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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

[…] 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)., virus-like particles (vlps) were generated as previously described (). briefly, the btcalv/a10 and btnov vp1 sequences […]


High resolution AFM structure of DNA G wires in aqueous solution

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

[…] parallel-stranded g-quadruplex crystal structure. the constraint files were generated using dev-c + + . minimal energy structures were identified and manually translated/rotated symmetrically using pymol to create longer models. fourteen full and four truncated ssdna strands generated g-wires of ~ 11 nm length. central k+ ions were added (33 in total) in between tetrads and on the exterior […]


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

PMCID: 5958116
PMID: 29773800
DOI: 10.1038/s41467-018-04434-y

[…] 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., nad1, nad1(k36e), and nad1(r39a) at 0.1 mm were incubated with or without 0.4 mm pa or pip2 at room temperature for 30 min. protein complexes […]


Structure guided Discovery of Dual recognition Chemibodies

PMCID: 5954141
PMID: 29765112
DOI: 10.1038/s41598-018-25848-0

[…] 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)., the atomic coordinates and structural factors of dpp-iv and 11a19 fab-(peg)6-inhibitor complex have been deposited in the protein data bank under accession […]


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

PMCID: 5950140
PMID: 29759072
DOI: 10.1186/s12929-018-0444-2

[…] 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., we have found statistically significant association between the risk of ad […]


Vaccine elicited receptor binding site antibodies neutralize two New World hemorrhagic fever arenaviruses

PMCID: 5951886
PMID: 29760382
DOI: 10.1038/s41467-018-04271-z

[…] refinement statistics are listed in supplementary table . we used sbgrid-supported applications to complete our structural studies, validated structures using molprobity, and made figures with the pymol molecular graphics system, schrödinger, llc., elisas in figs.  and and in supplementary figure  were done in duplicate twice (n = 2) with representative data shown. neutralization and entry […]

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