Re-image coordinates based on crystal space group symmetry operations and asymmetric unit volume.
xtalsymm <mask> group <space group> [collect [centroid]] [ first | reference | ref <name> | refindex <#> ] [na <na>] [nb <nb>] [nc <nc>]
<mask> Atom mask defining the asymmetric unit within the larger system (required).
group <space group> The space group to which the system belongs. Omit spaces in the name. Example: P22(1)2(1) .
[collect] Optional flag to have all solvent particles, not just the asymmetric units, re-imaged. This will trigger CPPTRAJ to compute the unit cell volume that constitutes the asymmetric unit and thereby classify all particles for re-imaging.
[centroid] If specified along with collect, re-image solvent molecules by centroids, not individual atom coordinates. This is useful for keeping water molecules intact.
[first | reference | ref <name> | rendex <#>] Reference structure to use for determining crystal symmetry.
[na <na>] [nb <nb>] [nc <nc>] The number of times the crystal unit cell is replicated along the ‘a’, ‘b,’ or ‘c’ axes (for orthorhombic unit cells, these are the x, y, and z axes) of the simulation; default is 1. Many crystal unit cells are too small in one or more dimensions for our simulation cutoffs, and replicating the unit cell is an effective way to counter imaging artifacts even for larger unit cells.
Calculate the optimal approach for superimposing symmetry-related subunits of the simulation back onto one another. The calculation assumes that the system is a simulation of an X-ray structure in its native crystal lattice, and all copies of the asymmetric unit among the entire system, and devises plans for re-imagining their coordinates to superimpose them back on the original asymmetric unit. The space group information can be found in a PDB X-ray structure used as the initial coordinates for a simulation. All 230 space groups are supported, and a scan of the PDB was made to ensure that common variants of the names are included (P2(1)22(1) is the same as P22(1)2(1), but with different axis conventions). If your space group is not understood, contact the Amber mailing list. This command is compute intensive, especially for simulations that are supercells containing many crystallographic unit cells.
This command will cause CPPTRAJ to locate all asymmetric units from within the topology, then determine what wrapping, if any, has occurred in order to bring about an optimal re-alignment based on the space group symmetry operations. The user need not worry about wrapping or drift of the simulation over time the asymmetric units will be re-imaged frame by frame. Coordinate modifications due to this action are permanent and will act the results of subsequent actions and analyses.