read and write PDB files using matlab

These two programs accept and output a variety of PDB file-formatted data

Both programs use data structures to store information about PDBs. I find these programs useful both for dealing with PDBs and visualizing 3D point information

-- example usage: plot the atoms of 3IJU.pdb --

PDBdata = pdb2mat('3IJU.pdb'); % read in data from PDB file
plot3(PDBdata.X, PDBdata.Y, PDBdata.Z, '.'); % make a 3D plot of data

-- example usage: translate the atoms of 3IJU.pdb by 10 angstroms in x direction --

PDBdata = pdb2mat('3IJU.pdb'); % read in data from PDB file
PDBdata.X = PDBdata.X + 10; % translate coordinates
PDBdata.outfile = '3IJU_tran10angXdir.pdb'; % update file name
mat2pdb(PDBdata); % output data in PDB format

-- example usage: make a PDB with 30 atoms in random places within a 10 angstrom box --
data.X = rand(1,20)*10;
data.Y = rand(1,20)*10;
data.Z = rand(1,20)*10;
mat2pdb(data)

%% -- pdb2mat.m --
%
% It's function is simple: give it a PDB file and out comes a
% matlab-friendly data structure. In cumbersomely large PDB's (such as those that
% include solvent), this can shave off a good amount of time relative to
% many programs. Unfortunately there is no easy way to hasten the slowest
% step, which is turning strings into doubles.
%

%% -- mat2PDB.m --
%
% this function creates a PDB from coordinate data. Represent all inputs as
% a structure field for it to be read. The output format is as given in
% online documentation (as of July 2012 when writing this program)
% http://www.wwpdb.org/documentation/format33/sect9.html#ATOM

To speed up the program, comment out any lines for data not being used. Commenting one line that converts numeric data speeds the program up by roughly 7-8%.

example usage : this plots the atoms of 3IJU.pdb

atoms = fastPDBRead('3IJU.pdb')
plot3(atoms.X, atoms.Y, atoms.Z, '.');