Tcl packages

These packages are used by Pestifer for certain system preparation tasks. They are not intended to be run directly by users, but rather are used by Pestifer’s Tcl API. The procedures they define are available in the Pestifer Tcl API, and can be used in your own VMD scripts. The PestiferUtil package is automatically loaded by the pestifer_init procedure. Others must be loaded explicitly using the package require command.

For example, if you want to use the brot procedure from the PestiferCRot package, you would include the following lines at the beginning of your Tcl script:

package require PestiferCRot
namespace import PestiferCRot::*

Sources for each package are included below for reference.

autools.tcl

PestiferAUTools – This is a Pestifer Tcl package for VMD that provides tools for manipulating asymmetric units (AUs) of macromolecular complexes. It allows for the generation of a new PDB file containing an asymmetric unit and appropriate BIOMT operations to build a complex based on aligning the base chains onto congruent chains of any other subunits. The package provides the following main procedures:

make_au_from_aligning: Generates a new PDB file containing an asymmetric unit and BIOMT transformations based on aligning the base chains onto congruent chains of other subunits.

overlay_protomers: Aligns protomer chains based on a specified residue range and returns the RMSD values for the alignment.

[source]

axes.tcl

PestiferAxes – This is a Pestifer Tcl package for VMD that provides tools for computing approximate symmetry axes of macromolecular complexes. It allows for the generation of an approximate axis around which protomers are arranged, based on the coordinates of symmetry-related atoms in each protomer. The package provides the following main procedures:

axis: Computes the approximate symmetry axis based on parallel arrays of atom coordinates.

get_axis: Computes the symmetry axis for a given molecule, frame, and selection string.

get_center: Computes the geometric center of symmetry-related atoms in a molecule.

get_tilt: Computes the tilt angle between two axes defined by different sets of chains.

get_tilt_z: Computes the tilt angle of a trimer axis with respect to the z-axis.

[source]

crot.tcl

PestiferCRot – This is a Pestifer Tcl package for VMD that provides tools for manipulating protein backbone and side chain torsion angles. It allows for the folding of alpha helices, rotation of phi, psi, and omega angles, and side chain rotations around chi angles. The package provides the following main procedures:

residues_in_same_chain: Checks if two residues are in the same chain.

get_phi_psi_omega: Measures phi, psi, and omega angles at a residue.

fold_alpha: Folds a section of residues into an alpha helix.

brot: Generalized bond rotation for proteins, allowing for phi, psi, omega, and chi rotations.

Crot_phi, Crot_phi_toCterm, Crot_psi, Crot_psi_toCterm, Crot_omega, SCrot_chi1, SCrot_chi2, Crot_psi_special: Specific procedures for rotating phi, psi, omega angles and side chain chi angles in proteins.

new_alpha: Folds a run of new residues into an alpha helix.

Crot_psi_special: Special case for psi rotation in a specific context.

Crot_omega: Rotates residues C-terminal to a specified residue around the peptide bond.

Crot_phi, Crot_phi_toCterm: Rotates residues C-terminal to a specified residue around the phi angle.

Crot_psi, Crot_psi_toCterm: Rotates residues C-terminal to a specified residue around the psi angle.

SCrot_chi1, SCrot_chi2: Rotates side chains around chi1 and chi2 angles.

[source]

declash.tcl

PestiferDeclash – This is a Pestifer Tcl package for VMD that provides tools for declashing protein loops and pendant groups. It allows for the minimization of steric clashes in protein structures by applying a simple Metropolis algorithm to alter the conformation of raw model-built protein gap loops or pendant groups. The package provides the following main procedures:

declash_loop: Applies a Metropolis algorithm to minimize clashes in protein gap loops.

declash_pendant: Applies a Metropolis algorithm to minimize clashes in pendant groups.

[source]

environ.tcl

PestiferEnviron – This is a Pestifer Tcl package for VMD that provides tools for manipulating the environment of a molecular system, particularly for bilayer systems. It allows for the apportioning of residues to upper and lower leaflets of a bilayer, and for writing PSFGEN segments based on residue types and labels. The package provides the following main procedures:

leaflet_apportionment: Apportion residues to upper and lower leaflets based on their center of mass relative to the bilayer center of mass.

write_psfgen: Write PSFGEN segments for a molecule based on specified segment types, labels, indices, and maximum residues per segment.

[source]

getlinks.tcl

PestiferGetLinks – This is a Pestifer Tcl package for VMD that provides tools for extracting links and disulfide bonds from a molecular structure. It allows for the identification of glycan links and disulfide bonds based on specific atom selections and bonding criteria. The package provides the following main procedures:

getlinks: Extracts glycan links from a specified molecule.

getssbonds: Extracts disulfide bonds from a specified molecule.

The links are formatted as “C1_RRR1_A1-C2_RRR2_A2” and disulfide bonds as “C1_RRR1_A1-C2_RRR2_A2”, where C1 and C2 are the atoms involved in the link, RRR1 and RRR2 are the residue numbers, and A1 and A2 are the chain identifiers.

[source]

multimer.tcl

PestiferMultimer – This is a Pestifer Tcl package for VMD that provides tools for computing geometric properties of multimers, such as opening angles and rotation matrices. It allows for the calculation of opening angles between protomer selections and the generation of rotation matrices for aligning protomers. The package provides the following main procedures:

opening_angles: Computes the opening angles between a list of selections based on their geometric centers.

opening_angles_trace: Computes opening angles for a trace of selections across multiple frames of a molecule.

rotation_matrices: Computes rotation matrices for aligning selections based on their geometric centers.

rotation_matrices_trace: Computes rotation matrices for a trace of selections across multiple frames of a molecule.

[source]

util.tcl

PestiferUtil – This is a Pestifer Tcl package for VMD that provides utility functions for various tasks such as splitting PSF files, verifying molecule states, and manipulating molecular data.

[source]