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PyMOL specifications


Unique identifier OMICS_03802
Name PyMOL
Alternative name AxPyMol
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes


  • PyKnot




No version available



  • person_outline Rhold C. Lua
  • person_outline Thomas Holder

Publication for PyMOL

PyMOL citations


Bat Caliciviruses and Human Noroviruses Are Antigenically Similar and Have Overlapping Histo Blood Group Antigen Binding Profiles

PMCID: 5964351
DOI: 10.1128/mBio.00869-18
call_split See protocol

[…] nce was determined by the use of the Modeller platform from the Bioinformatics Toolkit from the Max Planck Institute using GII.4.2012/NSW0514 as the template (). Dimeric models were created using The PyMOL Molecular Graphics System, version (Schrödinger, LLC). […]


High resolution AFM structure of DNA G wires in aqueous solution

Nat Commun
PMCID: 5958085
PMID: 29773796
DOI: 10.1038/s41467-018-04016-y

[…] ained dynamics with constraints of 5, 4, 3, 2, 1, and 0.5 kcal mol−1 Å−2. Finally, simulations were run unrestrained at 1 atm and 300 K for a duration of 1 ns. Molecules were visualized using VMD and Pymol. Molecular structures were averaged over the 1 ns unrestrained simulation and used for AFM simulations. […]


X ray structure of a carpet like antimicrobial defensin–phospholipid membrane disruption complex

Nat Commun
PMCID: 5958116
PMID: 29773800
DOI: 10.1038/s41467-018-04434-y
call_split See protocol

[…] d Rfree values of 0.2031 and 0.2519, respectively. All data collection and refinement statistics are summarized in Table . All programs were accessed via the SBGrid suite. Figures were prepared using PyMol. Movies were prepared using Chimera. […]


Structure guided Discovery of Dual recognition Chemibodies

Sci Rep
PMCID: 5954141
PMID: 29765112
DOI: 10.1038/s41598-018-25848-0
call_split See protocol

[…] re of rat DPP-IV with Fab 11A19 (PDB code: 4FFV) as a search model. Model building and refinement were carried out in COOT and REFMAC in CCP4, respectively. All structural figures were prepared using PyMOL (Schrodinger Inc, San Diego, CA). […]


CHAT gene polymorphism rs3810950 is associated with the risk of Alzheimer’s disease in the Czech population

J Biomed Sci
PMCID: 5950140
PMID: 29759072
DOI: 10.1186/s12929-018-0444-2
call_split See protocol

[…] p:// and homology modelling software MODELLER []. Search for hydrogen bond network was done via VMD [], Schrodinger Maestro software (Schrodinger, L. Biologics Suite 2017–1) and PyMOL (The PyMOL Molecular Graphics System, Version 2.0 Schrödinger, LLC.) as well as the visualization device. […]


Computer aided design of amino acid based therapeutics: a review

Drug Des Devel Ther
PMCID: 5958949
DOI: 10.2147/DDDT.S159767

[…] shown in . The X-ray crystallographic structures of Aldesleukin (PDB ID: 1M47; ) and Leuprolide (PDB ID: 1YY2; ) were obtained from the Protein Data Bank (PDB; and visualized by PyMol tool. The structure of Spaglumic acid was retrieved (in MOL format) from PubChem database ( with the PubChem ID 188803 () and visualized using PyMol. Aldesleuki […]


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