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 all the best options.
ReadySet! also adds hydrogens to the model which is a good thing.
Nigel
On 3/3/09 11:17 AM, Eric Liu wrote:
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.
PDB file elbow.stau_pdb.001.pdb written.
Bonding file elbow.stau_pdb.001.bonding.py
<http://elbow.stau_pdb.001.bonding.py> written.
Edit bonding file to reflectALTERNATIVELY
Re-run eLBOW with the --reel option and the molecule wil be loaded
into REEL. Edit the bonds and save the results as "fixed.cif" to
allow eLBOW to load the bonding. the desired bond.
I guess stausporine was quite complicated molecule. How do I rerun the
elbow with reel option? What other programs you can use to generate
compound library file?
Thanks!
Eric
--
Nigel W. Moriarty, Ph.D.
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709
Fax : 510-486-5909
Email : nwmoria...@lbl.gov
Web : CCI.LBL.gov
