NMA Scripts

Coarse grain

Takes a protein structure or biological assembly and coarse grains to select a set amount of CB atoms Command:

coarseGrain.py <options> --pdbFile <pdb file> --atomType <string>

Inputs:

Input (*required)	Input type	Flag	Description
PDB file *	File	--pdb	PDB structure to coarse grain. Can also accept biological assembly (.pdb1)
Atom type *	String	--atomType	Specify the type of atom to be selected in CG models. Only CA or CB accepted.
Coarse grain level	Comma Separted String	--cg	Level/Levels by which to coarse grain protein. Lower is less coarse grained E.g –cg 4 OR E.g –cg 1,3,5 Default: 4
Starting atom	Integer	--startingAtom	Residue number of the starting atom. Default: 1
Output file	File	--output	Specify a name for the PDB output file. Default: ComplexCG.pdb

Outputs:

Output	Description
PDB file/s	Coarse grained protein/s or macromolecule/s

ANM

Constructs an elastic network model of a protein complex and solves for the eigenvalues and eigenvectors of the system.

Compile:

g++ -I cpp/src/ ANM.cpp -o ANM

Command:

ANM <options> --pdb <pdb file> --atomType <atom type>

Inputs:

Input (*required)	Input type	Flag	Description
PDB file *	File	--pdb	PDB input file
Atom type *	String	--atomType	Specify the type of atom to be selected in CG models. Only CA or CB accepted.
Cutoff	Integer	--cutoff	Cuttoff radius in Å. Default: 15

Outputs:

Output	Description
W matrix	Text file of \(3N\) eigenvalues
VT matrix	Text file of \(3N\)x\(3N\) eigenvectors. Printed in rows
U matrix	Text file of \(3N\)x\(3N\) eigenvectors. Printed in columns

Mean square fluctuation

Calculates and returns the diagonals of the correlation matrix for a given set of modes.

The user can also compare the msf between two protein complexes. Let’s say that the user has performed NMA on two coarse grained models of the same protein, and now wants to compare if the additional coarse graining decreased the accuracy. If we obtain the same mean square fluctuations for each residue, then in each model we can say that the results are comparable regardless of the coarse graining level. Obviously, we must compare only the residues that are common in each model. Hence, we specify common residues.

Command:

meanSquareFluctuations.py <options> --pdb <PDB file> --wMatrix <text file> --vtMatrix <text file> --atomType <string>

Inputs:

Input (*required)	Input type	Flag	Description
PDB file *	File	--pdb	PDB input file
W matrix file *	File	--wMatrix	W values from ANM script for PDB
VT matrix file *	File	--vtMatrix	VT values from ANM script for Comparison PDB
Atom type *	String	--atomType	Specify the type of atom to be selected in CG models. Only CA or CB accepted.
Comparison PDB	File	--pdbC	When assigned, calculates mean square fluctuations based on common residues between the two systems.
W matrix file for pdbC	File	--wMatrixC	When assigned, calculates W values from ANM for Comparison PDB
VT matrix file for pdbC	File	--vtMatrixC	When assigned, calculates VT values from ANM for Comparison PDB
Selected modes	String OR Colon Separated String OR Comma Separated String	--modes	MSFs will be calculated over specified modes. Options: 1) Single mode E.g –modes 7; 2) A range E.g –modes 7:20; 3) A list E.g –modes 8,9,11 If unspecified MSFs will be calculated for the first twenty slowest modes (7:27)

Outputs:

Output	Description
The following are generated for the PDB and Comparison PDB (if pdbC was assigned)
MSF text file	MSF for all residues, calculated over all modes
MSF modes text file	MSF for all residues, calculated for a specific mode range
Common residue MSF text file	MSF for all common residues, calculated over all modes
Common residue MSF modes text file	MSF for all common residues, calculated over a specific mode range

Assembly Covariance

Calculates and plots Covariance matrices

The user can compare the Covariance between different regions in the biological assembly, or can calculate the Covariance across the full assembly complex. The user also has the option to perform the calculation over a specified list of modes or a mode range. The function also has a zoom option that allows the user to create a Covariance plot for a particular chain within a particular asymmetric unit.

Command:

assemblyCovariance.py <options> --pdb <PDB file> --wMatrix <text file> --vtMatrix <text file> --atomType <string>

Inputs:

