Write to file using Protein Data Bank (PDB) format
pdbwrite(File, PDBStruct)
PDBArray = pdbwrite(File, PDBStruct)
File | Character vector or string specifying either a file name or a path and file name for saving
the PDB-formatted data. If you specify only a file name, the file is saved to the
MATLAB® Current Folder. Tip After you save the MATLAB structure to a local PDB-formatted file, you can use the |
PDBStruct | MATLAB structure containing 3-D protein structure coordinate
data, created initially by using the getpdb or pdbread functions.Note You can edit this structure to modify its 3-D protein structure
data. The coordinate information is stored in the |
PDBArray | Character array in which each row corresponds to a line in a PDB record. |
pdbwrite( writes
the contents of the MATLAB structure File, PDBStruct)PDBStruct to
a PDB-formatted file (ASCII text file) whose path and file name are
specified by File. In the output file, File,
the atom serial numbers are preserved. The atomic coordinate records
are ordered according to their atom serial numbers.
Tip
After you save the MATLAB structure to a local PDB-formatted
file, you can use the molviewer function
to display and manipulate a 3-D image of the structure.
PDBArray = pdbwrite(File, PDBStruct)PDBStruct,
to PDBArray, a character array in which
each row corresponds to a line in a PDB record.
Note
You can edit PDBStruct to modify
its 3-D protein structure data. The coordinate information is stored
in the Model field of PDBStruct.
Use the getpdb function to retrieve
structure information from the Protein Data Bank (PDB) for the green
fluorescent protein with identifier 1GFL , and
store the data in the MATLAB structure gflstruct.
gflstruct = getpdb('1GFL');Find the x-coordinate of
the first atom.
gflstruct.Model.Atom(1).X ans = -14.0930
Edit the x-coordinate of
the first atom.
gflstruct.Model.Atom(1).X = -18;
Note
Do not add or remove any Atom fields, because
the pdbwrite function does not allow the number
of elements in the structure to change.
Write the modified MATLAB structure gflstruct to
a new PDB-formatted file modified_gfl.pdb in the Work folder
on your C drive.
pdbwrite('c:\work\modified_gfl.pdb', gflstruct);Use the pdbread function
to read the modified PDB file into a MATLAB structure, then confirm
that the x-coordinate of the first atom
has changed.
modified_gflstruct = pdbread('c:\work\modified_gfl.pdb')
modified_gflstruct.Model.Atom(1).X
ans =
-18