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 ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
