ReadMe PSIMAP js

From PSIMAP

This program means psimap_js on Linux or PSIMAP_js.exe or PSIMAP_GUI_js.exe on Microsoft Windows.

Contents 1 1. Introduction 1.1 1.1. PSIMAP interface 1.2 1.2. File format 1.3 1.4. Path 2 2. HOW TO USE THIS PROGRAM 2.1 2.1 options

1. Introduction

1.1. PSIMAP interface

Before defining interface between two domains, we have to define the distance between two residues. Definition Residue distance: The minimun distance between two atoms in two residues, except the cases when two atoms in one residue. Definition interface : Given t and n and two domains, if there are n residues in each domain and for each residue in one domain there is at least one residue in the other domain where the distance between the two residues is less than or equal to t, then pairs of such residues are interface. Interacting atom means an atom in one domain that have at least one atom in the other domain and the distance between the two atoms is less than or equal to the specified value. Interacting residue means a residue that contains at least one interacting atom.

1.2. File format

This program uses only one kind of file format: PDB-style Astral file. Each astral file contains all atoms in one domain.

1.3. Domain and protein ID.

Suppose PID is a PDB ID for a protein. Then, IDs for each domain in the protein look like: dPIDa1.pdb where 'a' means chain, '1' means domain number. IDs for domain number and chain should be one character. This program doesn't consider file extension.

1.4. Path

2. HOW TO USE THIS PROGRAM

Domain interaction information will be saved into a working directory as a name yyyy_MM_dd_hh_mm_ss_domain_interaction_info.txt file where heading string is the time you launch this program.

2.1 options

-a : Path that contains astral files. This program searchs all subfolders of the specified path. N.B: Astral files for the same PDB ID should be in the same folder. For example, if you put d1d23ab.ent in /test/tt and d1d23ac.ent in /test/tg, the program can't check if there is interface between d1d23ab.ent and d1d23ac.ent because they are not in the same path.


-r : Path to which atoms in residues that contain an interacting atom will be saved in PDB-style format

-i : Path to which interacting atoms and their information will be saved. Refer to 1.1 about interacting atom.

-t : Distance threshold to define interacting atoms.

-n : Number threshold for residue numbers in defining interface. Please refer to 1.1 for more detail.

-o : Option for residue atoms to be saved. If you set this value 'R', all atoms of interacting residues are saved; if 'I', only interacting atoms are saved. Please refer to 1.1 about interacting residue.