[phenixbb] Problem with smiles string in elbow

Edward A. Berry BerryE at upstate.edu
Thu Jul 13 15:43:25 PDT 2017

I'm not getting the expected result with this string:
When used with coot Lidia it gives the expected result
(upper picture). But when I run elbow like this:
    phenix.elbow --smiles="COC(=O)C(=COC)c1ccccc1COC(N1C)=CC(=N1)C(=C2O)C=C(Cl)C=C2" --output="Y7303" --id="Y03"

the result is the lower picture. In particular the
pyrazole ring (arrow) gets distorted, but other bond lengths are way off.

I want to use elbow because it names the atoms as numbered
in the order they appear in the smiles string, irrespective
of the element. This is good because this is one of a series of
compounds in some of which C's are replaced by N's and vice versa
so it helps to have the same number for atoms in the same position.

What does work is to save the structure as .mol from Lidia and
feed that to elbow, which gives the right structure and the elbow
atom names. But it would be good to find out why it isn't working directly.

my elbow is:
  electronic Ligand Builder & Optimisation Workbench (eLBOW) 1.12rc1-2801 None
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Builder.gif
Type: image/gif
Size: 10118 bytes
Desc: not available
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20170713/450cde3b/attachment-0001.gif>

More information about the phenixbb mailing list