ePMV overview

Hundreds of features to describe here- we'll update this list in September 2011

Molecule formats supported

ePMV can read the following molecule formats (just like PMV), either throught the gui ([Browse] button) or from the command : self.readMolecule("filename").

1. .pdb, .pdbqt, .cif, .mol, .dlg, .pqr

Theses molecule can be fecthed directly from a webserver, either throught the gui (Fetch button) or from the command : self.fetch("ID"):

1. PDB,CIF

2. PDBTM

3. OMP

Representations

Atom representations

Backbone representations

    • Secondary structure as cartoon ribbons, using the "Ribbons" check buttons or the command: self.displayExtrudedSS("moleculename")

    • Spline and extruded spline, using the "Spline" and the "Loft" check buttons. These host specific commands are not part of PMV.

    • Armature, a skeletal representation of the proteins using jointed atoms or domains that can be manipulated using Inverse Kinematics. The armature can be animated or simulated and bound to any mesh including ribbons and molecular surfaces.

Surface Representations

    • Molecular Surface (MSMS), using the "MSMSurf" check buttons or the command: self.displayMSMS("moleculename")

    • Coarse Molecular Surface, using the "CoarseMolSurf" check buttons.

    • Metaballs, using the "Metaballs" check buttons. This ePMV host-specific command is not part of PMV.

Biological unit Representations

In modern PDB file the biological unit of a molecule is represented by the "REMARK 350 BIOMT" which define the transformation matrices to apply in order to build the unit. If you fetch or load a PDB file that contains the BIOMT field you can build the unit for any choosen geometry (for instance surface).

Coloring methods

Each representation based on PMV can be colored with the following schemes:

    • Atoms Type (CPK)

    • Atoms by polarity (David Goodsell)

    • Residues Type (namely or shapely)

    • Secondary Structure Type

    • Chains

    • Temperature Factor

    • Surface accessible to solvent

    • Rainbow from N to C termini

The default colors can be changed throught the Edit->Colors palettes menu.

An additional method can interpolate volume data onto a mesh surface (e.g an APBS electrostatic grid can be mapped onto an MSMS surface)

Advanced features

    • ePMV selection string instructions

    • Trajectories e.g., from molecular dynamics, can be read and played from Gromacs (.xtc,.trj)

    • Grid data isocontouring representations from divers format (MRC,DX,MAP,CCP4,...)

Extensions

1. Protein-ligand scoring with AutoDock or PyRosetta

2. Modeller optimization and molecular dynamics

3. Augmented Reality

Theses features are all accessible from the gui provided for each host (see here for more details).

Other feature of either PMV or the host can be access using script (python). For instance:

* coloring a MSMS surface using an APBS computation.

* superimposing one molecule onto another

* adding charges

* removing waters

* setting up particle systems or physics objects

* ...