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LOOS 4.1.0
The Lightweight Object Oriented Structural analysis library/toolkit
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Track residue-residue contacts across a trajectory
Compute stacking interactions, eg. for an RNA molecule, over a trajectory
Compute the average structure for a set of molecules from a trajectory, using an iterative scheme.
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.
A PERL tool for creating "blurrogram" style figures with Pymol.
Write out the bounding box for a selection of atoms from a structure file.
Compute the frame-frame distance matrix for a trajetory in contact space
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.
Loop over a trajectory and count the number of contacts between two sets of atoms.
Compute a 2D radial distribution function in cylindrical coordinates. In Packages/PyLOOS.
Compute the thickness of the membrane around a centering selection
Compute a pair-distribution function for a macromolecule, like you might estimate from a scattering experiment
Track dihedrals of sets of chemically connected angles
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.
Calculates movement centroids over a trajectory
Fit charges on a mesh composed of spherical shells to reproduce the electrostatic potential due to solvent around a solute
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.
Determine what fraction of contacts with a probe belong to the specified targets
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.
Given two selections and a trajectory, compute the time series of the angle between their principal components. Also useful for measuring domain hinge motions.
Writes a new trajectory replacing each selection with 3 particles
Detect lipid chains that have made their way inside a membrane protein
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.
Display information about the metadata for a model
Calculate a pair-wise RMSD for multiple trajectories
Report the fraction of native contacts found over the course of a trajectory
Computes the orientational correlation function for a polymer chain (eg protein or RNA)
Extract embedded OCTAVE data from a LOOS output/log. This is used with aligner.
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.
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
Computes the packing score between a set of ligand molecules and each residue of a macromolecule. Useful for identifying binding sites.
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.
Histogram the radius of gyration for a selection of atoms a trajectory. Optionally, it can break your selection into individual molecules, if for example you have multiple solutes in the system. It can also write a time-series of these radii of gyration to a file.
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.
Applies the non-negative matrix factorization algorithm developed by Plante and Weinstein
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.
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. See rad-gyr for a more modern implementation.
Computes rmsds between a selection and either its average conformation or a reference model, optionally aligning the selection.
Loops over a trajectory and computes the pairwise RMSDs for a selection of atoms.
Calculate the RMSD between all pairs of frames from two different sets of trajectories
Identify RNA conformers using the RNA Suites approach of Richardson et al., RNA, 2008, 465–481
Computes the chi-1 and chi-2 angles for a given selection over an entire trajectory.
Add segids to a model that lacks them
Compute X-ray scattering using the spherical scattering approximation
Print a bunch of useful information about the system to stdout
Given 4 selections, compute the torsion angle for their centroids. This program loops over a trajectory and writes the torsion angle time series.
Print out the total charge of a system
Calculate the normalized transition between two structures over a trajectory.
1.10.0