Hi all, We have been finalising a structure with a ligand complexed to heme. I have been checking the close to final structure and I noticed that the ligand looks distorted away from what one would expect. We use Phenix.refine We initially used the grade server for our restraints files. I also just used elbow to generate a new one. Looking at both, the restraints look reasonable (similar in both) however the initial output pdb from elbow is distorted further. The angles /lengths looked reasonable and are similar to small molecule structures (CCDC). The planarity of a bi-phenyl moiety is very distorted. [cid:[email protected]] Are we missing something? Do we need to tell phenix.refine to not over refine the model? Should elbow give a distorted model? Apologies if this is all online but my uni cant seem to access phenix.org! Thanks in advance Joel Joel Tyndall | BSc(Hons) PhD Associate Professor in Medicinal Chemistry School of Pharmacy | He Rau Kawakawa University of Otago | Te Whare Wānanga o Otāgo PO Box 56 9054 Dunedin | Ōtepoti New Zealand | Aotearoa Ph: 64 3 479 7293 Skype: jtyndall Website | pharmacy.otago.ac.nz
