-Original Message-
From: CCP4 bulletin board on behalf of William G. Scott
Sent: Tue 03-Mar-09 9:06 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] elbow and compound library
Hi Eric:
You could try generating a SMILES string for your compound using this:
http://www.molinspiration.com/cgi-bin
Hi Eric:
You could try generating a SMILES string for your compound using this:
http://www.molinspiration.com/cgi-bin/properties
(or search to see if one is available) and feed that into elbow, eg:
elbow.builder --
smiles
=
"CC12C
(C(CC(O1)N3C4=CC=CC=C4C5=C6C(=C7C8=CC=CC=C8N2C7=C53)C(NC6=O
Eric
Staurosporine is a standard ligand in the Monomer library in PHENIX and
will work directly with phenix.refine.
I should mention that if you have the atom names different from the
monomer library
phenix.ready_set model_including_stau.pdb
will run eLBOW on the ligands in the model using
Hi Eric,
You can try the Dundee prodrg server:
http://davapc1.bioch.dundee.ac.uk/prodrg/
Good luck,
Eric
__
Eric Larson, PhD
MSGPP Consortium
Department of Biochemistry
Box 357742
University of Washington
Seattle, WA 98195
On Tue, 3 Mar 2009, Eric Liu wrote:
Hi All,
Hi All,
I downloaded a stausporine PDB file and used elbow to generate the cif file
for my ccp4 refinement. It gave the following error message:
0:00 Bondise Bondise Bondise Bondise Bondise Bondise Bondise Bondise Bondise
B
Failed to determine the bonding of a fragment of the molecule.
