[phenixbb] eLBOW / REEL and chirality

L. Costenaro (IBB) lionel.costenaro at bioinf.uab.es
Thu Jul 24 09:54:02 PDT 2014

Dear all,

I am making the restraints file (CIF) for a ligand with two chiral carbons,
using eLBOW (AM1 QM, output: retain original chirality) from a SMILES
description and obtain the following:

Atom   input_chirality   input_smiles   output_vol_sign   output_R/S
C20    S                       C at H               negative
S                  S
C37    R                       C@@H            positive
S                  S

Although the volume_sign in the output cif file correspond to the input
chiralities, the output pdb has the wrong chirality for the carbon C37: S
instead of the desired R.

I think the "retain original chirality" option is what I need to keep the
input chirality, but apparently it doesn't. How should I proceed to get a
pdb with the correct chiralities?

Best regards,

PS: phenix version 1.9-1692, linux X86_64

PS2: in REEL, the action "Find unique code" make phenix (not REEL) crash
(all windows close) without error message
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