-packages
7. Copy that path and paste it in Chimera> Favorites> Add to Favorites/Tools> Locations. Click Save. A new InsiliChem submenu will be available under Tools.

Documentation will be updated here (https://tangram-suite.readthedocs.io/en/latest/tangram_plip.html) at some point, but the usage is straight-forward once it is installed. Just go to Tools> Insilichem> Tangram PLIP, select your opened compound, and voilà. I reckon the install process is not very intuitive because of the added dependencies, so in some future I might port PLIP to be Chimera only (no openbabel deps), thus simplifying the process.

Let me know if you need something else.

Cheers,
Jaime.


El vie., 9 nov. 2018 a las 7:57, Francois Berenger (<mlists at ligand.eu<mailto:mlists at ligand.eu>>) escribió:
Hello,

Recently, I stumbled upon this open source tool:

PLIP - Protein-Ligand Interaction Profiler
Analyze and visualize non-covalent protein-ligand interactions in PDB
files

 From the abstract:
---
[...]
detection and visualization of [...] seven interaction types (hydrogen
bonds, hydrophobic contacts, pi-stacking, pi-cation interactions, salt
bridges, water bridges and halogen bonds).
---

Website:
http://plip.biotec.tu-dresden.de

Open-source code:
https://github.com/ssalentin/plip

Paper:
https://academic.oup.com/nar/article-pdf/43/W1/W443/17435622/gkv315.pdf
or
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4489249/

And, when I am inside chimera looking at a protein-ligand complex,
it would be super nice if this tool could be launched from within
chimera (as in a menu "Tools -> Surface/Binding Analysis -> PLIP
analysis (visualize non-covalent interactions)").
Or, maybe it could be a toggable button inside of ViewDock.

Best regards,
Francois.

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