Sampath Natarajan wrote:
Dear all,
I solved a structure with four molecules in the assymetric unit which
form a dodecameric oligomeric structure in the biological process. I
need to create the symmetrical molecules to find out the cavity size of
the entire molecule. I tried in coot, but I was not able to save the PDB
file for the entire moleule. I could get only 4 molecules again. Could
anyone help me to get dodecameric pdb file? Thanks in advance.
PDBSET does this very nicely with "symgen" and "chain" keywords:
This is for P3; if you have higher symmetry you might need to
try different symops to see which generate the dimer, and perhaps
add unit translations, to make it come together right. Symops
for each spacegroup are listed in $SYMOP.
#!/bin/csh -f
pdbset xyzin tetra.pdb xyzout dodeca.pdb <<eof
symgen x, y, z
symgen -Y,X-Y,Z
symgen Y-X,-X,Z
!select chain A B C D
chain symm 2 A I
chain symm 2 B J
chain symm 2 C K
chain symm 2 D L
chain symm 3 A Q
chain symm 3 B R
chain symm 3 C S
chain symm 3 D T
eof
