Align structure to a reference.

align <mask> [<refmask>] 
             [move <mask>]
             [ 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.


There is no difference in the alignment made by the align command and the best-fit rms command. They both use the same algorithm under the hood to perform the fitting; the main difference is that using the rms command, it will generate an RMSD data set.