NMFF-AFM flexible fitting

Modeling Conformational Transitions of Biomolecules from Atomic Force Microscopy Images using Normal Mode Analysis, Wu, Xuan; Miyashita, Osamu; Tama, Florence, DOI: 10.1021/acs.jpcb.4c04189

Usage

To perform a flexible fitting, follow these steps:

1. Create a Directory: Begin by creating a new directory where all necessary files will be stored.

2. Prepare Required Files: Place the following files into the newly created directory:

• PDB File: A PDB file representing the initial conformation. Filenames must not contain #, spaces, or any of the following special characters: @, !, $, %, ^, &, *, (, ), +, =, {, }, [, ], |, , :, ;, ", ', <, >, ,, ?, /, or ~.
• TSV File: The TSV file containing the target figure data.
• TOML File: An input TOML file with the required configuration settings (detailed below).

3. Optional: Reference Conformation for RMSD Calculation:

An RMSD curve will be generated by default, plotting the RMSD between the deformed conformation at each step and the initial conformation. If you want to calculate RMSD relative to a reference conformation:

• Place an additional PDB file (the reference conformation) in the same directory.
• Set calculate_rmsd_to_reference = 'yes' and input the name of the reference PDB in the TOML file.
• This will add an extra curve to the resulting figure, representing the RMSD relative to the reference conformation.

4. In the above directory, activate the virtual environment with the required modules (detailed in the Requirements section) using:

$ python path/to/nmff_afm.py parameter.toml

Configuration

Example file

This is an example of the parameter file.

num_iterations = 70
original_conformation = '4ake' # No need to add the suffix
target_conformation = '1ake' # No need to add the suffix
which_type_of_target = 'tsv'
combined_amplitude = 25
res_x = 0.5 # in nanometer
res_y = 0.5 # in nanometer
res_z = 0.64 # in Angstrom
size_x = 6.0 # This range represents half the size of the generated image in x-axis
size_y = 6.0 # This range represents half the size of the generated image in y-axis
first_mode = 1
last_mode = 16
mode_selection = 'slope' # ['slope', 'maxcc', 'maxcc_force_move']
how_many_threads = 8

# Whether to calculate the RMSD to a reference PDB file
calculate_rmsd_to_reference = 'yes' # ['yes', 'no']
file_name_of_reference_pdb = '1ake' # No need to add the suffix

# Shape of the probe
radius_of_probe = 2.0 # in nanometer
angle_of_probe = 10 # in degree

Parameters in the Input File

• num_iterations: Int
  A number indicating how many times the input PDB file will be deformed.
• original_conformation: String
  A name of initial PDB file. The suffix will be added.
• target_conformation: String
  A name of target figure. The suffix will be added.
• combined_amplitude: Int
  A nmber of the overall amplitude used in the deformation.
• res_x: Float
  A number of the resolution used in simulating AFM images in x-axis.
  It uses Nanometer as the unit of measurement.
• res_y: Float
  A number of the resolution used in simulating AFM images in y-axis.
  It uses Nanometer as the unit of measurement.
• res_z: Float
  A number of the resolution used in simulating AFM images in z-axis.
  It uses Angstrom as the unit of measurement.
• size_x: Float
  A number of the range of the simulated AFM images in x-axis. This range starts from the negative half-axis and ends at the positive half-axis.
  It uses nanometers as the unit of measurement.
• size_y: Float
  A number of the range of the simulated AFM images in y-axis. This range starts from the negative half-axis and ends at the positive half-axis.
  It uses nanometers as the unit of measurement.
• first_mode: Int
  A number of the lowest frequency used in deforming the initial PDB file.
• last_mode: Int
  A number of the highest frequency used in deforming the initial PDB file.
• mode_selection: String
  A string for selecting the mode for selecting the largest mode. By deafult, slope.
• how_many_threads: Int
  A number indicating how many threads using in the flexible fit-in.
• calculate_rmsd_to_reference: String
  The string indicating whether to calculate the RMSD to a reference conformation.
• file_name_of_reference_pdb: String
  A name of a PDB file used as the reference for RMSD calculation. The suffix will be added.
• radius_of_probe: Float
  A number indicating the radius of the simulated probe used generating the pseudo-AFM images.
  It uses nanometers as the unit of measurement.
• angle_of_probe: Float
  A number indicating the angle of the simulated probe used generating the pseudo-AFM images.

Installation

Requirements

Before running the calculation, several softwares should be installed first:

 • Pro-Fit: Available at Pro-Fit

 • afmize: Available at afmize

 • NMA scripts: Available at NMA scripts

To install all required Python modules, run:

pip install -r requirements.txt

Environment variable

Before running a flexible fitting, add the following environment variables to your system:

# Path the excutable file of afmize
export AFMIZE_PATH=/to/your/afmize_directory/afmize

# Path of the folder containing NMA program and scripts. rtb2, makebloc.pl and movemode.pl should be saved in this folder.
export NMA_FOLDER=/to/your/nma_directory

# Path the excutable file of Pro-Fit
export PRO_FIT_PATH=/to/your/profit_directory/profit