def Mutagenesis(kinase1, model, template,peptide_instance):
"""superposition the model and template, remove template and leave peptide behind """
"""replace peptide with instance peptide"""
list_name = peptide_instance
with open(input_data_folder+list_name,'r') as f:
instances = f.readlines()
instance = [x.strip() for x in instances]
print "your peptide: ", instance
for pep in instance:
cmd.delete('all')
cmd.fetch(model) # model_candidate, ex.chk1,chk2...
cmd.remove("hetatm") #remove the nonstandard residues
cmd.fetch(template) #mutagenesis template, ex.2phk
peptide_template = cmd.get_fastastr( "/"+template+'//B') #get the peptide from the template and generate another one for mutagenesis
peptide_template = peptide_template + 'G' #peptide of 2phk is 7 amino acid long, when our input peptide is 8 aa, we need to plus one character
for aa in peptide_template[6:].lower(): #creat template_peptide for mutagenesis
cmd._alt(aa)
firstaa = AAcode_1_to_3(peptide_template[6]) #translate template_peptide to 3 letter
low_firstaa = firstaa[0].lower()
cmd.alter(low_firstaa, 'chain = "B"') #select this template_peptide
cmd.show_as("cartoon")
cmd.align(model, template) #superpostion of model and template
cmd.align(low_firstaa,template) #superpostion of template_peptide and template
remove_part = "("+template+" and not resn ATP"+")"
cmd.select("remove_part",remove_part)
cmd.remove("remove_part") #remove the template except for ATP, there are only model and template_peptide
cmd.remove("resn hoh") #remove water
cmd.wizard("mutagenesis")
peptide_position = 0
for i in pep:
#the peptide_position starting point depends the first position of mutagenesis peptide
#pymol's peptide start from 1, not 0
mutagenesis_template = '/'+low_firstaa+ '///' + str(peptide_position + 2) # because of 2phk start at 2nd of peptide
#mutagenesis_template = '/' + template + '//B/' + str(peptide_position + 2)
cmd.get_wizard().do_select(mutagenesis_template) # select peptide position of mutation
replace_aminoacid = AAcode_1_to_3(pep)[peptide_position]
cmd.get_wizard().set_mode(replace_aminoacid) # select which residue want to mutate to
cmd.get_wizard().apply()
peptide_position += 1
filename = kinase1 + '_' + model + 'model_' + template + 'muta_' + pep + '.pdb' #build the canonical name
cmd.save(filename)
ATPchange(filename) #change ATP naming to the format of ATP.params
cmd.wizard(None)
return
def build_epz1_h():
"""Build epz1_h (epz1 with XL domains in alpha-helix)"""
cmd._alt('B'.lower()) # N-terminal actyl group
build_HP(0)
build_XL(1)
build_HP(0)
build_XL(1)
build_HP(0)
editor.attach_amino_acid('pk1', 'nhh')
cmd.save('/home/zyxue/labwork/pdb_backup/lele/epz1_h.pdb')
def build_XL(ssid=0):
"""
Build the cross-linking (XL) domain
:Parameters:
- `ssid`: secondary structure id
0: coil (default)
1: alpha-helix
2: antiparallel beta-sheet
3: parallel beta-sheet
"""
cmd.set('secondary_structure', ssid)
XL1 = 'AAAAAKAAKY'
linker = 'GVGTP'
XL2 = 'AAAAAKAAAKAAQF'
for aa in XL1:
cmd._alt(aa.lower())
# because of Pro in the linker, it has to be coil
cmd.set('secondary_structure', 0)
for aa in linker:
cmd._alt(aa.lower())
cmd.set('secondary_structure', ssid)
for aa in XL2:
cmd._alt(aa.lower())
def build_HP(ssid=0):
cmd.set('secondary_structure', ssid)
HP = 'GVPGVGVPGVGVPGVGVPGVGVPGVGVPGVGVPGV'
for aa in HP:
cmd._alt(aa.lower())
