Difference between revisions of "Enm explorer"

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Yang, Q., Sharp, K. A. 2008. Building alternate protein structures using the elastic network model. Proteins, 74:682-700. [http://onlinelibrary.wiley.com/doi/10.1002/prot.22184/full]
 
Yang, Q., Sharp, K. A. 2008. Building alternate protein structures using the elastic network model. Proteins, 74:682-700. [http://onlinelibrary.wiley.com/doi/10.1002/prot.22184/full]
  
The idea is to deform a protein structure along its normal modes while preserving physically reliable bonds and angles, as well as preserving secondary structure.  
+
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==
 
==Usage==
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  Enter .pdb file to deform:
 
  Enter .pdb file to deform:
  myfile_backbone.pdb
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  myfile_bb.pdb
  
 
  Enter maximum rms deviation cutoff:
 
  Enter maximum rms deviation cutoff:
 
  1.0
 
  1.0
 
   
 
   
  Enter maximum change in bond length (recommended 0.1-0.4):
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  Enter maximum change in bond length:
 
  0.4
 
  0.4
  
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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.  
 
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).  
 
The output is a crd file. You will now need to convert to a series of PDB files (credit Ryan Coleman).  

Revision as of 20:17, 8 October 2012

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:

~dahlia/software/3kenm/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 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