[ccp4bb] Monomer_lib_cif from PDB (Sketcher)
Dear CCP4 users, I just wonder if this problem can be solved using Sketcher. When i use Sketcher (PC or linux) in the CCP4 GUI to generate the monomer_lib.cif of a ligand (V3OAc.pdb) obtained from CCDC, the geometry of this ligand change (see V3Oand the attached files are used. Any comment is highly appreciated. stephen -- Dr. Stephen Sin-Yin Chui (徐先賢) Assistant Professor, Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China. Tel: 22415814 (Office), 22415818 (X-ray Diffraction Laboratory) V3OAc.pdb Description: Protein Databank data V3O_bondlist.cif Description: CIF chemical test V3O_libcheck.pdb Description: Protein Databank data V3O_mon_lib.cif Description: CIF chemical test
Re: [ccp4bb] Monomer_lib_cif from PDB (Sketcher)
On 10/08/11 18:42, Dr. STEPHEN SIN-YIN, CHUI wrote: Dear CCP4 users, I just wonder if this problem can be solved using Sketcher. When i use Sketcher (PC or linux) in the CCP4 GUI to generate the monomer_lib.cif of a ligand (V3OAc.pdb) obtained from CCDC, the geometry of this ligand change (see V3Oand the attached files are used. Any comment is highly appreciated. Hello Stephen, You just need to minimize the ligand (V30_libcheck.pdb). My understanding is that that is what typically happens for you when using Sketcher. Without the log files and/or button-press-tracking it is hard to know why this hasn't happened already. So just feed it into Refmac or your favourite other minimizer and it will turn out much closer to how you expect (I expect). (As an aside, I believe that the CCDC take a dim view of distributing work derived from their database.) Paul.
