crdtransform

Transform a COORDS set in one of several ways.

crdtransform <input crd set> [name <output crd set>]
             { rmsrefine [mask <mask>] [mass] [rmstol <tolerance>] | normcoords | trim [metric <metric>] [{ntrimmed <#>|cutoff <val>}]
             [criterion {comp|medoid}]    }

<input crd set> COORDS set to transform.
[name <output crd set>] COORDS set to create; if not specified <input crd set> will be modified.
rmsrefine Do iterative RMS refinement.
[mask <mask>] Mask of atoms to fit during refinement.
[mass] Mass-weight the refinement.
[rmstol <tolerance>] Tolerance (in Ang.) below which RMS-refinement will stop.
normcoords Normalize coordinates between 0.0 and 1.0 using the minimum and maximum coordinate values.
trim Remove trajectory frames using extended similarity metrics.
[metric <metric>] Metric to use; default MSD.
[{ntrimmed <#>|cutoff <val>} # of frames or fraction of trajectory to trim.
[criterion {comp|medoid}] Trim frames by comparitive similarity (i.e. trim most dissimilar frames) or comparison to medoid (i.e. trim most dissimilar to medoid frame).

Transform a COORDS set in one of several ways. Does not yet work with TRAJ data sets. The iterative RMS refinement is similar to the procedure outlined by Klem et al. (J. Chem. Theory Comput. 2022, 18, 3218-3230). The extended similarity metrics are those defined by Racz et al. (J. Comp.-Aid. Mol. Design, 2022, 36, 157-173).