On 23/03/2017 17:55, Mark Saper wrote:
I have a situation where I manually edited my PDB file to rename MET to MSE,
then made
the appropriate change to change all “ SD" atoms in MSE to “SE “. When I
optimize the
geometry with Real Space Refine Zone, the amide proton (H) moves several Å way
I get this too (after mutating to MSE in coot) - it's because there is an inconsistency in
the dictionary. Most amino acids have a dictionary according to their polypeptide form, but
MSE dictionary is a peptide with monomer Hydrogen atoms.
Noted, thanks.
Work around is to hand-edit the MSE.cif dictionary. Rename HN1 to HN, copy the H-N bond
length and angle of H, N, CA from MET.cif and delete HN2.
and the
Torsions error goes to 2.24.
Do you get bad torsions when you idealize too?
Paul.
