LOOS  v2.3.2

General purpose tools

averager

Compute the average structure for a set of molecules from a trajectory, using an iterative scheme.

atomic-rdf

Compute the radial distribution function for 2 selections of atoms taken from a trajectory, treating each selection as a set of individual atoms. For contrast, see rdf.

blurrogram.pl

A PERL tool for creating "blurrogram" style figures with Pymol.

bounding

Write out the bounding box for a selection of atoms from a structure file.

cluster-structures.py

Perform clustering analysis on a trajectory using the k-means algorithm on the basis of RMSD. In Packages/PyLOOS.

contact-time

This tool computes the number of contacts between a probe selection and a set of target selections. The output is in the form of a matrix and can be normalized by either total number of contacts (across the row) or by the maximum # of contacts per target (down the column). In addition, it can automatically split the probe into separate molecules, based on their segids, and compute the inter-probe contacts as well.

contacts

Loop over a trajectory and count the number of contacts between two sets of atoms.

cylindrical-density.py

Compute a 2D radial distribution function in cylindrical coordinates. In Packages/PyLOOS.

domain.py

Describe the motion of two selections within a single macromolecule, including distance and the angle and torsion formed the their first principal moments. In Packages/PyLOOS.

drifter

Calculates movement centroids over a trajectory

exposure

Computes the degree of exposure of a set of selections over time. The exposure is defined as the average density of a probe selection within a spherical shell about each target atom. This tool can be used to determine how exposed to solvent a selection is, or alternatively how buried a selection is.

gmxdump2pdb.pl

Converts a Gromacs/MARTINI system into a PDB and minimal PSF with connectivity. Constraints (and bonds to hydrogens) can be added, and the connectivity for water can be inferred.

helix_kink

Given two selections and a trajectory, compute the time series of the angle between their principal components. Also useful for measuring domain hinge motions.

interdist

Calculates distances between a selection and an aribtrary set of other selections over a trajectory. The distance computed can be the distance between the centroids, the minimum distance between any atom in any group, or the max distance between any atom in any group.

octavex

Extract embedded OCTAVE data from a LOOS output/log. This is used with aligner.

paxes

Computes the magnitude of the principal axes of a set of selections over the trajectory. This can be used to analyze shape changes over time.

packing_score

Computes the packing score, a measure of the contact between two selections, over the course of a trajectory. Originally defined in Grossfield et al, PNAS, 2006, 103, 4888-4893

protein_tilt.py

Compute the overall tilt of a membrane protein relative to the membrane normal by averaging the tilts of the individual transmembrane helices. In Packages/PyLOOS.

ramachandran

Computes a ramachandran map for a given selection of a specified range of frames in a trajectory (or all frames). Note that some torsions may be missing for the residues at the ends of the selection. To avoid this, expand your selection by a residue in both directions, then use the "--skip" flag.

rdf

Computes the radial distribution function for two selections averagd over a trajectory. The selections are split up by molecule and the center of mass is used. For example, selecting all water molecules will cause it to compute the radial distribution of the centers of mass of individual water molecules. For contrast, see atomic-rdf.

rgyr

Compute the radius of gyration for a selection of atoms. Optionally, it can break your selection into individual molecules, if for example you have multiple solutes in the system.

rmsd2ref

Computes rmsds between a selection and either its average conformation or a reference model, optionally aligning the selection.

rmsds

Loops over a trajectory and computes the pairwise RMSDs for a selection of atoms.

rotamer

Computes the chi-1 and chi-2 angles for a given selection over an entire trajectory.

torsion

Given 4 selections, compute the torsion angle for their centroids. This program loops over a trajectory and writes the torsion angle time series.

transition_contacts
Calculate the normalized transition between two structures over a trajectory.