Calculate symmetry-corrected RMSD.

symmrmsd [<name>] [<mask>] [<refmask>] [out <filename>] [nofit] [mass] [remap] [ first | reference | ref <name> | refindex <#> | previous | reftraj <name> [parm <parmname> | parmindex <#>] ]

[<name>] Output data set name.
[<mask>] Mask of atoms to calculate RMSD for; if not specified, calculate for all atoms.
[<refmask>] Reference mask; if not specified, use <mask>.
[out <filename>] Output data file name.
[nofit] Do not perform best-fit RMSD (not recommended).
[mass] Mass-weight the RMSD calculation.
[remap] Re-arrange atoms according to symmetry. See below for more details.

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 file associate trajectory <name> with specified topology; if not specified the first topology is used.

Perform symmetry-corrected RMSD calculation. This is done by identifying potential symmetric atoms in each residue, performing an initial best-fit, then determining which configuration of symmetric atoms will give the lowest RMSD using atomic distance to reference atoms.

Note that when re-mapping, all atoms in the residues of interest should be selected to prevent cases where selected symmetric atoms are swapped but the atoms they are bonded to are not. Also, occasionally larger symmetric structures (e.g. 6 membered rings) may become distorted due to only part of the residue being corrected for symmetry. This appears to happen about 4% of the time but does not overly inflate the RMSD. The ’check’ command can be used after symmrmsd to look for such distortions.

Warning: the symmetry correction is generally robust enough to account for symmetries in the standard amino and nucleic acid residues, but has not been extensively tested on residues with more extended types of symmetry.