[Chimera-users] crystallographic symmops and lattice translations in Chimera

Tom Goddard goddard at cgl.ucsf.edu
Sat Dec 15 16:29:31 PST 2007

Hi Boaz,

  Chimera can apply lattice translations in a variety of ways, though 
there isn't currently a simple flexible command for this.  The 
Multiscale tool (menu Tools / Higher-Order Structure) can make a 3 by 3 
by 3 array of unit cells, and you can drag to select and delete unwanted 
monomers.  The Unit Cell tool (same menu) can translate the unit cell 
origin (values 0-1) and reposition all asym units to have their centers 
in the cell.  That only allows translation by a fraction of a unit 
cell.  The Crystal Coordinates script on the experimental features web 
page can write out PDB files for a block of unit cells.  That has to be 
downloaded separately:


Another trick is you could open two copies of your PDB translate one by 
one unit cell length along x with a command line "move x 123.5" then 
apply the Unit Cell tool to both copies.  You'd have to get the unit 
cell size in x by looking at the CRYST1 record in the PDB file.

  The Unit Cell tool has a button "Outline unit cell" that displays an 
outline box for the unit cell of a chosen PDB model.


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