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:name.surn...@astrazeneca.com> > > > > Please consider the environment before printing this e-mail > > > > > -------------------------------------------------------------------------- > AstraZeneca UK Limited is a company incorporated in England and Wales with > registered number: 03674842 and a registered office at 2 Kingdom Street, > London, W2 6BD. > Confidentiality Notice: This message is private and may contain confidential, > proprietary and legally privileged information. If you have received this > message in error, please notify us and remove it from your system and note > that you must not copy, distribute or take any action in reliance on it. Any > unauthorised use or disclosure of the contents of this message is not > permitted and may be unlawful. > Disclaimer: Email messages may be subject to delays, interception, > non-delivery and unauthorised alterations. Therefore, information expressed > in this message is not given or endorsed by AstraZeneca UK Limited unless > otherwise notified by an authorised representative independent of this > message. No contractual relationship is created by this message by any person > unless specifically indicated by agreement in writing other than email. > Monitoring: AstraZeneca UK Limited may monitor email traffic data and content > for the purposes of the prevention and detection of crime, ensuring the > security of our computer systems and checking Compliance with our Code of > Conduct and Policies. -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A
pgpWMgT9ZBW3Y.pgp
Description: PGP signature
