PDB (.pdb)

• Import supports Version 2.3 and previous versions of the PDB format, as well as several common variants.

IMPORT

• Import["file.pdb"] reads a PDB file and returns a stylized rendering of the protein.

• Mathematica provides a variety of 3D rendering styles for macromolecules.

• Import["file.pdb"] returns a Graphics3D object.

• Import["file.pdb", elem] imports the specified element from a PDB file.

• Import["file.pdb", {elem, sub_a, sub_b, ...}] imports a subelement.

• Import["file.pdb", {{elem₁, elem₂, ...}}] imports multiple elements.

• The import format can be specified with Import["file", "PDB"] or Import["file", {"PDB", elem, ...}].

• See the reference pages for full general information on Import.

• ImportString supports the PDB format.

ELEMENTS

• General Import elements:

	"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

• Graphics element:

"Graphics3D"

PDB file rendered as a Graphics3D object

• Import uses the "Graphics3D" element by default for the PDB format.

• Data representation elements:

	"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

• When reading an incomplete chain which is missing one or more residues from PDB, Mathematica will represent it as a sequence of individual subchains.

• Mathematica uses the standard IUB/IUPAC abbreviations for amino acid residues:

	A	alanine (Ala)
	C	cysteine (Cys)
	D	aspartic acid (Asp)
	E	glutamic acid (Glu)
	F	phenylalanine (Phe)
	G	glycine (Gly)
	H	histidine (His)
	I	isoleucine (Ile)
	K	lysine (Lys)
	L	leucine (Leu)
	M	methionine (Met)
	N	asparagine (Asn)
	P	proline (Pro)
	Q	glutamine (Gln)
	R	arginine (Arg)
	S	serine (Ser)
	T	threonine (Thr)
	V	valine (Val)
	W	tryptophan (Trp)
	Y	tyrosine (Tyr)
	X	unspecified or unknown amino acid (Unk)

• The following abbreviations are used to represent nucleic acids:

	A	adenosine
	C	cytidine
	G	guanosine
	I	inosine
	T	thymidine
	U	uridine
	X	unspecified or unknown nucleic acid

• When importing a PDB file that describes multiple 3D models of the same molecule, the following Import elements can be used to read the geometries of all models:

	"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

• Meta-information elements:

	"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
	"Title"	document title

OPTIONS

• General rendering options:

	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

• With the default setting "ViewPoint"->Automatic, Mathematica automatically calculates the optimal viewing angle for the imported molecule model.

• Selecting a rendering style:

"Rendering"

"Structure"

specifies the visualization method

• Possible settings for "Rendering" are:

	"BallAndStick"	displays atoms and bonds as a ball-and-stick model
	"Structure"	stylized rendering of the protein backbone
	"Spacefilling"	atoms shown as overlapping spheres
	"Wireframe"	bonds rendered as lines

SEE ALSO

• "FASTA"  "MOL"  "XYZ"

MORE ABOUT

• 3D Geometry & Modeling Formats

• Importing & Exporting

• Listing of All Formats

• Scientific & Medical Data Formats

EXAMPLES

CLOSE ALL

Basic Examples

Import a large PDB file from the RCSB Protein Data Bank website: In[1]:= Out[1]= Read the title of this PDB file: In[2]:= Out[2]= Import the labels for each chain in the above molecule: In[3]:= Out[3]=   Show the Import elements available in a smaller sample file: In[1]:= Out[1]= Get the name of the organism referenced in this file: In[2]:= Out[2]= Import the residue sequence: In[3]:= Out[3]= This gives the same sequence as a string of single-character abbreviations: In[4]:= Out[4]= Get structural information about this molecule: In[5]:= Out[5]= Show the protein backbone in a stylized form: In[6]:= Out[6]= Show the same protein, using standard colors for each residue: In[7]:= Out[7]= This imports the sample file as a ball-and-stick graphic: In[8]:= Out[8]= Show the same protein as a wireframe model: In[9]:= Out[9]= Import residue data: In[10]:= Out[10]= This imports the sample file, rendering atoms as space-filling spheres: In[11]:= Out[11]=   Import a DNA model: In[1]:= Out[1]=