pdbread

Read data from Protein Data Bank (PDB) file

Syntax

PDBStruct = pdbread(File)

PDBStruct = pdbread(File,Name=Value)

Description

PDBStruct = pdbread(File) reads data from a PDB-formatted text file and stores the data in a structure containing a field for each PDB record.

PDBStruct = pdbread(File,Name=Value) uses additional options specified by one or more name-value arguments.

Examples

Read Protein Structural Information from PDB File

Use the getpdb function to retrieve structure information for the nicotonic receptor protein from the Protein Data Bank, and save the data as a PDB-formatted file in the current folder.

PDBtoFile = getpdb('1abt',ToFile="nicotonic_receptor.pdb");

Read the data from the PDB-formatted file into a structure.

PDBStruct = pdbread("nicotonic_receptor.pdb")

PDBStruct = struct with fields:
            Header: [1×1 struct]
             Title: [2×60 char]
          Compound: [8×37 char]
            Source: [2×10 char]
          Keywords: 'TOXIN'
    ExperimentData: 'SOLUTION NMR'
           Authors: 'V.J.BASUS,G.SONG,E.HAWROT'
      RevisionDate: [1×5 struct]
           Journal: [1×1 struct]
           Remark1: [1×1 struct]
           Remark2: [1×1 struct]
           Remark3: [1×1 struct]
           Remark4: [2×59 char]
         Remark100: [3×59 char]
         Remark210: [25×59 char]
         Remark215: [6×59 char]
         Remark300: [6×59 char]
         Remark350: [13×59 char]
         Remark465: [13×59 char]
         Remark500: [168×59 char]
      DBReferences: [1×2 struct]
          Sequence: [1×2 struct]
             Helix: [1×1 struct]
             Sheet: [1×5 struct]
            SSBond: [1×5 struct]
       CISPeptides: [1×2 struct]
            Cryst1: [1×1 struct]
           OriginX: [1×3 struct]
             Scale: [1×3 struct]
             Model: [1×4 struct]
      Connectivity: [1×10 struct]
            Master: [1×1 struct]

Read the data from only the second model into a structure.

PDBStruct = pdbread("nicotonic_receptor.pdb",ModelNum=2);
PDBStruct.Model

ans = struct with fields:
    MDLSerNo: 2
        Atom: [1×1205 struct]
    Terminal: [1×2 struct]

Input Arguments

File — Name of PDB file

character vector | string | character array | column vector of strings

Name of PDB file, specified as one of the following.

• Character vector or string specifying a filename, a path and filename, or a URL pointing to a file. The file must be a PDB-formatted file (ASCII text file). If you specify only a filename, that file must be on the MATLAB^® search path or in the current folder.

• Character array or column vector of strings that contains the text of a PDB-formatted file.

For more information about PDB formatting, visit https://www.wwpdb.org/documentation/file-format.

Tip

You can use the getpdb function with the ToFile property to retrieve protein structure data from the PDB database and create a PDB-formatted file.

Data Types: char | string

Name-Value Arguments

Specify optional pairs of arguments as Name1=Value1,...,NameN=ValueN, where Name is the argument name and Value is the corresponding value. Name-value arguments must appear after other arguments, but the order of the pairs does not matter.

Example: PDBStruct = pdbread(File,ModelNum=2,TimeOut=10)

ModelNum — Model number to read

positive integer

Model number to read from File, specified as a positive integer. If ModelNum does not correspond to an existing model number in File, then the function reads the coordinate information of all the models.

Example: PDBStruct = pdbread(File,ModelNum=2) reads only the second model from the file.

Data Types: double

TimeOut — Connection timeout

5 (default) | positive scalar

Connection timeout (in seconds) to read data from the PDB database, specified as a positive scalar.

Example: PDBStruct = pdbread(File,TimeOut=10) waits 10 seconds to receive a response from the PDB database.

Data Types: double

Output Arguments

PDBStruct — PDB data

structure

PDB data, specified as a structure with a field for each PDB record. The following table summarizes the possible PDB records and the corresponding fields in PDBStruct.

PDB Database Record	Field in the MATLAB Structure
HEADER	Header
OBSLTE	Obsolete
TITLE	Title
CAVEAT	Caveat
COMPND	Compound
SOURCE	Source
KEYWDS	Keywords
EXPDTA	ExperimentData
AUTHOR	Authors
REVDAT	RevisionDate
SPRSDE	Superseded
JRNL	Journal
REMARK 1	Remark1
REMARK N Note N can be any number from 2 through 999.	Remarkn Note n can be any number from 2 through 999.
DBREF	DBReferences
SEQADV	SequenceConflicts
SEQRES	Sequence
FTNOTE	Footnote
MODRES	ModifiedResidues
HET	Heterogen
HETNAM	HeterogenName
HETSYN	HeterogenSynonym
FORMUL	Formula
HELIX	Helix
SHEET	Sheet
TURN	Turn
SSBOND	SSBond
LINK	Link
HYDBND	HydrogenBond
SLTBRG	SaltBridge
CISPEP	CISPeptides
SITE	Site
CRYST1	Cryst1
ORIGXn	OriginX
SCALEn	Scale
MTRIXn	Matrix
TVECT	TranslationVector
MODEL	Model
ATOM	Atom
SIGATM	AtomSD
ANISOU	AnisotropicTemp
SIGUIJ	AnisotropicTempSD
TER	Terminal
HETATM	HeterogenAtom
CONECT	Connectivity

Several fields of PDBStruct are structures containing subfields.

• The Sequence field contains sequence information in the following subfields:

  • NumOfResidues

  • ChainID

  • ResidueNames — Contains the three-letter codes for the sequence residues

  • Sequence — Contains the single-letter codes for the sequence residues

  Note

  If the sequence has modified residues, then the ResidueNames subfield might not correspond to the standard three-letter amino acid codes. In this case, the Sequence subfield contains the modified residue code in the position corresponding to the modified residue. The modified residue code is provided in the ModifiedResidues field.

• The Model field is a structure or array of structures that contains coordinate information. If PDBStruct contains one model, then Model is a structure containing coordinate information for that model. If PBStruct contains multiple models, then Model is an array of structures containing coordinate information for each model. The Model field contains the following subfields:

  • Atom

  • AtomSD

  • AnisotropicTemp

  • AnisotropicTempSD

  • Terminal

  • HeterogenAtom

• The Atom field is an array of structures containing the following subfields:

  • AtomSerNo

  • AtomName

  • altLoc

  • resName

  • chainID

  • resSeq

  • iCode

  • X

  • Y

  • Z

  • occupancy

  • tempFactor

  • segID

  • element

  • charge

  • AtomNameStruct — Contains three subfields: chemSymbol, remoteInd, and branch

Version History

Introduced before R2006a