Forgot your password?
New user?
Document Actions
List of Pmv Commands
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 |
|---|---|---|
| APBSCommands.py |
Graphic User Interface (GUI) for Adaptive Poisson-Boltzmann Solver (APBS). Read Molecular Electrostatics tutorial to learn more. |
Yes |
| SLCommands.py | An interface to Spatial Geometry library that implements Binary Space Partitioning (BSP) Trees. | No |
| aboutCommands.py | Implements Help → About menu. |
Yes |
| amberCommands.py | GUI for running energy minimization and molecular dynamics using Amber94 force field. |
No |
| bondsCommands.py | Used for building, add or removing bonds. Edit → Bonds. |
Yes |
| coarseMolSurfaceCommands.py | Compute → Coarse Molecular Surface. |
Yes |
| colorCommands.py | Color → by Atom, Residue, Chain, Molecule and other properties. |
Yes |
| colorPaletteCommands.py | Edit → color palettes → Edit Color By Atom Type Palette. |
Yes |
| controlPanelCommands.py | Control Panel Widget (deprecated). |
No |
| dashboardCommands.py | Dashboard for a quick access to various commands. |
Yes |
| deleteCommands.py | Delete items from MoleculeViewer. Edit → Delete. |
Yes |
| displayCommands.py | Display → Lines, Label, Stick and Balls, CPK, etc.. |
Yes |
| editCommands.py | Edit → Atoms, Charges, Hydrogens and Misc. |
Yes |
| extrusionCommands.py | Used for extruding Secondary Structure. |
Yes |
| fileCommands.py | File → "Read Molecule" and other file related reading and writing. |
Yes |
| genparserCommands.py | File → "Define Pdb Specifications" and "Read PDB with Gen Parser..." menu. |
No |
| grid3DCommands.py | 3D grid and volume rendering widget. Available through Grid3D menu and toolbar icon. Read 3D Grid/Volume Rendering Widget tutorial to learn more. |
Yes |
| gridCommands.py |
Reads AutoGrid maps; displays isosurfaces and orthoslices. |
No |
| hbondCommands.py | Adds Hydrogen Bonds menu and various options such as Build, Display and Edit. |
No |
| helpCommands.py | Builds Help menu. |
Yes |
| interactiveCommands.py | Used to implement keyboard and mouse bindings. |
Yes |
| labelCommands.py | Display → Label. |
Yes |
| measureCommands.py | Display → Measure. | Yes |
| msmsCommands.py | Compute → Molecular Surface. |
Yes |
| mvCommand.py | Base class for command objects for a molecule viewer. |
Yes |
| povrayCommands.py | Povray GUI. |
No |
| repairCommands.py | Adds 'Check For Missing Atoms', 'Check For Close Contacts' and 'Repair Missing Atoms' menus under Edit → Misc. |
No |
| sdCommands.py | Adds a menu for SurfDock which is general tool for predicting protein-protein interactions. | No |
| secondaryStructureCommands.py | Display → Secondary Structure. |
Yes |
| selectionCommands.py | Implements Select menu and its options (e.g. Select From String). |
Yes |
| setangleCommands.py | Edit → 'Torsion Angles' → 'Set Torsions'. |
Yes |
| splineCommands.py | Compute → Spline. |
Yes |
| superImposeCommands.py | Compute → Superimpose. |
No |
| superimposeCommandsNew.py | Compute → 'Superimpose Atom Pairs'. |
Yes |
| traceCommands.py | Display → Trace. |
No |
| trajectoryCommands.py | Use to read and play GROMACS trajectories. Add new Trajectory top level menu. |
No |
| updateCommands.py | Help → Update. |
Yes |
| vectfieldCommands.py |
Used to display VU files. |
No |
| visionCommands.py | Integrates Vision with PMV. |
Yes |
| writeMsmsAsCommands.py | Saves MSMS as STL or Mathematica .m file. |
No |
New VISION Screencasts