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Included in psico
This command or function is available from psico, which is a PyMOL extension.

Module psico.mcsalign

mcsalign aligns two small-molecule selections based on Maximum-Common-Substructure.


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


mcsalign mobile, target [, mobile_state [, target_state
    [, cycles [, timeout [, method ]]]]]


  • 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}


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

See Also