Lab Journal - Task 5 (PAH)

Model calculation

Modeller

To use Modeller we follow the tutorial written by the students 2011.

• First the target sequence must be provided into PIR-format (2pah has one Lysine at the end and therefore is one aa longer than P00439???):

>P1;2pah
sequence:2pah:::::::0.00: 0.00
MSTAVLENPGLGRKLSDFGQETSYIEDNCNQNGAISLIFSLKEEVGALAKVLRLFEENDV
NLTHIESRPSRLKKDEYEFFTHLDKRSLPALTNIIKILRHDIGATVHELSRDKKKDTVPW
FPRTIQELDRFANQILSYGAELDADHPGFKDPVYRARRKQFADIAYNYRHGQPIPRVEYM
EEEKKTWGTVFKTLKSLYKTHACYEYNHIFPLLEKYCGFHEDNIPQLEDVSQFLQTCTGF
RLRPVAGLLSSRDFLGGLAFRVFHCTQYIRHGSKPMYTPEPDICHELLGHVPLFSDRSFA
QFSQEIGLASLGAPDEYIEKLATIYWFTVEFGLCKQGDSIKAYGAGLLSSFGELQYCLSE
KPKLLPLELEKTAIQNYTVTEFQPLYYVAESFNDAKEKVRNFAATIPRPFSVRYDPYTQR
IEVLDNTQQLKILADSINSEIGILCSALQKIK*

An example python script for template: 1j8u:

from modeller import *
env = environ()
aln = alignment(env)
mdl = model(env, file='1j8u.pdb', model_segment=('FIRST:@', 'END:'))
aln.append_model(mdl, align_codes='1j8u', atom_files='1j8u')
aln.append(file='target.pir', align_codes='2pah')
aln.align2d()
aln.check()
aln.write(file='/mnt/home/student/waldraffs/masterpracitcal/Task5/alignments/1j8u-2pah-2d.ali', alignment_format='PIR') 
aln.malign()
aln.check()
aln.write(file='/mnt/home/student/waldraffs/masterpracitcal/Task5/alignments/1j8u-2pah.ali', alignment_format='PIR')

from modeller import *
from modeller.automodel import *    
log.verbose()   
env = environ() 
a = automodel(env,
            alnfile  = '/mnt/home/student/waldraffs/masterpracitcal/Task5/alignments/1j8u-2pah.ali',   
            knowns   = '1j8u',              
            sequence = '2pah',
            assess_methods=(assess.DOPE, assess.GA341))
a.starting_model= 1                
a.ending_model  = 1                
a.make()