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<div>Hi!</div>
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<div>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:</div>
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<div>- PLIPGUI: The extension -> <a href="https://github.com/insilichem/tangram_plipgui">
https://github.com/insilichem/tangram_plipgui</a></div>
<div>- libtangram: Some common code for Tangram extensions -> <a href="https://github.com/insilichem/libtangram">
https://github.com/insilichem/libtangram</a></div>
<div>- PLIP: The code itself, with no dependencies <br>
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<div>- Openbabel: Plip needs it.<br>
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<div>- In some cases, I had to install lxml and future, as well.</div>
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<div>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
<span style="font-family:monospace,monospace">pip install -t <location> <packages></span> 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:
<a href="https://tangram-suite.readthedocs.io/en/latest/install.html#install-only-one-specific-extension">
https://tangram-suite.readthedocs.io/en/latest/install.html#install-only-one-specific-extension</a>. Make sure that PLIP does not install numpy, because it will be incompatible with Chimera's. To sum up:</div>
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<div>1. Install Miniconda for Py2.7 if you haven't. <a href="https://conda.io/miniconda.html">
https://conda.io/miniconda.html</a><br>
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<div>2. Create a new environment: conda create -n plip -c openbabel python=2.7 lxml openbabel</div>
<div>3. Activate the environment: conda activate plip<br>
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<div>4. Install PLIP with no deps: pip install pip install <a href="https://github.com/ssalentin/plip/archive/master.zip">
https://github.com/ssalentin/plip/archive/master.zip</a> --no-deps # so it does not try to install numpy and openbabel again</div>
<div>5. Install PLIPGUI: pip install future <a href="https://github.com/insilichem/libtangram/archive/master.zip">
https://github.com/insilichem/libtangram/archive/master.zip</a> <a href="https://github.com/insilichem/tangram_plipgui/archive/master.zip">
https://github.com/insilichem/tangram_plipgui/archive/master.zip</a></div>
<div>6. Obtain extensions path: echo ${CONDA_PREFIX}/lib/python2.7/site-packages</div>
<div>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.<br>
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<div>Documentation will be updated here (<a href="https://tangram-suite.readthedocs.io/en/latest/tangram_plip.html">https://tangram-suite.readthedocs.io/en/latest/tangram_plip.html</a>) 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.</div>
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<div>Let me know if you need something else.</div>
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<div>Cheers,</div>
<div>Jaime.<br>
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<div class="gmail_quote">
<div dir="ltr">El vie., 9 nov. 2018 a las 7:57, Francois Berenger (<<a href="mailto:mlists@ligand.eu">mlists@ligand.eu</a>>) escribió:<br>
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Hello,<br>
<br>
Recently, I stumbled upon this open source tool:<br>
<br>
PLIP - Protein-Ligand Interaction Profiler<br>
Analyze and visualize non-covalent protein-ligand interactions in PDB <br>
files<br>
<br>
From the abstract:<br>
---<br>
[...]<br>
detection and visualization of [...] seven interaction types (hydrogen <br>
bonds, hydrophobic contacts, pi-stacking, pi-cation interactions, salt <br>
bridges, water bridges and halogen bonds).<br>
---<br>
<br>
Website:<br>
<a href="http://plip.biotec.tu-dresden.de" rel="noreferrer" target="_blank">http://plip.biotec.tu-dresden.de</a><br>
<br>
Open-source code:<br>
<a href="https://github.com/ssalentin/plip" rel="noreferrer" target="_blank">https://github.com/ssalentin/plip</a><br>
<br>
Paper:<br>
<a href="https://academic.oup.com/nar/article-pdf/43/W1/W443/17435622/gkv315.pdf" rel="noreferrer" target="_blank">https://academic.oup.com/nar/article-pdf/43/W1/W443/17435622/gkv315.pdf</a><br>
or<br>
<a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4489249/" rel="noreferrer" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4489249/</a><br>
<br>
And, when I am inside chimera looking at a protein-ligand complex,<br>
it would be super nice if this tool could be launched from within<br>
chimera (as in a menu "Tools -> Surface/Binding Analysis -> PLIP <br>
analysis (visualize non-covalent interactions)").<br>
Or, maybe it could be a toggable button inside of ViewDock.<br>
<br>
Best regards,<br>
Francois.<br>
<br>
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</blockquote>
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