|MIME type: chemical/x-pdb|
Protein Data Bank PDB files.
3D molecular model file.
Used in bioinformatics applications and on the web for storing and exchanging molecule models.
PDB is an acronym for Protein Data Bank.
Plain text format.
Stores structure information for large biological molecules such as proteins and nucleic acids.
Does not store chemical bond information.
Developed in 1971 at Brookhaven National Laboratory.
Maintained by the Research Collaboratory for Structural Bioinformatics (RCSB).
|"Elements"||list of elements and options available in this file|
|"Rules"||full list of rules for each element and option|
|"Options"||list of rules for options, properties, and settings|
|"Graphics3D"||PDB file rendered as a Graphics3D object|
|"Residues"||residue sequences as an array of three-letter abbreviations|
|"Sequence"||residue sequences given as a list of strings|
|"ResidueAtoms"||list of residue atoms|
|"ResidueChainLabels"||list of chain labels|
|"ResidueRoles"||functional roles of residue atoms|
|"ResidueCoordinates"||3D coordinates of residue atoms|
|"AdditionalAtoms"||atoms that are not constituents of a chain|
|"AdditionalCoordinates"||3D coordinates of additional atoms|
|"SecondaryStructure"||rules describing the large-scale structure of a chain|
|"VertexCoordinates"||atomic coordinates, typically given in picometers|
|"VertexTypes"||all atoms or groups constituting the molecule, typically given as a list of chemical element abbreviations|
|D||aspartic acid (Asp)|
|E||glutamic acid (Glu)|
|X||unspecified or unknown amino acid (Unk)|
|"ResidueCoordinatesList"||residue coordinates for each model|
|"AdditionalCoordinatesList"||3D coordinates of additional atoms for each model|
|"VertexCoordinatesList"||atomic coordinates for each model, typically given in picometers|
|"Author"||author information as referenced in the file|
|"Comments"||user comments stored in the file, given as a list of strings|
|"DepositionDate"||when the file was added to the database|
|"Organism"||organism in which this protein occurs|
|"References"||bibliographic references, given as a list of rules|
|ImageSize||Automatic||specifies the overall size of the graphics to display|
|Background||White||specifies what background color to use|
|ColorFunction||Automatic||function to apply to determine the coloring of secondary structure visualizations|
|ViewPoint||Automatic||point in space from which the 3D model is to be viewed|
Import a large PDB file from the RCSB Protein Data Bank website:
Read the title of this PDB file:
Import the labels for each chain in the above molecule:
Show the Import elements available in a smaller sample file:
Get the name of the organism referenced in this file:
Import the residue sequence:
This gives the same sequence as a string of single-character abbreviations:
Get structural information about this molecule:
Show the protein backbone in a stylized form:
Show the same protein, using standard colors for each residue:
This imports the sample file as a ball-and-stick graphic:
Show the same protein as a wireframe model:
Import residue data:
This imports the sample file, rendering atoms as space-filling spheres:
Import a DNA model:
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