File Formats

Currently, only PDB files are supported.

VistaPDB Manual -> File Formats

File Formats

PDB (Protein Data Bank) files are the only file type currently supported by VistaPDB. PDB files are standardized file types that specify macromolecular structures resulting from studies using x-ray diffraction or NMR specrometry. These files can be deposited into a database provided by the Resources for Studying Biological Macromolecules. You can use VistaPDB to search for PDB files. Alternatively you can visit RCSB to browse, search, and download PDB files.

  • Multiple Models: some PDB files contains multiple models. In such an instance, VistaPDB will ask users which model to open. To overlay multiple models upon one another, users can add multiple layers from the same file using the different models.
  • Chains: Many PDB structure files are co-crystal structures containing multiple macromolecules. VistaPDB opens these files into a single layer with multiple chains, each chain representing a different macromolecule in the structure. Rotations and translations occur to every chain in a layer. To move the chains individually, go to Layers -> Split to create a new layer for each chain in the model.

VistaPDB allows users to save structures and alignments to files. This file format is identical in nature to a PDB file format, with the addition record lines not described in the RCSB PDB File Format Standard. The extension for these files is .pdv. VistaPDB indicates in the REMARK record fields the origin of the structure.

  • Each layer is saved into the file as a separate model.
  • TRANS: The trans record identifies transformations applied to models.
    • COLUMNS      FORMAT         DESCRIPTION
    • 1-5           "TRANS"      
    • 10-12          REAL        Model Number
    • 31-38          REAL(3.5)   Angle Rotation around X axis
    • 39-46          REAL(3.5)   Angle Rotation around Y axis
    • 47-54          REAL(3.5)   Angle Rotation around Z axis
    • 55-60          REAL(3.5)   Translation From Model Midpoint
  • ALIGN The align record saves alignments made during structure analysis.
    • COLUMNS       FORMAT        DESCRIPTION
    • 1-5           "ALIGN"      
    • 10-70          NAME     NAME OF THE ALIGNMENT
  • ALIGNS The align record saves alignments made during structure analysis.
    • COLUMNS     RECORD NAME     DESCRIPTION
    • 1-5          "ALIGNS"      
    • 10-70        SEQUENCE        SEQUENCE