try using this sed script for the moment, Paul is updating coot to handle the newest pdb v3.2 hydrogen names. regards Mark
On Wed, 29 Oct 2008, [ISO-8859-1] Maria H?kansson wrote: > Regarding protons in coot version 0.5, > > I am using shelx to refine my 1.2 ? data and I am refining the > hydrogen atoms. Subsequent rebuilding in > coot is difficult though since hydrogens often does not "follow" when > you do side chain rebuilding using > > add alternative conformation > edit chi angles > real space refine > rotate translate zone > > and so on > > For the moment I have quit transfering hydrogens to coot and add the > hydrogens every refinment cycle, though > it would be good I think if I could see them in coot without bothering > about wrong positions. > > Best regards, > > Maria > >> Maria H?kansson, Ph.D. > >> tel: +46 (0) 76 8585 706 > >> Senior Scientist, Max-lab, Lund University > >> fax: +46 46 222 47 10 > >> Ole R?mers v?g 1 (P.O. Box 188) > >> www.maxlab.lu.se > > > > >
s/HA3\(.\)GLY/HA1\1GLY/g s/HB3\(.\)ARG/HB1\1ARG/g s/HB3\(.\)ASN/HB1\1ASN/g s/HB3\(.\)ASP/HB1\1ASP/g s/HB3\(.\)CYS/HB1\1CYS/g s/HB3\(.\)GLN/HB1\1GLN/g s/HB3\(.\)GLU/HB1\1GLU/g s/HB3\(.\)HIS/HB1\1HIS/g s/HB3\(.\)LEU/HB1\1LEU/g s/HB3\(.\)LYS/HB1\1LYS/g s/HB3\(.\)MET/HB1\1MET/g s/HB3\(.\)MSE/HB1\1MSE/g s/HB3\(.\)PHE/HB1\1PHE/g s/HB3\(.\)PRO/HB1\1PRO/g s/HB3\(.\)SER/HB1\1SER/g s/HB3\(.\)TRP/HB1\1TRP/g s/HB3\(.\)TYR/HB1\1TYR/g s/HG3\(.\)ARG/HG1\1ARG/g s/HG3\(.\)GLN/HG1\1GLN/g s/HG3\(.\)GLU/HG1\1GLU/g s/HG3\(.\)LYS/HG1\1LYS/g s/HG3\(.\)MET/HG1\1MET/g s/HG3\(.\)MSE/HG1\1MSE/g s/HG3\(.\)PRO/HG1\1PRO/g s/HD3\(.\)ARG/HD1\1ARG/g s/HD3\(.\)LYS/HD1\1LYS/g s/HD3\(.\)PRO/HD1\1PRO/g s/HE3\(.\)LYS/HE1\1LYS/g s/HG13\(.\)ILE/HG11\1ILE/g ######sed -f pdb4coot.sed old.pdb > new.pdb
