Hi Jan,
One of the little extensions I have written for coot (which you can download
from: https://www.dropbox.com/s/0b4bebwxw0p9x0e/oli_custom.py?dl=0 or at
cootscripts.tiddlyspace.com), might be handy for this (in the script it is the
function mutate_by_resnum).
It does not align the sequence for you, but if you have a pre-aligned sequence
(that is, the numbering matches your structure - paste in the whole seq
including the starting Met (which should equate to residue 1 in your
structure)) you can paste your sequence into the little text box that pops up,
and it will mutate every non-matching residue in the active chain (the one you
are centered on). It will automatically strip any non-sequence residues from
the input, and the sequence is not case-sensitive. The script for this function
alone is appended to this email.
Hope this helps,
Oliver.
Script follows:
def mutate_by_resnum():
def enter_seq(seq):
seq=str(seq).upper()
seq.replace(" ", "")
seq_dic={}
len_seq=len(seq)
n=0
nmax=len_seq+1
aa_dic={'A':'ALA','R':'ARG','N':'ASN','D':'ASP','C':'CYS','E':'GLU',
'Q':'GLN','G':'GLY','H':'HIS','I':'ILE','L':'LEU','K':'LYS','M':'MET',
'F':'PHE','P':'PRO','S':'SER','T':'THR','W':'TRP','Y':'TYR','V':'VAL'}
clean_seq=''
while (n<len_seq):
if ((not seq.isalpha()) and (seq[n].isalpha())):
clean_seq=clean_seq+seq[n]
n=n+1
seq=clean_seq
len_seq=len(seq)
n=0
while (n<len_seq):
value=aa_dic[seq[n]]
seq_dic[n+1]=value
n=n+1
mol_id=active_residue()[0]
ch_id=active_residue()[1]
sn=0
last_sn=chain_n_residues(ch_id,mol_id)-1
turn_off_backup(mol_id)
while (sn<=last_sn):
res=resname_from_serial_number(mol_id,ch_id,sn)
seqnum=seqnum_from_serial_number(mol_id,ch_id,sn)
ins_id=str(insertion_code_from_serial_number(mol_id,ch_id,sn))
if ((res in aa_dic.values()) or (res=="MSE")) and (res!=seq_dic[seqnum]):
mutate(mol_id,ch_id,seqnum,ins_id,seq_dic[seqnum])
delete_residue_sidechain(mol_id,ch_id,seqnum,ins_id,0)
sn=sn+1
turn_on_backup(mol_id)
generic_single_entry("Enter raw amino acid sequence (must be complete!)",
"MLKYG","Mutate active chain to match sequence using PDB numbering",
enter_seq)
add_simple_coot_menu_menuitem(menu,
"Mutate active chain to template sequence (numbering must match sequence!)",
lambda func: mutate_by_resnum())
