ToPDB

convert_data2pdb

Purpose

convert_data2pdb application is intended to convert a set of coordinate values into PDB file. This is specially useful for visualizing 3D data as a "atoms" with any of the PDB visualization systems. e.g.: VMD, rasmol, molmol, etc.

The input data to this program is a text file with the following format:

3 1000
12 34 54
-12 45 76
...
2 45 76

The first line indicates the dimension of the vectors (in this case 3) and the number of vectors (in this case 1000). The rest of the lines are the coordinates vectors. Each line is a vector and each column is a vectors' component. In case the data file is composed by vectors of more than 3 dimension, then only the first three components will be taken into account.

Usage

$ convert_data2pdb ...

Paramteres

• `` The input data file
• `` The output file name (in PDB format)
• `` Indicates the size in angstrom of each atom (neuron). Default: 1
• `` Offset applied to each atom in the X axis. Default: 0
• `` Offset applied to each atom in the Y axis: Default:offX
• `` Offset applied to each atom in the Z axis: Default:offX

Examples and notes

$ convert_data2pdb -iname results.dat -oname results.pdb

In this example, theresults.dat file will be converted into an atomic coordinates file and the results is saved inresults.pdb.

If the input file is the following:

4 4
12 54 56 0.3
15 65 98 0.9
9 65 14 0.1
98 32 19 0.0

The output file will be:

ATOM 1 XMIP XMIP 1 12.000 54.000 56.000 0.00 0.00 XMIP
ATOM 2 XMIP XMIP 1 15.000 65.000 98.000 0.00 0.00 XMIP
ATOM 3 XMIP XMIP 1 9.000 65.000 14.000 0.00 0.00 XMIP
ATOM 4 XMIP XMIP 1 98.000 32.000 19.000 0.00 0.00 XMIP

Note that only the first three components were used for generating the PDB file.

--Main.AlfredoSolano - 26 Jan 2007