Embedded Files
Hundreds of features to describe here- we'll update this list in September 2011
Hundreds of features to describe here- we'll update this list in September 2011
Molecule formats supported
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
Representations
Atom representations
Atom representations
Space filling (CPK), using the [Atoms] check buttons or the command: self.displayCPK("moleculename")
Sticks and balls, using the [Sticks] check buttons or the command: self.displaySticksAndBalls("moleculename")
Lines, using a presets or the command: self.displayLines("moleculename")
Backbone 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
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
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
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
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
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
* ...
Page updated
Google Sites
Report abuse