Table 5.

Examples of tools and packages that are included with LOOS.

Core Tools
aligner	Optimally align trajectory
contact-time	Time-series of atom contacts
density-dist	Electron, mass, or charge density along z-axis
merge-traj	Merge and subsample trajectories
order_parameters	Order parameters analogous to 2H quadrupolar splitting for lipid chains
rdf	Radial distribution function
rmsds	All-to-all RMSD for one or two trajectories
svd	Singular Value Decomposition of a trajectory (PCA)
xy_rdf	Radial distribution function in the x,y-plane
Convergence Package
block_average	Block average of arbitrary time-series data
coscon	Cosine content of a trajectory
decorr_time	Decorrelation time of a trajectory
bcom, boot_bcom	Block covariance overlap method for determining convergence and sampling
Density Package
blobid	Segment a density grid and find non-contiguous blobs of density
grid2xplor	Convert density grid to X-plor electron density map format for visualization
near_blobs	Find residues in a trajectory that are near a blob of density
water-hist	3D histogram of atoms in a trajectory
Elastic Network Models
anm	Anisotropic network model
enmovie	Visualize ENM motions by generating a trajectory based on an ENM solution
vsa	Vibrational subsystem analysis
Hydrogen Bonds
hbonds	Find occupancies of putative hydrogen bonds in a trajectory
hcontacts	Time-series of possible intra- and inter-molecular hydrogen bonds
hcorrelation	Time-correlation of putative hydrogen bonds