That's right. The S-OH configuration is imposed by the CIF dictionary
for the ligand that you are using in REFMAC. You can edit the dictionary
with e.g., jligand, save a local copy and feed that copy to REFMAC - it
will override the library definition of the ligand.
On 25/06/2021 10:58, Peat, Tom (Manufacturing, Parkville) wrote:
Hello Shipra,
If you have defined the small molecule with a cif dictionary file
(used for refinement in REFMAC), then take a look at that file and see
whether it is correctly defined.
You can manually edit these files or remake them using any number of
programs to get the parameters you think are correct.
Best of luck, tom
Tom Peat, PhD
Proteins Group
Biomedical Program, CSIRO
343 Royal Parade
Parkville, VIC, 3052
+613 9662 7304
+614 57 539 419
tom.p...@csiro.au
------------------------------------------------------------------------
*From:* CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of
Shipra Bijpuria <shipra.bijpu...@gmail.com>
*Sent:* Friday, June 25, 2021 7:04 PM
*To:* CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK>
*Subject:* [ccp4bb] S=O converted to S-OH during refinement
Hello everyone,
I am trying to refine a protein-ligand complex structure.
The ligand is a small molecule and at one end has Sulfur that has
three branches of O, NH and CH3.
Sulfur is attached to oxygen by a double bond (S=O). After fitting the
ligand, I did refinement using Refmac5 with default settings.
But after the refinement the S=O gets converted to S-OH. Please let me
know how can I retain the S=O during refinement.
Thanks,
Shipra
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--
Industry and Medicine Applied Crystallography
Macromolecular Crystallography Unit
___________________________________
Phones : (351-21) 446-9100 Ext. 1669
(351-21) 446-9669 (direct)
Fax : (351-21) 441-1277 or 443-3644
email : mat...@itqb.unl.pt
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