Input (*required)	Input type	Flag	Description
PDB file *	File	--pdb	PDB input file
W matrix file *	File	--wMatrix	W values from ANM script for PDB
VT matrix file *	File	--vtMatrix	VT values from ANM script for Comparison PDB
Atom type *	String	--atomType	Specify the type of atom to be selected in CG models. Only CA or CB accepted.
Selected modes	String OR Colon Separated String OR Comma Separated String	--modes	Covariance will be calculated over specified modes Options: 1) All modes E.g –modes all; 2) Single mode E.g –modes 7; 3) A range E.g –modes 7:20; 4) A list E.g –modes 8,9,11 If unspecified, Covariance will be calculated for all modes.
Asymmetric Units	String OR Comma Separated String	--aUnits	Covariance will be calculated and plotted for specified asymmetric units Options: 1) Single unit E.g –aUnits 5; A list of units E.g –aUnits 1,3 If unspecified, Covariance will be calculated for the first asymmetric unit in the assembly.
Zoom	Comma Separated String	--zoom	If specified, Covariance will be calculated and plotted for a specified chain in a specified unit. Only format accepts is: [Unit,Chain] E.g –zoom 1,2 OR E.g –zoom 1,B (Chain specifier must match chain label in PDB file) The above calculates the covariance for the second chain in the first asymmetric unit.
VMin	float	--vmin	Minimum axes value for plot Default: -0.1
VMax	float	--vmax	Maximum axes value for plot Default: 0.1

Outputs:

Output	Description
Covariance Plots	Covariance Matrices plotted as a Linear Segmented Color map
Matrix text files	Covariance Matrices printed in .txt format

Conformation mode

Identifies modes responsible for the conformational change of a molecule.

Command:

conformationMode.py <options> --pdbConf <PDB file> --pdbANM <PDB file> --vtMatrix <text file> --atomType <string>

Inputs:

Input (*required)	Input type	Flag	Description
Unaligned PDB file *	File	--pdbConf	PDB file of the conformational change
PDB *	File	--pdbANM	PDB file that was used to run ANM
VT matrix file *	File	--vtMatrix	Eigenvetors obtained from ANM script
Atom type *	String	--atomType	Specify the type of atom to be selected in CG models. Only CA or CB accepted.
Output file	File	--output	Specify a name for the output file. Default: ModesOfConfChange.txt

Outputs:

Output	Description
Conformation file	Text file with the overlap and correlation of each mode

Combination mode

Calculates the combined overlap and correlation for specified set of modes to a known conformational change. This script also calculates the overlap and correlation per chain in each asymmetric unit for the specified modes. This allows the user to determine which parts of the complex, in each mode, contribute the most to the overall conformational change.

Command:

combinationMode.py <options> --pdbConf <PDB file> --pdbANM <PDB file> --vtMatrix <text file> --modes <comma separated string> --atomType <string>

Inputs:

Input (*required)	Input type	Flag	Description
Unaligned PDB file *	File	--pdbConf	PDB file of the conformational change
PDB *	File	--pdbANM	PDB file that was used to run ANM
VT matrix file *	File	--vtMatrix	Eigenvetors obtained from ANM script
Modes *	Integer	--modes	Calculate the overlap for a combination of specific modes. Numbers are separated by commas: 1,5,7
Atom type *	String	--atomType	Specify the type of atom to be selected in CG models. Only CA or CB accepted.
Output file	File	--output	Specify a name for the output file. Default: ModeSpecificConfChange.txt

Outputs:

Output	Description
Combination file	Text file with the overlap and correlation of each mode as well as the combined overlap and correlation for the modes specified
Break down per unit file	Text file with the overlap and correlation calculated for each chain in each asymmetric unit in the complex. Calculations are performed for each specified mode.

Mode visualisation

Generates a set of frames, where eigenvectors are plotted as a set of unit vectors multiplied by an increasing factor in each frame. Vectors are also plotted as arrows that can be viewed in the tool VMD

Command:

visualiseVector.py <options> --pdb <PDB file> --vtMatrix <text file> --mode <int> --atomType <string> --direction <int>

Inputs:

Input (*required)	Input type	Flag	Description
Coarse grained PDB file *	File	--pdb	Coarse grained PDB input file
Mode index value *	Ingeter	--mode	Value specifying the index of the mode
VT matrix file *	File	--vtMatrix	VT values from ANM script
Atom type *	String	--atomType	Specify the type of atom to be selected in CG models. Only CA or CB accepted.
Direction	Boolean integer (1 or -1)	--direction	Direction of overlap correction. Default = 1
Arrow head	float	--head	Radius of cone that forms the head of each vector arrow
Arrow tail	float	--tail	Radius of cylinder that forms the tail of each vector arrow
Arrow length	float	--arrowLength	Specify a factor by which to increase or decrease the length of each arrow E.g –arrowLength 2 doubles the default length and –arrowLength 0.5 halves the default length
Colours	Comma Separted String	--colourByChain	Colour the vectors arrows of each chain. E.g for a two chain protein –colourByChain blue,red will colour the arrows of Chain A as blue and Chain B as red
Asymmetric Units	String OR Comma Separated String	--aUnits	Vector frames and arrows will be plotted for specified asymmetric units Options: 1) Single unit E.g –aUnits 5 A list of units E.g –aUnits 1,3
Chain	String	--chain	Draws arrows only for the specified chain. This option only accepts a single chain

Outputs:

Outputs are generated in output/VISUALISE directory by default.

Output	Description
PDB file	Output PDB to be opened in VMD
Arrows file	Tcl script that can be copied into the VMD TK console