Protein Data Viewer for Windows.
The PDVWIN program allows the user to view proteins and other molecules with coordinates in the PDB format of the Brookhaven Protein Data Bank. Currently, files for proteins and nucleic acids which conform to the PDB standard can be viewed. Other molecules can be viewed as Heteroatoms (HETATOM) as long as the coordinates are defined in standard HETATM lines, and are accompanied by an appropriate CONECT matrix.
The program has the following features:
- Models are displayed as stick, or ball and stick, structures
- A Render window allows display of 3-D sphere models
- View modes include
- Mono (with color)
- Stereo crossed-eye (with color)
- Stereo wall-eyed (with color)
- Stereo through red/green or blue/red pairs (simple viewer with filters needed)
- PDB Information window reads the header section of the file, and decodes secondary structural information, hetero groups, etc. The window includes a comprehensive set of coloring tools to allow separate coloring of atoms, chains, spans, prosthetic groups.
- Profile menu allows coloring of the model according to physico-chemical indices (hydropathy, structural propensity, volume, charge, etc.), or according to the sequence profile (hydropathy profile, prediction profile, etc.), or a moment profile (amphipathy, conservation moment, side-chain volume moment, etc.).
- Toggles allow independent display of side-chains, backbone, CA-backbone, heteroatoms, hydrogen bonds, waters.
- A Highlights menu allows highlighting of residues by name or number, or of hetatoms. Selected groups can be colored, decorate with atom circles, numbered, or displayed with increased line-thickness.
- A 3-D cursor allows identification of atoms, residues, distances, neighbors, or centering of the model, or placing of text (in 3-D) anywhere on the screen.
- The program will calculate and file psi and phi angles for spans, chains, or the complete molecule (proteins only).
- Models can be printed (WYSWYG) on the Windows Printer in either portrait or landscape views, and in all mono or stereo options.
- Rendered pictures can be saved to file for decoration by paint programs.
Click here for PDVWIN Manual.
Ribosome model of pufX protein
Rendered picture of pufX protein
Photosystem II. Space filling model
Qb-site of photosystem II
Donor side of photosystem II
Ribosome model of LHCII helix
A decorated picture of the Qi-site