MVP: Macromolecular Visualization and Processing

Dong Xu and Yang Zhang

Purpose:

Sometimes, our aim is not only to see 3D molecular structures, but also to get derived computational results from the structures and visualize them simultaneously. Currently, MVP is mainly for the illustration and processing of structure-related information which is useful in structure prediction.

Downloadable Version 1.0:

Windows executable

Linux executable

Project page for Version 2.0: (new)

MVP-Fit: Flexible Manual Fitting of Atomic Models into a Cryo-Electron Microscopy Density Map

Development Information:

Language: C++, OpenGL

GUI design: wxWidgets

Compiler and dependence: MSVS in Windows; GCC+GTK in Linux

Highlights:

1. Secondary strucutre estimation and visualization for alpha-carbon backbone

During the protein tertiary structure prediction, the decoy may only contains alpha carbons. However, we still want to check out if the backbone conformation is possible to form hydrogen bond after add mainchain heavy atoms.



2. Visualization of trajectories after Monte Carlo or molecular dynamics simulation



3. Depth calculation and visualization

Depth is the minimum distance to the surface. It reveals the hydrophobic property of each residue.

per atom	per residue

 

Basic Components:

1. Protein tertiary structure (styles, colors)

backbone, charge	spacefill, CPK	wireframe, amino type	stick, shapely
strands, acidity	ribbons, structure	cartoon, group	ballstick, hydropathy

2. Cryo-EM density maps

pointcloud	mesh	isosurface

3. Contact visualization

If predicted contact is consistent with that in the native structure, then the line is solid red, else is dash blue.



4. Principal axes

Using Principal Component Analysis (PCA), transform the structure to the standard position.

before PCA	after PCA

5. RNA and DNA visualization