scipion-chem Goto Github PK

Documentation under development, sorry for the inconvenience

Base Scipion plugin defining objects and protocols for CHEMoinformatics and virtual drug screening

Full documentation can be found in the Scipion Chem official documentation page.

You will need to use 3.0.0 version of Scipion to run these protocols. To install the plugin, you have two options:

• Stable version (Currently not available)

scipion3 installp -p scipion-chem

OR

• through the plugin manager GUI by launching Scipion and following Configuration >> Plugins

• Developer's version

1. Download repository:

git clone https://github.com/scipion-chem/scipion-chem.git

2. Switch to the desired branch (master or devel):

Scipion-chem is constantly under development. If you want a relatively older an more stable version, use master branch (default). If you want the latest changes and developments, user devel branch.

cd scipion-chem
git checkout devel

3. Install: The following comand will launch the installation of the plugin, together with some third-party programs

scipion3 installp -p path_to_scipion-chem --devel

• External software

External software currently installed by scipion-chem:

• OpenBabel and RDKit: the main small molecule handlers and converters
• MGLTools: additional utils for small molecules, docking, ... (includes AutoDockTools)
• JChemPaint: Java program to manually draw small molecules.
• PyMol: main viewer of Scipion-Chem for small molecules and structures
• VMD: secondary viewer of Scipion-Chem for structures and Molecular Dynamics
• AliView: main viewer for sequences
• PLIP: specialized viewer for docking interactions in PyMol

Status devel version:

Status production version: