pdbread
Read data from Protein Data Bank (PDB) file
Description
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 residuesSequence
— 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, theSequence
subfield contains the modified residue code in the position corresponding to the modified residue. The modified residue code is provided in theModifiedResidues
field.The
Model
field is a structure or array of structures that contains coordinate information. IfPDBStruct
contains one model, thenModel
is a structure containing coordinate information for that model. IfPBStruct
contains multiple models, thenModel
is an array of structures containing coordinate information for each model. TheModel
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
, andbranch
Version History
Introduced before R2006a
See Also
genpeptread
| getpdb
| pdbdistplot
| pdbsuperpose
| pdbtransform
| pdbwrite
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