Prof. Robert J. Lancashire wrote: Bob,
I see a note about PDB files and symmetry. Is it that you can make use
of the section in the header like that given below?
REMARK PDB: Mineral
1001 1
REMARK cubic crystal with a=b=c=8.0832
1001 1
REMARK Space group 227 Fd-3m
1001 1
REMARK Atomic coordinates are stored in orthogonalised format
1001 1
REMARK All bonds are stored in connectivity arrays (CONECT)
1001 1
SEQRES 1 A 1 A
1001 1
CRYST1 8.083 8.083 8.083 90.00 90.00 90.00 Fd-3m 8
1001 1
ORIGX1 1.000000 0.000000 0.000000 0.00000
1001 1
ORIGX2 0.000000 1.000000 0.000000 0.00000
1001 1
ORIGX3 0.000000 0.000000 1.000000 0.00000
1001 1
SCALE1 1.000000 0.000000 0.000000 0.00000
1001 1
SCALE2 0.000000 1.000000 0.000000 0.00000
1001 1
SCALE3 0.000000 0.000000 1.000000 0.00000
1001 1
------------------
Right. Exactly.
1) If you just
load xxx.pdb
you will see no difference from before.
2) If you use
load xxx.pdb
unitcell on
you will see a single entity in its proper unit cell, with parameters
3) If you use
load "xxx.pdb" {1 1 1}
you will see the proper number of entities in one unit cell. Jmol will
use the SCAL1,2,3 lines to generate the fractional coordinates
internally, apply the symmetry indicated by the spacegroup in the CRYST1
line, and return the coordinates to Cartesians. Having done that, you can
show symmetry
show spacegroup
select symop=2 # atoms generated by symmetry operator 2
select site=3 # crystallographic site equivalent on all entities
select specialPosition # or NOT
select symmetry # or NOT
4) If you use
load "xxx.pdb" {1 1 1} spacegroup "P -4"
you will see the unit cell and entities as though for the spacegroup P
-4. Name can be a Hall symbol, a Hermann-Maugin symbol, or an
international table number. See the end of
http://cci.lbl.gov/sginfo/hall_symbols.html for specifics.
5) If you use
load "xxx.pdb" {1 1 1} spacegroup "x,y,z;-x,-y,-z"
you are designing your own space group
6) If you use
load "xxx.pdb" {1 1 1} unitcell {10.0 2.0 2.0 120 90 90}
you are defining your own unit cell.
7) If you use
load "myfile.xyz" {1 1 1} spacegroup "P -1" unitcell {20.0 10.0 12.0
90 90 90}
then you are generating the spacegroup and unitcell for standard xyz
cartesian data. Jmol converts the Cartesian coordinates into fractional
coordinates, applies the symmetry, and returns the coordinates to
Cartesians.
It's pretty powerful.
Bob
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