Mcsalign
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Included in psico | |
Module | psico.mcsalign |
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mcsalign aligns two small-molecule selections based on Maximum-Common-Substructure.
Installation
mcsalign is available from the psico package and requires rdkit and csb.
All dependencies are available from Anaconda Cloud:
conda install -c schrodinger pymol conda install -c schrodinger pymol-psico conda install -c rdkit rdkit conda install -c speleo3 csb
Usage
mcsalign mobile, target [, mobile_state [, target_state [, cycles [, timeout [, method ]]]]]
Arguments
- mobile = str: atom selection of mobile object
- target = str: atom selection of target object
- mobile_state = int: object state of mobile selection {default: -1 = current state}
- target_state = int: object state of target selection {default: -1 = current state}
- cycles = int: number of weight-refinement iterations for weighted RMS fitting {default: 5}
- timeout = int: MCS search timeout in seconds {default: 10}
- method = indigo or rdkit {default: check availability}
Example
Align Cytochrome C and Hemoglobin based on their Heme moieties:
fetch 3zcf 4n8t, async=0 zoom /4n8t//A/HEM, animate=2, buffer=3 import psico.mcsalign mcsalign /3zcf//A/HEC, /4n8t//A/HEM
Align a set of small molecules to a reference
fetch ala ile arg trp met extra_fit *, ala, method=mcsalign