Its obviously not going to be possible to give a unique
chain letter for every chain in 27 cells, but forget renaminmg
the chains and its very easy to generate the models to look at-
might even do it in a triple-nested foreach loop in csh.
After generating the whole cell as suggested by David or Eleanor,
#untested script!
foreach A (-1 +0 +1)
foreach B (-1 +0 +1)
foreach C (-1 +0 +1)
pdbset xyzin wholecell.pdb xyzout sym$A$B$C.pdb <<eof
symgen X$A,Y$B,Z$C
eof
end
end
end
awk '$1~/CRYST1|SCALE/ wholecell.pdb > new.pdb
foreach sym??????.pdb
awk '$1~/ATOM|HETATM/' $file >> new.pdb
end
echo END >>new.pdb
and open new.pdb in some viewer that doesn't object to duplicate chain names
Tim Gruene wrote:
Hi Dave,
as first step you apply all symmetry operators of the space group to the
pdb-file in order to fill the unit cell, and store all copies in the same
PDB-file. You can do this with pdbset and the symgen keyword, see
http://www.ccp4.ac.uk/dist/html/pdbset.html#symgen
Check with coot that all copies are indeed in the asymmetric unit.
Once you have filled the unit cell, read in the PDB-file with moleman2 and run
xyz frac
write mypdb.frac
in order to get the fractional coordinates.
Now you run a loop over x,y,z to add -1, 0, 1 in order to get the cube of unit
cells and re-convert to orthogonal coordinates with moleman2.
It's actually quicker than it sounds.
Cheers, Tim
On Thu, Jun 30, 2011 at 01:52:17PM +0100, Hargreaves, David wrote:
Does anyone have a rigorous method (or script) for generating an
extended lattice e.g 3x3x3 unit cells from any pdb file?
Any help gratefully received,
Dave
David Hargreaves
Associate Principal Scientist
_____________________________________________________________________
AstraZeneca
DECS, CP&SS
Mereside, 50F49, Alderley Park, Cheshire, SK10 4TF
Tel +44 (0)01625 518521 Fax +44 (0) 1625 232693
David.Hargreaves @astrazeneca.com<mailto:[email protected]>
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