Enm explorer - Revision history

TBalius at 19:24, 14 February 2018

2018-02-14T19:24:12Z

← Older revision		Revision as of 19:24, 14 February 2018
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	Use:		Use:
	~rgc/Source/sharp_src/pdbcrd2pdbs.py pdbName crdName outputPdbPrefix		~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

TBalius at 16:16, 2 February 2018

2018-02-02T16:16:50Z

← Older revision		Revision as of 16:16, 2 February 2018
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	WARNING: '''The rms cutoff must be a float!'''		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.		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.
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	Use:		Use:
	~rgc/Source/sharp_src/pdbcrd2pdbs.py pdbName crdName outputPdbPrefix		~rgc/Source/sharp_src/pdbcrd2pdbs.py pdbName crdName outputPdbPrefix



	[[Category:Docking]]		[[Category:Docking]]
	[[Category:Tutorials]]		[[Category:Tutorials]]

TBalius at 19:56, 31 January 2018

2018-01-31T19:56:12Z

← Older revision		Revision as of 19:56, 31 January 2018
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	Input should be a pdb '''with backbone atoms only'''.		Input should be a pdb '''with backbone atoms only'''.

	Run:		Run on cluster0:

	~dahlia/software/3kenm/enm_explorer_drw/enm_explorer 1		~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:		Enter .pdb file to deform:

Frodo at 01:04, 11 March 2014

2014-03-11T01:04:49Z

← Older revision		Revision as of 01:04, 11 March 2014
Line 41:		Line 41:
	[[Category:Docking]]		[[Category:Docking]]
	[[Category:Tutorials]]		[[Category:Tutorials]]
	~~[[Category:Preparation for docking]]~~

Frodo at 16:12, 14 February 2014

2014-02-14T16:12:16Z

← Older revision		Revision as of 16:12, 14 February 2014
Line 40:		Line 40:

	[[Category:Docking]]		[[Category:Docking]]
	[[Category:~~Tutorial~~]]		[[Category:Tutorials]]
	[[Category:Preparation for docking]]		[[Category:Preparation for docking]]

Frodo at 03:38, 14 February 2014

2014-02-14T03:38:29Z

← Older revision		Revision as of 03:38, 14 February 2014
Line 37:		Line 37:
	Use:		Use:
	~rgc/Source/sharp_src/pdbcrd2pdbs.py pdbName crdName outputPdbPrefix		~rgc/Source/sharp_src/pdbcrd2pdbs.py pdbName crdName outputPdbPrefix


			[[Category:Docking]]
			[[Category:Tutorial]]
			[[Category:Preparation for docking]]

Therese: 7 revisions

2012-10-08T20:17:36Z

7 revisions

New page

==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. [http://onlinelibrary.wiley.com/doi/10.1002/prot.22184/full]

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

Rgc: link to paper

2012-02-13T21:07:31Z

link to paper

New page

==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. [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.

==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_backbone.pdb

Enter maximum rms deviation cutoff:
1.0

Enter maximum change in bond length (recommended 0.1-0.4):
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.

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