LOOS  v2.3.2
Trajectory manipulation

Trajectory manipulation tools

A set of tools for manipulating structure and trajectory files, found in the Tools/ directory:

aligner

Align structures in a trajectory against the average using an iterative refinement scheme. Can read any LOOS trajectory format, but will write the aligned trajectory as a DCD.

center-molecule

A more flexible tool for centering molecules. Can use different subsets for calculating the center, controlling what is translated, and what goes to the output. It can also reimage the molecule and center only within the x,y plane.

center-pdb

Read in a structure file, shift its centroid to the origin, and write a new pdb file to stdout.

clipper

Manually clip a model using arbitrary sets of clipping planes. Outputs a PDB.

concat-selection

Concatenates atoms from a trajectory into a single PDB. Useful for seeing where something has been...

convert2pdb

Read in a structure file in a LOOS-supported format, and write it out as a pdb file.

dcdinfo

Extract the header information from a CHARMM/NAMD dcd file. Will verify the number of frames present and report periodic box information.

dumpmol

Outputs the low-level AtomicGroup representation for a model. Useful for double-checking LOOS' parsing of a file.

frame2pdb

Extract a frame from a trajectory and write it as a pdb file.

merge-traj

Merges a series of trajectory files into a single DCD file. If you give it a pre-existing merged file to work from, it simply appends the new data to it by counting frames in the merged DCD and skipping that many frames in the input; this enormously reduces the time needed to merge large data sets. It also has options to produce a second down-sampled trajectory, to translate and reimage each frame such that a particular set of atoms is centered at the origin, and to fix imaging such that molecules aren't broken across the periodic image.

model-select

Takes a model (PDB, PSF, etc) and a selection string. Parses the selection, then applies it to the PDB and writes the output to stdout. This tool is used mainly for checking your selection strings to make sure you're actually selecting what you intend to select.

model2matlab

Takes a PDB and a selection and an optional selection and writes out the coordinates to stdout in matlab format.

porcupine

Creates a faux-PDB containing atoms/bonds that represent a "porcupine" figure for a column vector from a matrix. This can be used to visualize the direction of motion from SVD and ENM results.

rebond

Distance-based search for bonds, that are explicitly added to the output PDB. Use this tool to visualize your ENM networks, or to reconnect CA traces from SVD results...

recenter-trj

Loop over a trajectory, translating the entire system such that the selected portion remains at the origin, and reimaging the rest on a molecule by molecule basis. It can also just do translations in the z-dimension, or just in the xy-plane (these options are useful for membrane systems). The model file must have connectivity information, and the trajectory must have periodic box information. This program writes a DCD file as output.

reimage-by-molecule

Reads a trajectory, and writes a new DCD which has been reimaged on a molecule by molecule basis. The model file must have connectivity information, and the trajectory must have periodic box information.

renum-pdb

Used primarily to renumber atoms/residues in a PDB...but it can work with any LOOS-supported format.

rmsfit

Superimpose two structures using Kabsch RMS alignment.

serialize-selection

Takes a trajectory consisting of N copies of a selection and turns it into a trajectory that is N times as long, but with only one copy of the selection.

smooth-traj

Smooths a trajectory by computing a windowed-average structure. Weighting within the window can either be uniform or cosine-weighted.

subsetter

Subsets a trajectory (stripping out any atoms that don't match the given selection), and writes a new DCD file. Can be used to concatenate trajectories, pull specific frames out, as well as adjusting periodic box information and centering the trajectory on a selection. Since trajectories are often stored in files with an ascending numerical sequence name (i.e. frame_1.dcd, frame_2.dcd, etc), and since the shell globbing doesn't sort these in numerical order, a command such as

subsetter foo model.pdb frame_*.dcd

will not concatenate your frames in the order you want. You can tell subsetter to sort the input trajectories so that they are in numerical order by using the "--sort" flag. For more detailed information, use the "--fullhelp" option with subsetter.

traj2dcd

Converts a LOOS-supported format to a DCD.

trajinfo
Similar to dcdinfo, but works with generic trajectories. Can report box information and the centroid of a selection. Useful for verifying trajectory header information and extracting the number of frames and atoms in a trajectory.