PyMol
Pairwise superposition from Wizard menu.
Artem
On Fri, Sep 3, 2010 at 6:44 AM, Rex Palmer wrote:
> This is not really protein crystallography but we are trying to model build
> a ligand into a protein binding site. A similar ligand is already in place
> and we want to replace this by init
Hi Rex,
the command
phenix.superpose_ligands 1.pdb 2.pdb
will do it.
1.pdb and 2.pdb are two PDB files containing the ligands. The output
result will be in overlay_1_pdb_2_pdb.pdb file. The algorithm is based
on graph matching, and it is good for ligand-sized molecules. The atom
labels can
Dear Rex,
if I understood corrctly what you are looking for you could also use Gerard
Kleywegt's lsqman, where you can pick the atoms which you want to use for
superpositioning.
Tim
On Fri, Sep 03, 2010 at 12:44:03PM +0100, Rex Palmer wrote:
> This is not really protein crystallography but we ar
Dear Rex,
You can try SPDB viewer if it serves your purpose.
Gauri
Palmer
Sent: Friday, September 03, 2010 1:44 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] superpositioning two ligands
This is not really protein crystallography but we are trying to
model build a ligand into a protein binding site. A similar ligand
On 03/09/10 12:44, Rex Palmer wrote:
This is not really protein crystallography but we are trying to model
build a ligand into a protein binding site. A similar ligand is
already in place and we want to replace this by initially
superimposing a phenyl ring which is common to both ligands. We
u
Fri. Sept 3rd 2010
EBI
Try ProFit
ttp://www.bioinf.org.uk/software/profit/
as you can give the atom names you want to fit.
Miri
On Fri, 3 Sep 2010, Rex Palmer wrote:
This is not really protein crystallography but we are trying to model build a
ligand into a protein binding site. A
simila
This is not really protein crystallography but we are trying to model build a
ligand into a protein binding site. A similar ligand is already in place and we
want to replace this by initially superimposing a phenyl ring which is common
to both ligands. We understand that such superpositioning ca
