NMD File

This module defines input and output functions for NMD format.

NMD Format

Description

NMD files (extension .nmd) are plain text files that contain at least normal mode and system coordinate data.

NMD files can be visualized using Normal Mode Wizard. ProDy functions writeNMD() and parseNMD() can be used to read and write NMD files.

Data fields

Data fields in bold face are required. All data arrays and lists must be in a single line and items must be separated by one or more space characters.

coordinates: system coordinates as a list of decimal numbers
Coordinate array is the most important line in an NMD file. All mode array lengths must match the length of the coordinate array. Also, number of atoms in the system is deduced from the length of the coordinate array.
coordinates 27.552 4.354 23.629 24.179 4.807 21.907 ...
mode: normal mode array as a list of decimal numbers

Optionally, mode index and a scaling factor may be provided in the same line as a mode array. Both of these must precede the mode array. Providing a scaling factor enables relative scaling of the mode arrows and the amplitude of the fluctuations in animations. For NMA, scaling factors may be chosen to be the square-root of the inverse-eigenvalue associated with the mode. Analogously, for PCA data, scaling factor would be the square-root of the eigenvalue.

If a mode line contains numbers preceding the mode array, they are evaluated based on their type. If an integer is encountered, it is considered the mode index. If a decimal number is encountered, it is considered the scaling factor. Scaling factor may be the square-root of the inverse eigenvalue if data is from an elastic network model, or the square-root of the eigenvalue if data is from an essential dynamics (or principal component) analysis.

For example, all of the following lines are valid. The first line contains mode index and scaling factor. Second and third lines contain mode index or scaling factor. Last line contains only the mode array.

mode 1 2.37    0.039 0.009 0.058 0.038 -0.011 0.052  ...
mode 1    0.039 0.009 0.058 0.038 -0.011 0.052  ...
mode 2.37    0.039 0.009 0.058 0.038 -0.011 0.052  ...
mode 0.039 0.009 0.058 0.038 -0.011 0.052 0.043  ...

name: name of the model

The length of all following data fields must be equal to the number of atoms in the system. NMWiz uses such data when writing a temporary PDB files for loading coordinate data into VMD.

atomnames: list of atom names
If not provided, all atom names are set to “CA”.
resnames: list of residue names
If not provided, all residue names are set to “GLY”.
chainids: list of chain identifiers
If not provided, all chain identifiers are set to “A”.
resids: list of residue numbers
If not provided, residue numbers are started from 1 and incremented by one for each atom.
bfactors: list of experimental beta-factors
If not provided, all beta-factors are set to zero. Beta-factors can be used to color the protein representation.

NMD files may contain additional lines. Only lines that start with one of the above field names are evaluated by NMWiz.

Autoload Trick

By adding a special line in an NMD file, file content can be automatically loaded into VMD at startup. The first line calls a NMWiz function to load the file itself (xyzeros.nmd).

nmwiz_load xyzeros.nmd
coordinates 0 0 0 0 0 0  ...
mode 0.039 0.009 0.058 0.038 -0.011 0.052 ...
mode -0.045 -0.096 -0.009 -0.040 -0.076 -0.010 ...
mode 0.007 -0.044 0.080 0.015 -0.037 0.062 ...

In this case, VMD must be started from the command line by typing vmd -e xyzeros.nmd.

parseNMD(filename, type=None)[source]

Returns NMA and AtomGroup instances storing data parsed from filename in .nmd format. Type of NMA instance, e.g. PCA, ANM, or GNM will be determined based on mode data.

writeNMD(filename, modes, atoms)[source]

Returns filename that contains modes and atoms data in NMD format described in NMD Format. .nmd extension is appended to filename, if it does not have an extension.

Note

  1. This function skips modes with zero eigenvalues.
  2. If a Vector instance is given, it will be normalized before it is written. It’s length before normalization will be written as the scaling factor of the vector.
pathVMD(*path)[source]

Returns VMD path, or set it to be a user specified path.

getVMDpath()[source]

Deprecated for removal in v1.5, use pathVMD() instead.

setVMDpath(path)[source]

Deprecated for removal in v1.5, use pathVMD() instead.

viewNMDinVMD(filename)[source]

Start VMD in the current Python session and load NMD data.