Writing TCL scripts for VMD

This module defines TCL file for VMD program. Questions/Problems: karolami@pitt.edu

prody.dynamics.vmdfile.calcChainsNormDistFluct(coords, ch1, ch2, cutoff=10.0, percent=5, rangeAng=5, filename='ch_ndf_out', loadToVMD=False)[source]

Calculate protein-protein interaction using getNormDistFluct() from GNM model. It is assigned to protein complex.

Parameters:

  • coords (ndarray.) – a coordinate set or an object with getCoords method.

  • ch1 ('A' or other letter as a string) – first chain name

  • ch2 (string) – second chain name

  • cutoff (float) – cutoff distance (Å) for pairwise interactions in Kirchhoff matrix, default is 10.0 Å

  • percent (int or float) – percent of the highest and lowest results displayed in _VMD program, default is 5%

  • rangeAng (int or float) – cutoff range of protein-protein interactions, default is 5 Å

  • filename (str) – name of tcl file from _VMD program

By default files are saved as filename and loaded to VMD program. To change it use loadToVMD=False.

UNDER PREPARATION.. problems with not complete structures

prody.dynamics.vmdfile.writeDeformProfile(stiffness, pdb, filename='dp_out', select='protein and name CA', pdb_selstr='protein', loadToVMD=False)[source]

Calculate deformability (plasticity) profile of molecule based on mechanical stiffness matrix (see [EB08]).

Parameters:

  • stiffness (:class:`~numpy.ndarray) – mechanical stiffness matrix

  • pdb (ndarray) – a coordinate set or an object with getCoords method

Note: selection can be done using select and pdb_selstr. select defines model selection (used for building ANM model) and pdb_selstr will be used in VMD program for visualization.

By default files are saved as filename and loaded to VMD program. To change it use loadToVMD=False.

Mean value of mechanical stiffness for molecule can be found in occupancy column in PDB file.

prody.dynamics.vmdfile.writeVMDstiffness(stiffness, pdb, indices, k_range, filename='vmd_out', select='protein and name CA', loadToVMD=False)[source]

Returns three files starting with the provided filename and having their own extensions:

  1. A PDB file that can be used in the TCL script.

(2) TCL file containing vmd commands for loading PDB file with accurate vmd representation. Pair of residues with selected k_range of effective spring constant are shown in VMD respresentation with solid line between them. If more than one residue is selected in indices, different pair for each residue will be colored in the different colors.

(3) TXT file containing pair of residues with effective spring constant in selected range k_range.

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.

Parameters:

  • stiffness (ndarray) – mechanical stiffness profile calculated with calcMechStiff()

  • pdb (ndarray, Atomic) – a coordinate set or an object with getCoords method

  • indices (list) – an amino acid number or a pair of amino acid numbers

  • k_range (int, float, list) – effective force constant value or range of values

  • select (Select, str) – a selection or selection string default is ‘protein and name CA’

  • loadToVMD (bool) – whether to load VMD and run the tcl file default is False