Hi Markus, Did you load the .cif file into Coot before real space refinement? File -> Import CIF dictionary … When you do that, Coot should be able to refine the link and that might then also help for the refinement in Refmac.
Bernhard Bernhard C. Lechtenberg, PhD Postdoctoral Associate Riedl Lab Cancer Metabolism and Signaling Networks Program NCI-Designated Cancer Center [cid:[email protected]] 10901 N. Torrey Pines Road, La Jolla, CA 92037 T 858.646.3100 ext. 4216 E [email protected]<mailto:[email protected]> Science Benefiting Patients® On Jan 15, 2019, at 12:49 PM, Markus Heckmann <[email protected]<mailto:[email protected]>> wrote: 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://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgist.github.com%2Fort163%2Fe6b8411f45e5224f7d46fc36c3324e6f&data=02%7C01%7Cblechtenberg%40SBPDISCOVERY.ORG%7Cddcea39782f54aa79e0008d67b2b4211%7C0b162723004547deb0699f1a7aa955a1%7C0%7C0%7C636831823062844471&sdata=YuhoO%2B6giCrJwZ9R4Njw2UBpkp6c85PZHA%2FSYiBwZnw%3D&reserved=0 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://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2Fwebadmin%3FSUBED1%3DCCP4BB%26A%3D1&data=02%7C01%7Cblechtenberg%40SBPDISCOVERY.ORG%7Cddcea39782f54aa79e0008d67b2b4211%7C0b162723004547deb0699f1a7aa955a1%7C0%7C0%7C636831823062844471&sdata=wGACGXp67jTkq9Y5JBLznjZ8IG9VsuOxLBd1T29BYGw%3D&reserved=0 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
