Enm explorer

From DISI
Jump to: navigation, search

Overview

3KENM was developed by Qingyi Yang. Please use this reference:

Yang, Q., Sharp, K. A. 2008. Building alternate protein structures using the elastic network model. Proteins, 74:682-700. [1]

The idea is to deform a protein structure along its normal modes (elastic normal modes or ENM) while preserving physically reliable bonds and angles, as well as preserving secondary structure.

Usage

At the moment only mode "1" has been tested. All other modes of running the code are likely broken. Input should be a pdb with backbone atoms only.

Run on cluster0:

~dahlia/software/3kenm/enm_explorer_drw/enm_explorer 1

Run on cluster2:

/mnt/nfs/home/tbalius/zzz.programs/enm_explorer_drw/enm_explorer 1
Enter .pdb file to deform:
myfile_bb.pdb
Enter maximum rms deviation cutoff:
1.0

Enter maximum change in bond length:
0.4


WARNING: The rms cutoff must be a float!

  • The name prefix of the input file should be 4 characters long (????.pdb): for example 1m17.pdb.
  • If you run it once on the protein it will produe a pdb file called ????_backbone.pdb (this file columns up to and including the coordinates not beyond, no occ or b columns).
  • Copy this file to a new file name with 4 characters prefix eg bb1m.pdb
  • Run agin with the new backbone only file.

The file should also be backbone atoms

The larger the protein is, the more your individual bond lengths will be distorted. You will have to play with this parameter. If the output is only 1 frame, you need to increase this number.

As a note, the filename <prefix>_backbone.pdb is hardcoded, and naming your input file by that name will cause the program to crash.

The output is a crd file. You will now need to convert to a series of PDB files (credit Ryan Coleman).

Use:

~rgc/Source/sharp_src/pdbcrd2pdbs.py pdbName crdName outputPdbPrefix

This version was for cluster0, but is no longer here.

Here is a new version to convert a crd file to PDB files (written by Trent Balius):

/nfs/home/tbalius/zzz.scripts/convert_crd_to_pdb.py