PyMOL protocols

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PyMOL specifications


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


  • PyKnot



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  • person_outline Rhold C. Lua <>
  • person_outline Thomas Holder <>

Publication for PyMOL

PyMOL in pipelines

PMCID: 5750217
PMID: 29295993
DOI: 10.1038/s41467-017-02444-w

[…] the twin. therefore, untwined refinement was carried out further. unit cell parameters, data collection and refinement statistics are presented in table . all structural figures were prepared using pymol., all relevant data are available from the corresponding authors upon reasonable request. the coordinates of the refined models and structure factors have been deposited into the protein data […]

PMCID: 5773547
PMID: 29348627
DOI: 10.1038/s41598-018-19295-0

[…] and van der waals + electrostatic. amongst these, the balanced outputs were analyzed. the docking solution with largest (128) members (table ) was taken for further visualization using the pymol software., the atpase assay was performed by measuring phosphate release using a colorimetric method based on complex formation with malachite green and molybdate as described earlier […]

PMCID: 5774476
PMID: 29391779
DOI: 10.2147/DDDT.S149973

[…] of the ligand was performed by using the chemdraw ultra 12.0.2 and marvinsketch programs. the molecular docking process was performed by using the plants/protein–ligand ant system. meanwhile, the pymol program ( was used to see the hydrogen bonds in amino acid residues between the ligand and receptors., the in vitro cytotoxic activities were evaluated by using […]

PMCID: 5774825
PMID: 29352301
DOI: 10.1371/journal.pone.0191610

[…] the protein data bank as pdb file 4j2o. structural homologs for ab-wbjb were identified with dali searches [], last accessed in august 2017. all molecular views presented here were prepared using pymol []., to generate mutants m134a-wbjb and m134y-wbjb, isolated pet15b plasmids harbouring fnla gene were subjected to site-directed mutagenesis with a commercial kit (quikchange, stratagene) […]

PMCID: 5792426
PMID: 29346773
DOI: 10.1016/j.celrep.2017.12.075

[…] using i-tasser (). ssp2 model was further regularized by 1 ns molecular dynamics in explicit solvent followed by energy minimization (gromacs 2016.3; ). structural alignments were performed in pymol (version; schrodinger)., quantitative data were analyzed and presented using graphpad prism, and pairwise comparison was performed using unpaired t tests (two tailed). all replicates […]

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PyMOL in publications

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 […]

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 […]

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 […]

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 […]

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 […]

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PyMOL reviews

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