chainid = ' '
for i in range(len(lines)):
line = lines[i]
if len(line) > 5 and line[:6] == 'ENDMDL': break # Its an NMR model.
chainid = [i for i in chainid]
if (line[21] in chainid or ignorechain or removechain):
line_edit = line
if line[0:3] == 'TER':
continue
elif (line[0:6] == 'HETATM'):
ok = False
# Is it a modified residue ?
if modres.has_key(line[17:20]):
# if so replace it with its canonical equivalent !
line_edit = 'ATOM '+line[6:17]+modres[line[17:20]] + line[20:]
modifiedres = modifiedres + line[17:20] + ', '
# dont count MSEs as modiied residues (cos they're so common and get_pdb deal with them previosuly)
if line[17:20] != "MSE":
shit_stat_modres = True
ok = True
# other substitution (of atoms mainly)
if (line[17:20] == 'MSE'): # Selenomethionine
if (line_edit[12:14] == 'SE'):
line_edit = line_edit[0:12]+' S'+line_edit[14:]
if len(line_edit) > 75:
if (line_edit[76:78] == 'SE'):
line_edit = line_edit[0:76]+' S'+line_edit[78:]
if chainid == '_':
chainid = ' '
for line in lines:
if line.startswith('ENDMDL'): break # Only take the first NMR model
if len(line) > 21 and ( line[21] in chainid or options.allchains):
if line[0:4] != "ATOM" and line[0:6] != 'HETATM':
continue
line_edit = line
resn = line[17:20]
# Is it a modified residue ?
# (Looking for modified residues in both ATOM and HETATM records is deliberate)
if modres.has_key(resn):
# if so replace it with its canonical equivalent !
orig_resn = resn
resn = modres[resn]
line_edit = 'ATOM '+line[6:17]+ resn + line[20:]
if orig_resn == "MSE":
# don't count MSE as modified residues for flagging purposes (because they're so common)
# Also, fix up the selenium atom naming
if (line_edit[12:14] == 'SE'):
line_edit = line_edit[0:12]+' S'+line_edit[14:]
if len(line_edit) > 75:
if (line_edit[76:78] == 'SE'):
line_edit = line_edit[0:76]+' S'+line_edit[78:]
else:
shit_stat_modres = True
chainid = ' ' for i in range(len(lines)): line = lines[i] if len(line)>5 and line[:6]=='ENDMDL':break #Its an NMR model. if (chainid == line[21] or ignorechain): line_edit = line if line[0:3] == 'TER': continue elif (line[0:6] == 'HETATM'): ok = False ## Is it a modified residue ? if modres.has_key( line[17:20] ): ## if so replace it with its canonical equivalent ! line_edit = 'ATOM '+line[6:17]+modres[line[17:20]] +line[20:] modifiedres = modifiedres + line[17:20] + ', ' ## dont count MSEs as modiied residues (cos they're so common and get_pdb deal with them previosuly) if line[17:20] != "MSE": shit_stat_modres = True ok = True ## other substitution (of atoms mainly) if (line[17:20]=='MSE'): #Selenomethionine if (line_edit[12:14] == 'SE'): line_edit = line_edit[0:12]+' S'+line_edit[14:] if len(line_edit)>75: if (line_edit[76:78] == 'SE'): line_edit = line_edit[0:76]+' S'+line_edit[78:]
chainid = " "
for line in lines:
if line.startswith("ENDMDL"):
break # Only take the first NMR model
if len(line) > 21 and (line[21] in chainid or options.allchains):
if line[0:4] != "ATOM" and line[0:6] != "HETATM":
continue
line_edit = line
resn = line[17:20]
# Is it a modified residue ?
# (Looking for modified residues in both ATOM and HETATM records is deliberate)
if modres.has_key(resn):
# if so replace it with its canonical equivalent !
orig_resn = resn
resn = modres[resn]
line_edit = "ATOM " + line[6:17] + resn + line[20:]
if orig_resn == "MSE":
# don't count MSE as modified residues for flagging purposes (because they're so common)
# Also, fix up the selenium atom naming
if line_edit[12:14] == "SE":
line_edit = line_edit[0:12] + " S" + line_edit[14:]
if len(line_edit) > 75:
if line_edit[76:78] == "SE":
line_edit = line_edit[0:76] + " S" + line_edit[78:]
else:
shit_stat_modres = True