Hi Javier, The deuterium exchange should not change the chemistry of the residues (neglecting the minor changes in bond lengths), so the cif-file should be exactly the same for the deuterated amino acids. The _chem_comp_atom.atom_id (e.g. HA) in your monomer library (which is also a cif-file) should correspond to the third column of your pdb-file, so that coot know what hydrogen that should be. The only difference in your pdb-file compared to an X-ray structure with hydrogens is the element symbol in the last column.
HTH, Esko _____________________ Esko Oksanen, PhD Instrument Scientist - Neutron Macromolecular Crystallography European Spallation Source ESS AB P.O Box 176, SE-221 00 Lund, Sweden Visiting address: Tunavägen 24, Lund Switchboard: +46 46 888 00 00 Phone: +46 46 888 30 36 Mobile: +46 721 79 20 36 E-mail: [email protected]<mailto:[email protected]> www.esss.se<http://www.esss.se/> The European Spallation Source is a Partnership of 17 European Nations committed to the goal of Collectively building and operating the world's leading facility for research using neutrons by the second quarter of the 21st Century On Aug 2, 2013, at 7:15 PM, Javier Gonzalez wrote: Dear all, I'm refining a neutron structure and I would like to know whether there are available geometry dictionaries for deuterated aminoacids, in order to input them into Coot. At least the version I have (Coot 0.7, revision 4459) is unable to handle aminoacids whose exchangeable H atoms are replaced by D. I would rather avoid the hassle of having to edit manually the .cif files for all aminoacids. Thanks in advance, Javier -- Javier M. Gonzalez Protein Crystallography Station Bioscience Division Los Alamos National Laboratory TA-3, Building 4200, Room 202 Mailstop T001 work: (505) 667-9376 (temporary)
