Of
martyn.w...@stfc.ac.uk
Sent: 30 June 2011 15:08
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] generate large symmetry model
As well as pdbset, you can use pdbcur. A combination of keywords genunit, symop
and symcommit.
I’d probably use genunit (applicable to whatever spacegroup you have
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
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
Well - you have a problem of chain IDS,
but pdbset xyzin asymm.pdb xyzout whole-cell.pdb
symgen P212121 (say)
end
will generate a whole unit cell,
then
pdbset xyzin whole-cell.pdb xyzout whole-cell-+100
symgen x+1,y,z
end
etc
will move that unitcell.pdb
You would have to put them all
[mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Hargreaves, David
Sent: 30 June 2011 13:52
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] generate large symmetry model
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
Apologies for suggesting a non-CCP4 solution, but UCSF Chimera can do that and
more (interactively!):
Tools - Higher Order Structure - Unit cell
Petr
On Jun 30, 2011, at 2:52 PM, Hargreaves, David wrote:
Does anyone have a rigorous method (or script) for generating an extended
lattice
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
PDBCur (CCP4) should be able to generate the unit cell at once, which then
should be translated to 3x3x3 cube. All may be done within a single run of
PDBCur, a simple keyword input is required. Same job is doable with PDBSet.
Eugene
On 30 Jun 2011, at 15:36, Petr Leiman wrote:
Apologies for
You can do this with PyMOL with the supercell script:
http://pymolwiki.org/index.php/Supercell
Cheers,
Thomas
On 06/30/2011 02:52 PM, 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
