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pdbtransform

Apply linear transformation to 3-D structure of molecule

Syntax

pdbtransform(PDB, Transf)
PDBTX = pdbtransform(PDB, Transf)

... = pdbtransform(..., 'ModelNum', ModelNumValue, ...)
... = pdbtransform(..., 'Segment', SegmentValue, ...)

Input Arguments

PDB

Protein structure represented by any of the following:

  • String specifying a unique identifier for a protein structure record in the Protein Data Bank (PDB) database.

  • Variable containing a PDB-formatted MATLAB® structure, such as returned by getpdb or pdbread.

  • String specifying a file name or a path and file name. The referenced file is a PDB-formatted file. If you specify only a file name, that file must be on the MATLAB search path or in the MATLAB Current Folder.

TransfMATLAB structure representing a linear transformation, which is applied to the coordinates of the molecule represented by PDB. Transf contains the following fields:
  • T — Orthogonal rotation and reflection component.

  • b — Scale component.

  • c — Translation component.

    Tip   You can use the Transf structure returned by the pdbsuperpose function as input.

ModelNumValue

Positive integer that specifies the model to which to apply the transformation, when PDB contains multiple models. By default, the first model is considered.

SegmentValue

Specifies the extent to which the linear transformation is applied. SegmentValue can be either:

  • 'all' — The transformation is applied to the entire PDB input.

  • String specifying the boundaries and the chain to consider. It uses either of the following formats: 'start-stop:chain' or 'chain'. Omitting the boundaries indicates the entire chain.

Output Arguments

PDBTX Transformed PDB-formatted MATLAB structure.

Description

pdbtransform(PDB, Transf) applies the linear transformation specified in Transf, a MATLAB structure representing a linear transformation, to the coordinates of the molecule represented by PDB, which can be any of the following:

  • String specifying a unique identifier for a protein structure record in the PDB database.

  • Variable containing a PDB-formatted MATLAB structure, such as returned by getpdb or pdbread.

  • String specifying a file name or a path and file name. The referenced file is a PDB-formatted file. If you specify only a file name, that file must be on the MATLAB search path or in the MATLAB Current Folder.

PDBTX = pdbtransform(PDB, Transf) returns PDBTX, the transformed PDB-formatted MATLAB structure.

... = pdbtransform(...'PropertyName', PropertyValue, ...) calls pdbtransform with optional properties that use property name/property value pairs. You can specify one or more properties in any order. Each PropertyName must be enclosed in single quotation marks and is case insensitive. These property name/property value pairs are as follows:


... = pdbtransform(..., 'ModelNum', ModelNumValue, ...)
specifies the model to which to apply the transformation, when PDB contains multiple models. ModelNumValue is a positive integer. By default, the first model is considered.

... = pdbtransform(..., 'Segment', SegmentValue, ...) specifies the extent to which the linear transformation is applied. SegmentValue can be either:

  • 'all' — The transformation is applied to the entire PDB input.

  • String specifying the boundaries and the chain to consider. It uses either of the following formats: 'start-stop:chain' or 'chain'. Omitting the boundaries indicates the entire chain.

Examples

  1. Create a MATLAB structure that defines a linear transformation.

    transf.T = eye(3);  transf.b = 1;  transf.c = [11.8 -2.8 -32.3];
  2. Apply the linear transformation to chain B in the thioredoxin structure, with a PDB identifier of 2trx.

    pdbtx = pdbtransform('2trx', transf, 'segment', 'B');

See Also

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