Purpose

This is a simple yet useful viewer for Protein Data Bank (PDB) files. It should be able to read any .pdb file exported from the website. It includes three example files which can instantly be loaded via the menu.

Features

This PDB viewer has the following features:

• Full 3D view of primary and secondary structure of the given Protein sequence, based on the coordinates given by PDB.
• Fully rotatable and zoomable view of the protein structure.
• Different 3D views:
  • Atom view - shows the atoms and atom bonds.
  • Cartoon view - stylized secondary structure for alpha helices and beta sheets are beautifully shown within the coil structure.
  • Toggle a ribbon view following the backbone structure of the protein. Showing the twisting of the structure as it evolves through its coil space.
  • Toggle atoms to be shown or hidden
  • Toggle bonds to be shown or hidden
  • Toggle C-beta atoms to be shown or hidden
• Mark any number of residues in the primary structure view (sequence view) and mark all atoms associated with the marked residue in the 3D view.
• Carry out BLAST-p queries for the loaded protein and show the acquired hits in BLAST-Text format

Restrictions

• Only shows primary and secondary structure of the residues including C-beta atoms, but excluding any residual atoms.
• For Glycin the residual H-Atom is treated as a C-beta atom. But with the correct positioning

Dependencies

• Apache Maven 3 for the build.
• JavaFX runtime. This is included in the Oracle JRE 8 or Oracle JDK 8.
• Git (not needed if you download a .tar.gz or .zip file from the website).

Donwload

Navigate to some directory in a terminal. This is where you want the code base (in the following <PROJECT_DIR>) to lie. Then run the following:

git clone https://github.com/pgrupp/pdb_viewer.git

Usage

The application runs using JavaFX and should be self-explanatory.

Build

To build the application Oracle Java SDK 8 and Maven 3 is required. Other dependencies are resolved by Maven.

Complete build

1. Compile the runnable JAR file and run tests.

mvn package

2. Run the application using the generated JAR file. Which should be located in <PROJECT_DIR>/target.

java -jar <PROJECT_DIR>/target/pdb_viewer-1.2.jar

Or just double-click the generated JAR file.

Run tests only

In order to only run the provided tests run the following command in the <PROJECT_DIR>.

mvn test

Compile only binaries

In order to simply compile the source code run the following command in the <PROJECT_DIR>.

mvn compile