2010
DOI: 10.1002/bmb.20450
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Conscript: RasMol to PyMOL script converter

Abstract: The aim of the Structural Biology Extensible Visualization Scripting Language (SBEVSL) project is to allow users who are experts in one scripting language to use that language in a second molecular visualization environment without requiring the user to learn a new scripting language. ConSCRIPT, the first SBEVSL release, is a plug-in for PyMOL that accepts RasMol scripting commands either as premade scripts or as line-by-line entries from PyMOL's own command line. The plug-in is available for download at http:… Show more

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Cited by 7 publications
(4 citation statements)
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“…Atomic coordinates of the yeast RNA pol II were retrieved from the Protein Data Bank (PDB, RCSB) with the accession number PDB 1WCM, and visualized with the PyMOL program (DeLano Scientific LLC) ( 23 ).…”
Section: Methodsmentioning
confidence: 99%
“…Atomic coordinates of the yeast RNA pol II were retrieved from the Protein Data Bank (PDB, RCSB) with the accession number PDB 1WCM, and visualized with the PyMOL program (DeLano Scientific LLC) ( 23 ).…”
Section: Methodsmentioning
confidence: 99%
“…For each charged residue (D,E,R,K,H), the nearest, oppositely charged amino acid residue was found, and the distance was measured from nitrogen on the positive residue to the closest oxygen on the negative residue; the minimum criterium for an SB was defined as at least one D or E side-chain carbonyl oxygen being within 4 Å from an R,K, or H side-chain nitrogen. 34 HB networks were initially identified using the PyMOL script list_hb.py; 35 the heteroatom-to-heteroatom distance cutoff was initially set to 3.2 Å (see the Results section) and the maximum angle was set to 180°. 36 SBs and HBs in the simulation trajectory files were also found using Visual Molecular Dynamics's (VMD) 33 SB and HB analysis tools.…”
Section: T H Imentioning
confidence: 99%
“…Each docking program employs one or multiple specific research algorithms to anticipate the final configurations of a binary complex [14] . To prepare for molecular docking, we used PyMOL (The PyMOL Molecular Graphics System, Version 2.0 Schrödinger, LLC), an application for generating images and animations of molecular structures, to remove water and ligands [15] . Hydrogen atoms were subsequently added by using AutoDock 4.2 and AutoDock Vina software, which facilitated subsequent molecular docking simulations of potential targets and their corresponding components [16] .…”
Section: Molecular Dockingmentioning
confidence: 99%