Dear all, I have a structure where CYS is bound to OCA (octanoic acid). I started with Jligand and created a CYS-OCA covalent link. It then output a CIF file (verified looks OK). Add the LINK record to PDB file:
LINK SG CYS A 161 C1 OCA A 902 CYS-OCA Place OCA to the model using Coot. When I now use RealSpaceRefinement, the OCA is placed on top of CYS itself. Coot does not recognise that OCA-CYS link but why? therefore, I just place OCA at Place it in *reasonable* position without any overlaps. All files are located at https://gist.github.com/ort163/e6b8411f45e5224f7d46fc36c3324e6f Now in REFMAC, input MTZ,PDB and the CIF file (from jligand). After refinement, I find that the oxygen in the OCA is pointing wrongly. The thioester bond is also NOT ideal distance (though density is good). Is there anything wrong with my procedure? *Shouldnt* the refinement optimise everything in OCA-CYS link? Best Markus ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
