PDB2descr

convert_pdb2descr

Purpose

This script reads a PDB file and creates a.descr file that can be used with create_phantom, project, etc. Each atom (that is not hydrogen) is replaced by a blob of unit weight. The output phantom is computed as if the sampling rate were 1Angstrom/pixel. That is, all features in the file have coordinates as if the sampling rate were 1Angstrom/pixel (always). The sampling rate supplied by the user is used to compute a scaling factor that transforms the phantom to the desired scale. The sampling rate by default is1 Angstrom/pixel.

Usage

$ convert_pdb2descr ... 

Parameters

• ``
• ``
• ``
• ``
• ``
• ``

The blob parameters by default are[blob radius6]= (angstroms),[blob alpha3.6]=,[blob order2]=. If you want to change the blob parameters, you must supply the three parameters at the same time.

Examples and notes

Translate a phantom at 1Angstrom/pixel of sampling rate

$ convert_psb2descr 1a6d.pdb 1a6d.descr

Translate a phantom at 3Angstrom/pixel of sampling rate

$ convert_pdb2descr 1a6d.pdb 1a6d.descr 3

Translate a phantom at 3Angstrom/pixel of sampling rate, changing the blob parameters

$ convert_pdb2descr 1a6d.pdb 1a6d.descr 3 3 10.4 2

--Main.AlfredoSolano - 30 Jan 2007