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Crystal symmetry

The format of the CRYST1 record is as follows:

1 - 6 Record name "CRYST1"
7 - 15 Real(9.3) a a (Angstroms).
16 - 24 Real(9.3) b b (Angstroms).
25 - 33 Real(9.3) c c (Angstroms).
34 - 40 Real(7.2) alpha alpha (degrees).
41 - 47 Real(7.2) beta beta (degrees).
48 - 54 Real(7.2) gamma gamma (degrees).
56 - 66 LString sGroup Space group.
67 - 70 Integer z Z value. # ignored by PyMOL

When you use the "load" command to read in a PDB file with symmetry information, matrix information should be output. Verify that this information is produced before attempting to display symmetry related molecules.

The "symexp" command is used to display symmetry related molecules in the crystal lattice about an atom selection. This commands creates a set of new objects with a common prefix. Each object in the series corresponds to one symmetry-related object, which can be treated independently. See "help symexp" or the reference section for usage information.

In order to visualize only symmetry-related atoms within a given distance, you need to break the process down into two steps. First, you use the symexp command to create complete symmetry-related objects. Then you use "hide" commands to restrict what is visible to only those areas which you are interested.

load foo.pdb # load PDB file with CRYST record
symexp sym,foo,(foo),5.0

This last command create symmetry related "foo" objects which pass within 5 angstroms of foo using the prefix "sym"

hide (not (foo expand 5))


With this last one you hide atoms greater than 5 A from foo.
NOTE: The symexp command can potentially create large numbers of objects. You will want to use the "delete" command with a wildcard "*" to remove all objects that share a common prefix.
delete sym* # deletes objects starting with "sym"
To open a crystal structure of a dimer from pdb with the symmetry coordinates easiest would be:
click on the 'A' button, select 'generate' and select 'symmetry mates'. From there you can select within how many Angstroms you want your symm molecules to be displayed. From the symmetry related molecules that get displayed you can select the one that completes the dimer.
Alternately:

symexp sym=pdb,(pdb),4.0 # Creates symmetry partners within 4 A of molecule pdb