[ccp4bb] Refmac bond restraints across special positions?
Colleagues, We have determined a structure of a palindromic DNA molecule, in which one half of the DNA is in the asymmetric unit. Is there a way to tell REFMAC that there are covalent bonds across asymmetric units? Without such "LINK" records in the PDB file, REFMAC treats this as a non-covalent interaction and pushes the two DNA halfs apart. The data are at a fairly high resolution, which helps, but the repulsion is still there. Any advice would be greatly appreciated! I imagine this situation is quite rare in macromolecular crystallography. Oleg -- Oleg Tsodikov, Ph.D. Associate Professor of Pharmaceutical Sciences University of Kentucky College of Pharmacy Department of Pharmaceutical Sciences BioPharm Bldg, Room 425 789 S. Limestone Lexington, KY 40536
Re: [ccp4bb] Refmac bond restraints across special positions?
I haven’t tried this in a long time, but in the old days, we would have simply refined one strand. On Mar 12, 2014, at 4:05 PM, Oleg Tsodikov wrote: > Colleagues, > > We have determined a structure of a palindromic DNA molecule, in which one > half of the DNA is in the asymmetric unit. Is there a way to tell REFMAC that > there are covalent bonds across asymmetric units? Without such "LINK" records > in the PDB file, REFMAC treats this as a non-covalent interaction and pushes > the two DNA halfs apart. The data are at a fairly high resolution, which > helps, but the repulsion is still there. > > Any advice would be greatly appreciated! I imagine this situation is quite > rare in macromolecular crystallography. > > Oleg > -- > Oleg Tsodikov, Ph.D. > Associate Professor of Pharmaceutical Sciences > University of Kentucky College of Pharmacy > Department of Pharmaceutical Sciences > BioPharm Bldg, Room 425 > 789 S. Limestone > Lexington, KY 40536 > >
Re: [ccp4bb] Refmac bond restraints across special positions?
Hi, > Is there a way to tell REFMAC that there are covalent bonds across asymmetric > units? Try this (example from 3gbi.pdb) for DNA: LINK PDC B 119 O3' DA B 125 1555 2555 1.61 LINK O3' DA B 125 PDC B 119 1555 3555 1.61 LINK PDG C 209 O3' DT D 108 1555 3555 1.61 LINK O3' DT D 108 PDG C 209 1555 2555 1.61 Best, Debanu. -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Craig Bingman Sent: Wednesday, March 12, 2014 2:10 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Refmac bond restraints across special positions? I haven't tried this in a long time, but in the old days, we would have simply refined one strand. On Mar 12, 2014, at 4:05 PM, Oleg Tsodikov wrote: > Colleagues, > > We have determined a structure of a palindromic DNA molecule, in which one > half of the DNA is in the asymmetric unit. Is there a way to tell REFMAC that > there are covalent bonds across asymmetric units? Without such "LINK" records > in the PDB file, REFMAC treats this as a non-covalent interaction and pushes > the two DNA halfs apart. The data are at a fairly high resolution, which > helps, but the repulsion is still there. > > Any advice would be greatly appreciated! I imagine this situation is quite > rare in macromolecular crystallography. > > Oleg > -- > Oleg Tsodikov, Ph.D. > Associate Professor of Pharmaceutical Sciences University of Kentucky > College of Pharmacy Department of Pharmaceutical Sciences BioPharm > Bldg, Room 425 > 789 S. Limestone > Lexington, KY 40536 > >
