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List of Pmv Commands

by Sargis Dallakyan last modified 2011-10-03 11:33
The following is a list of commands available in Pmv. Last column called "Loaded" shows whether a given command is loaded, by default, or not. The ones that are not loaded, can be loaded by using File → Browse Commands menu. This menu can also provide more up-to-date description of these commands.
Command Brief Summary
Loaded Graphic User Interface (GUI) for Adaptive Poisson-Boltzmann Solver (APBS). Read Molecular Electrostatics tutorial to learn more.
Yes Implements Help → About menu.
Yes Used for building, add or removing bonds. Edit → Bonds.
Yes Compute → Coarse Molecular Surface.
Yes Color → by Atom, Residue, Chain, Molecule and other properties.
Yes Edit → color palettes → Edit Color By Atom Type Palette.
Yes Dashboard for a quick access to various commands.
Yes Delete items from MoleculeViewer. Edit → Delete.
Yes Display → Lines, Label, Stick and Balls, CPK, etc..
Yes Edit → Atoms, Charges, Hydrogens and Misc.
Yes Used for extruding Secondary Structure.
Yes File → "Read Molecule" and other file related reading and writing.
Yes File → "Define Pdb Specifications" and "Read PDB with Gen Parser..." menu.
No 3D grid and volume rendering widget. Available through Grid3D menu and toolbar icon. Read 3D Grid/Volume Rendering Widget tutorial to learn more.
Reads AutoGrid maps; displays isosurfaces and orthoslices.
No Adds Hydrogen Bonds menu and various options such as Build, Display and Edit.
No Builds Help menu.
Yes Used to implement keyboard and mouse bindings.
Yes Display → Label.
Yes Display → Measure. Yes Compute → Molecular Surface.
Yes Base class for command objects for a molecule viewer.
Yes Povray GUI.
No Adds 'Check For Missing Atoms', 'Check For Close Contacts' and 'Repair Missing Atoms' menus under Edit → Misc.
No Adds a menu for SurfDock which is general tool for predicting protein-protein interactions. No Display → Secondary Structure.
Yes Implements Select menu and its options (e.g. Select From String).
Yes Edit → 'Torsion Angles' → 'Set Torsions'.
Yes Compute → Spline.
Yes Compute → Superimpose.
No Compute → 'Superimpose Atom Pairs'.
Yes Display → Trace.
No Use to read and play GROMACS trajectories. Add new Trajectory top level menu.
No Help → Update.
Used to display VU files.
No Integrates Vision with PMV.
Yes Saves MSMS as STL or Mathematica .m file.

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