Re: [ccp4bb] elbow and compound library

[William G. Scott]

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:



I got the smiles string here:
http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?sid=14717161


Here is the resulting cif file generated by the above command:

elbow.builder -- smiles = "CC12C (C(CC(O1)N3C4=CC=CC=C4C5=C6C(=C7C8=CC=CC=C8N2C7=C53)C(NC6=O)O)NC)OC"

elbow.cif
Description: Binary data

HTH,

Bill





On Mar 3, 2009, at 11:17 AM, Eric Liu wrote:

The compound is spelled lightly differently to what you wrote, so check to see if this is the right thing.

Hi All,


for my ccp4 refinement. It gave the following error message:



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 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.




with reel option? What other programs you can use to generate compound
library file?


Thanks!

Eric

I downloaded a stausporine PDB file and used elbow to generate the cif file 0:00 Bondise Bondise Bondise Bondise Bondise Bondise Bondise Bondise Bondise I guess stausporine was quite complicated molecule. How do I rerun the elbow