projection

Project coordinates along given eigenvectors.

projection [<name>] evecs <dataset name> [out <outfile>] [beg <beg>] [end <end>] [<mask>] [dihedrals <dataset arg>] [start <start>] [stop <stop>] [offset <offset>]

[<name>] Output data set name.
evecs <dataset name> Data set containing eigenvectors (modes).
[out <outfile>] Write projections to <outfile>.
[beg <beg>] First eigenvector/mode to use (default 1).
[end <end>] Final eigenvector/mode to use (default 2).
[<mask>] (Not dihedral covariance) Mask of atoms to use in projection; MUST CORRESPOND TO HOW EIGENVECTORS WERE GENERATED.
[dihedrals <dataset arg>] (Dihedral covariance only) Dihedral data sets to use in projection; MUST CORRESPOND TO HOW EIGENVECTORS WERE GENERATED.
[start <start>] Frame to start calculating projection.
[stop <stop>] Frame to stop calculating projection.
[offset <offset>] Frames to skip between projection calculations.

Data Sets Created:
DataSet indices correspond to mode #.
<name> (All execpt IDEA) Projection data set.
<name>[X] X component of mode (IDEA modes only).
<name>[Y] Y component of mode (IDEA modes only).
<name>[Z] Z component of mode (IDEA modes only).
<name>[R] Magnitude of mode (IDEA modes only).

Projects snapshots onto eigenvectors obtained by diagonalizing covariance or mass-weighted covariance matrices. Eigenvectors are taken from previously generated (e.g. with diagmatrix) or previously read-in (e.g. with readdata) eigenvectors with name <dataset name>. The user has to make sure that the atoms selected by <mask> agree with the ones used to calculate the modes (i.e., if mask = ’@CA’ was used in the “matrix” command, mask = ’@CA’ needs to be set here as well).