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  • Last update: 5 years ago
  • Total downloads: 37
  • Operating system: Linux, Mac OS X, Win All, BSD, Solaris
  • Publisher: Evan (2 other programs)
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scripts default icona fast method of reading data from PDB files (Scripts) Publisher's description

Some of the logic from this program was provided from PDBRead.m by Sachin Nikumbh.

Some of the logic from this program was provided from PDBRead.m by Sachin Nikumbh. The version I made is a trimmed down version of it that only outputs the data from one atom type (protein by default), and formats it as convenient cell variables. For smaller PDB files, the time difference between these programs is negligible, but for larger systems of more than 10,000 atoms it can shave off a minute or two.

The manual is as follows:

% -- Manual --
This program is the most speedy way to read a PDB file that I could come
up with. It's function is simple: give it a PDB file and out comes a
matlab-friendly matrix. In cumbersomely large PDB's (such as those that
include solvent), this can shave off a good ammount of time.

version 1.0
created by Evan Arthur: University of Michigan, Feb 8, 2012

It outputs 8 pieces of information about the PDB:

atomNum (index number of the atom)
atomName (elemental identification of the atom)
resName (name of the amino acid/residue)
resNum (index number of the amino acid)

X (X position of atom)
Y (Y position of atom)
Z (Z position of atom)
b_factor (this is extra information about an atom. In PDBQT's it holds
the partial charge, for CHARMM this is the chain name, and so on)

check the "Input" section below. The "outputStringID" string is the
only kind of atom this program records. 'ATOM' generally means only
protein data is output. Changing this to 'SOL', for instance, would
output only solvent data.

also, this script has not yet been optimized for PDB movies. If I get
requests for it, I will make changes for in the next version.

example usage:

atoms = PDBRead_short('3IJU.pdb')
plot3(atoms.X, atoms.Y, atoms.Z, '.');
--> this plots the atoms of 3IJU.pdb

System Requirements:

MATLAB 7.10 (2010a)
Program Release Status: New Release
Program Install Support: Install and Uninstall

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