align
Align structure to a reference.
align <mask> [<refmask>] [move <mask>] [mass] X [ first | reference | ref <name> | refindex <#> | previous | reftraj <name> [parm <name> | parmindex <#>] ]
<mask>
Target atoms to fit.
[<refmask>]
Reference atoms to fit (default is target mask).
[move <mask>]
Atoms to move when aligning (default is target mask).
[mass]
Mass-weight the fit. Reference keywords:
first
Use the first trajectory frame processed as reference.
reference
Use the first previously read in reference structure (refindex 0).
ref <name>
Use previously read in reference structure specified by filename/tag.
refindex <#>
Use previously read in reference structure specified by <#> (based on order read in).
previous
Use frame prior to current frame as reference.
reftraj <name>
Use frames from COORDS set <name> or read in from trajectory file <name> as references. Each frame from <name> is used in turn, so that frame 1 is compared to frame 1 from <name>, frame 2 is compared to frame 2 from <name> and so on. If <trajname>
runs out of frames before processing is complete, the last frame of <trajname>
continues to be used as the reference.
parm <parmname> | parmindex <#
> If reftraj
specifies a trajectory file, associate it with specified topology; if not specified the first topology is used.
Align structure using specified <mask>
onto reference. If ‘move’ is specified, only move atoms in the move mask.