These are the atom names you should have in your monomer. No mention of H_N4 there..
NH4 HN4 H H 0.000 0.000 0.000 0.000 NH4 N N NT 1.000 -0.581 0.302 -0.782 NH4 HN3 H H 0.000 -1.232 1.041 -0.516 NH4 HN2 H H 0.000 -0.024 0.609 -1.579 NH4 HN1 H H 0.000 -1.055 -0.583 -0.962 loop_ On 10 Aug 2012, at 16:17, Afshan Begum wrote: > Hello all, > I am refining my structures with REFMAC 5 and is failed. Actually i used > ammonium dihydrogen phosphate buffer during crystallization and in the map > file where i observed the density of ammonium ion (NH4). I get this ion from > the coot library but when i run refmac its failed even i gave the cif file > for this ion as a supplement but i could not get success so, if any body give > me suggestion how to solve this problem. > > I would be thankful to all. > this are the error message came from refmac log file > > > ERROR : atom :H4_N NH4 1 FF is absent in the library > ATTENTION: atom:N NH4 1 FF is missing in the structure > ERROR : atom :H4_N NH4 2 Fa is absent in the library > ATTENTION: atom:N NH4 2 Fa is missing in the structure > ERROR : atom :H4_N NH4 3 Fb is absent in the library > ATTENTION: atom:N NH4 3 Fb is missing in the structure > ERROR : atom :H4_N NH4 4 Fc is absent in the library > ATTENTION: atom:N NH4 4 Fc is missing in the structure > ERROR : atom :H4_N NH4 5 Fd is absent in the library > ATTENTION: atom:N NH4 5 Fd is missing in the structure > ERROR : atom :H4_N NH4 6 Fe is absent in the library > ATTENTION: atom:N NH4 6 Fe is missing in the structure > ERROR : atom :H4_N NH4 7 Ff is absent in the library > ATTENTION: atom:N NH4 7 Ff is missing in the structure > > Best Regards > > AFSHAN > >
