[HTML][HTML] A virtual alternative to molecular model sets: a beginners' guide to constructing and visualizing molecules in open-source molecular graphics software

S Phankingthongkum, T Limpanuparb�- BMC Research Notes, 2021 - Springer
… the two freely available molecular graphics programs, Avogadro and IQmol, … molecular
model sets. These simple exercises can be used in other class settings, other available programs

A Semester-Long Learning Path Teaching Computational Skills via Molecular Graphics in PyMOL

M Kjaergaard, LS Rasmussen, JN Vinther…�- The�…, 2022 - meridian.allenpress.com
… out basic visualization tasks using PyMOL scripts, while three-… molecular graphics software
with teaching of structural biochemistry allows a hands-on approach to analyzing molecular

Shortcuts for faster image creation in PyMOL

BHM Mooers�- Protein Science, 2020 - Wiley Online Library
… of the molecular graphics program PyMOL, which has more than 100,000 users.5 PyMOL is
open-source versions of PyMOL. The module is not easy to add to the incentive versions of …

[HTML][HTML] Boosting the full potential of PyMOL with structural biology plugins

S Rosignoli, A Paiardini�- Biomolecules, 2022 - mdpi.com
… use molecular graphics tool. This review outlines the plugins and features that make PyMOL
… and Linux on both the open source and incentive PyMOL builds provided by Schr�dinger Inc…

Geo-Measures: A PyMOL plugin for protein structure ensembles analysis

LP Kagami, GM das Neves, LFSM Timmers…�- …�Biology and Chemistry, 2020 - Elsevier
… Geo-Measures GUI is based on PyMOL (The PyMOL Molecular Graphics System, … ://pymol.org
), a widely used open source tool for biomolecular visualization. The choice of PyMOL was …

[HTML][HTML] pyProGA—a PyMOL plugin for protein residue network analysis

V Sladek, Y Yamamoto, R Harada, M Shoji, Y Shigeta…�- PLoS�…, 2021 - journals.plos.org
PyMOL package is widely used in molecular research [52] and thus enjoys a large degree
of familiarity in the chemical community. Additionally, PyMOLopen source nature of PyMOL

[PDF][PDF] MAGI-Dock: a PyMOL companion to Autodock Vina

J Kaftalli, A Bernini, G Bonetti, S Cristoni…�- European Review for�…, 2023 - europeanreview.org
… MAGI-Dock is a free open-source software available under … such box drawing is limited to a
few molecular graphics software5 … widely used macromolecular visualization tools, PyMOL7. …

Templates for writing PyMOL scripts

BHM Mooers, ME Brown�- Protein Science, 2021 - Wiley Online Library
… from lecture notes on molecular graphics, scripts used to … , the PyMOL Wiki (http://pymolwiki.org),
and the PyMOL mailing … use at the PyMOL prompt in interactive PyMOL sessions. Code …

PyVibMS: a PyMOL plugin for visualizing vibrations in molecules and solids

Y Tao, W Zou, S Nanayakkara, E Kraka�- Journal of Molecular Modeling, 2020 - Springer
… PyVibMS was written in Python and its open-source nature makes it flexible and sustainable.
As … In this work, a PyMOL plugin named PyVibMS is developed to visualize molecular and …

Visualizing protein structures—tools and trends

X Martinez, M Chavent, M Baaden�- Biochemical Society�…, 2020 - portlandpress.com
tools, we will briefly discuss Chimera (latest version called ChimeraX), Jmol (and more
recently JSmol), PyMol … about the progress of molecular graphics will conclude our collection of …