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.... 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@ligand.eu<mailto:mlists@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. _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu<mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
