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Command: unitcell

unitcell  atomic-model  [ symFromFile  true | false ] [ spacegroup  true | false ] [ ncs  true | false ] [ pack  true | false ] [ outline  true | false ] [ origin  f1,f2,f3 ] [ cells  N1,N2,N3 ] [ offset  M1,M2,M3 ]

unitcell info  atomic-model 

unitcell outline  atomic-model  [ origin  f1,f2,f3 ] [ close ]

unitcell delete  atomic-model  [ outline  true | false ]

The unitcell command builds crystallographic unit cells using symmetry information from the input coordinate file (PDB or mmCIF, but not small-molecule CIF). It can regenerate the full unit cell, multiple unit cells, or only those parts defined by crystallographic symmetry or noncrystallographic symmetry. The corresponding tool is Unit Cell; see limitations. See also: crystalcontacts, sym

One or more atomic models can be specified. Subcommands:.


Option descriptions are for PDB symmetry records, but the equivalent information from mmCIF is used in the same way.

symFromFile  true | false
Whether to apply crystallographic symmetry described by SMTRY1, SMTRY2, and SMTRY3 matrices in REMARK 290 lines of a PDB file (default true).
spacegroup  true | false
For files without crystallographic symmetry matrices, whether to use the space group name in the CRYST1 record of a PDB file to look up the crystallographic symmetry (default true). Space group names are the full Hermann-Mauguin symbols, e.g., P 1 21 1 rather than P 21 (see lists of names).
ncs  true | false
Whether to apply noncrystallographic symmetry described by MTRIX1, MTRIX2, and MTRIX3 matrices in a PDB file (default true). However, most MTRIX records describe how to transform one chain to match closely another chain that is already present in the PDB file, as indicated by a “1” in column 60; these MTRIX records are ignored.
pack  true | false
Whether to pack the structures so that their centers fall within one unit cell box (default true).
outline  true | false
Whether to show a white outline box of the unit cell (default false).
origin  f1,f2,f3
Shift the unit cell along its axes, where f1,f2,f3 are fractional coordinates in unit cell lengths (default 0,0,0 meaning no shift). Values of a coordinate that differ by integer amounts are equivalent; e.g., (0.3,0,0) is equivalent to (-0.7,0,0) and (4.3,0,0). Changing the origin may rearrange the copies and shift the outline (if present). The shift will occur in the direction that maintains the center of the original copy within the box.
cells  N1,N2,N3
Number of unit cells to generate along each of the unit cell axes, where N1,N2,N3 are positive integers (default 1,1,1 meaning a single unit cell).
offset  M1,M2,M3
Placement of the unit cell or block of cells relative to the cell containing the original structure. M1,M2,M3 are integers (default 0,0,0), and when more than one unit cell is generated, this is the position of the lower left front unit cell. For example, cells 3,1,1 and offset –1,0,0 would give a 3x1x1 block of cells with the original structure in the middle cell along the first axis.

UCSF Resource for Biocomputing, Visualization, and Informatics / March 2021