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)O)NC)OC"
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:
The compound is spelled lightly differently to what you wrote, so
check to see if this is the right thing.
HTH,
Bill
On Mar 3, 2009, at 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 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
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