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Plugin Update MOLE 2.5 is an updated version of channel analysis software in PyMOL
Official Release PyMOL v1.8.6 has been released on March 9, 2017.
Official Release PyMOL v1.8.4 has been released on October 4, 2016.
New Script dssr_block is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
New Plugin LiSiCA is a new plugin for 2D and 3D ligand based virtual screening using a fast maximum clique algorithm.
Official Release PyMOL v1.8.0 has been released on Nov 18, 2015.
PyMOL Open-Source Fellowship Schrödinger is now accepting applications for the PyMOL Open-Source Fellowship program! Details on
Official Release PyMOL, AxPyMOL, and JyMOL v1.7.6 have all been released on May 4, 2015.
New Plugin PyANM is a new plugin for easier Anisotropic Network Model (ANM) building and visualising in PyMOL.
New Plugin Bondpack is a collection of PyMOL plugins for easy visualization of atomic bonds.
New Plugin MOLE 2.0 is a new plugin for rapid analysis of biomacromolecular channels in PyMOL.
3D using Geforce PyMOL can now be visualized in 3D using Nvidia GeForce video cards (series 400+) with 120Hz monitors and Nvidia 3D Vision, this was previously only possible with Quadro video cards.
Older News See Older News.
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Type Python Script
Author(s) Zhenting Gao


RMSD between two structures of the same protein

  • programming
    • Platform
      • PyMOL
        • rms_cur
    • Feature
      • Output
        • RMSD of all atoms of each residues pairs
        • Least RMSD of all atoms of each residues pairs
          • symmetry of Phe, Tyr, His, Asp, Glu, Gln, Asn, Arg, Leu and Val needs to be considered
            • switch the atom name and then calculate the RMSD again
            • Selected least RMSD of a residue pair for report
              • RMSD of backbone atoms of each residues pairs
              • RMSD of C alpha atoms of each residues pairs
          • With defined residues pairs
            • Residue pair can be limited to within binding site
    • Workflow
      • Read reference and target pdb files
        • two structures should be superposed before using this function
  • Note
    • Python
    • PyMOL
      • Clean attributes
        • otherwise rms_cur will fail
      • How to get residue name?
        • residue name, residue index and etc. can only be read from an atom
  • Reference
A Random PyMOL-generated Cover. See Covers.