PyMOL pipeline

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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Publication for PyMOL

PyMOL citations

PMCID: 5894237

[…] using discovery studio (dassault systèmes biovia, discovery studio modeling environment, release 4.1, san diego: dassault systèmes, 2007). mutant models and 3d images were generated with pymol (the pymol molecular graphics system, version 1.8 schrödinger, llc)., the data are expressed as averages with the standard deviations (sds), and statistically significant differences were determined using […]

PMCID: 5936819

[…] with both pairs of histidines positioned closest to their respective heme-ligating positions was selected as a starting structure. from this structure, mutants bt6m1 and bt6m0 were generated using pymol version 1.7 (pymol molecular graphics system version 1.7, schrödinger, llc). hemes (0, 1, or 2) were manually docked into the bis-his sites of the structures., to relax the starting structure […]

PMCID: 5842395

[…] template was identified from pdb by a locally installed lomets meta-threading server. models were constructed by iterative tasser simulations. the generated pdb files were then visualized with pymol molecular graphics system., to investigate the transcriptional changes of ctls during the various stages of o. furnacalis, total rna samples were individually prepared from three different […]

PMCID: 5913616

[…] or phenix (adams et al., 2010). during this operation, care was taken to use the programs and scripts of the originators, as described in the respective pdb header., the figures were created with ‘pymol’ (version, schrödinger, llc)., the structure of o. sativa dwarf14 (osd14) was determined by x-ray crystallography to a resolution of 1.35 å from a construct lacking the first 51 […]

PMCID: 5874642

[…] of the modelled protein 3-d structure. the stereochemical parameters of the modelled structure were also ascertained in order to determine whether there is any structural violation during modelling. pymol 1.3 version was used to visualise and evaluate, as well as analyse, the generated 3-d model [21]. based on the fact that there is no existing vaccine against cancer, this present study […]

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