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 Håkansson wrote:
> Regarding protons in coot version 0.5,
>
> I am using shelx to refine my 1.2 Å 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 Håkansson, Ph.D.
> >> tel: +46 (0) 76 8585 706
> >> Senior Scientist, Max-lab, Lund University
> >> fax: +46 46 222 47 10
> >> Ole Römers väg 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
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