Basic usage¶
Once installed, the CryptoSite protocol can be run by means of a command line
tool (cryptosite
). Each component of the protocol is also a Python package,
which can be called directly from other Python software
(via import cryptosite
).
Overview¶
Running the basic protocol consists of these steps:
- Create a set of input files specifying the structure to probe, and basic CryptoSite parameters.
- Run
cryptosite setup
to calculate structural features and prepare input files for AllosMod. - Run AllosMod given the set of input files.
- Calculate additional features using the AllosMod output
(
cryptosite soap
,cryptosite pockets
,cryptosite am_bmi
,cryptosite analysis
). - Gather together all features into a single file (
cryptosite gather
). - Predict cryptic binding sites with an SVM using the complete set of features
as input (
cryptosite predict
). - Optionally visualize the results in
Chimera (
cryptosite chimera
).