Dear all, I am refining a structure that has a ligand which contains a thiol group and forms a disulfide with the cysteine. I created the cif file with the Dundee server for the ligand and modified the BME-cysteine link cif file to fit my ligand. I combined these two cif files and feed it to Refmac when I refine my structure, and in the starting pdb, I added the SSBOND and LINK records for the ligand-cysteine disulfide.
Here is the problem: after refinement, the length of this bond is restrained correctly, but the angles between the (ligand)CH2-S-S(cysteine) and S(ligand)-S-CH2(cysteine) are not restrained according to the values in my combined cif file. Any suggestions? Thank you very much! Best, Melody
