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Hi again :-)

I guess I spoke too soon.

The phenix.pdbtools command works as advertised, but the code I shared obviously (if I had cared to read it) changes MET to MSE.

Here is the correct version:
# code start
def mutate_all_mse_to_mets():
  mol_id=active_residue()[0]
  for ch_id in chain_ids(mol_id):
    for resn in range(0,chain_n_residues(ch_id,mol_id)):
      if (resname_from_serial_number(mol_id,ch_id,resn)=="MSE"):
        seqnum=seqnum_from_serial_number(mol_id,ch_id,resn)
        mutate(mol_id,ch_id,seqnum,'',"MET")
mutate_all_mse_to_mets()
# code end

I just tried it, and the script changes the coordinates of the mutated residues. The phenix.pdbtools version does not do that. Both methods seem to work though.

Best regards,
Folmer

2015-10-09 15:56 GMT+02:00 Folmer Fredslund <[log in to unmask]>:
Dear Eleanor,

I think it should be doable with this script by Oliver Clarke ([log in to unmask]" target="_blank">http:[log in to unmask])

Copy the code to a file and Calculate -> Run script

# code start
def mutate_all_mets_to_mse():
  mol_id=active_residue()[0]
  for ch_id in chain_ids(mol_id):
    for resn in range(0,chain_n_residues(ch_id,mol_id)):
      if (resname_from_serial_number(mol_id,ch_id,resn)=="MET"):
        seqnum=seqnum_from_serial_number(mol_id,ch_id,resn)
        mutate(mol_id,ch_id,seqnum,'',"MSE")
mutate_all_mets_to_mse()
# code end
There is also (if you are so inclined) phenix.pdbtools:
phenix.pdbtools convert_semet_to_met=true yourmodel.pdb
which works with the latest official version of phenix.

Best regards,
Folmer



2015-10-09 14:56 GMT+02:00 Eleanor Dodson <[log in to unmask]>:
Is there an easy way to mutate all MSE say to MET or do I have to do it one by one?
Eleanor



--
Folmer Fredslund



--
Folmer Fredslund