Tim has the more modern answer, but PDBSET
http://www.ccp4.ac.uk/html/pdbset.html is quite simple and scriptable.
If I recall correctly, the SYMGEN keyword may be of use.
>From the example in the documentation:
######################## Expand dimer to tetramer, rename chains, transform
#!/bin/csh -f
#
# Make tetramer from dimer
#
pdbset xyzin ecrproducts268.pdb xyzout ecrprodpqrtet.pdb <<eof-1
remark Tetramer generated from AB dimer
remark rotated to pqr frame
remark
! Generate other dimer by z-dyad in P21212
symgen x,y,z
symgen -x,-y,z
! Rename chains in second dimer: V & W are water chains
chain symmetry 2 A C
chain symmetry 2 B D
chain symmetry 2 V X
chain symmetry 2 W Y
! transform to molecular frame
transform -
0.87831 0.47808 0 -
0 0 -1. -
-0.47808 0.87831 0 -
0.0 -2.713 0.0
eof-1
Mark
On 1 August 2013 03:08, Chen Zhao <[email protected]> wrote:
> Dear all,
>
> I have been trying to search for some softwares/applications that can
> display the crystal space group "lattice" based on the input of cell
> dimension and space group. Ideally, it can also apply the arbitrary
> symmetry operation to a molecule with given orientation and position in the
> unit cell. It would be perfect if it can output a PDB file. Does anybody
> heard of something like that?
>
> I know it might not be too hard to be realized with a script simply
> modifying the coordinates, but unluckily I am not a programmer. And
> actually, even some simple PDB files of different space group, in which
> molecules are represented as dots, would be very helpful.
>
> Thank you so much!
>
> Sincerely,
> Chen Zhao
>
