# 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 call for template: 1j8u: <figtable id="mod_pyt">

``````from modeller import *
env = environ()
aln = alignment(env)
mdl = model(env, file='/mnt/home/student/waldraffs/masterpracitcal/Task5/1j8u.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()
```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() `````` ````Swissmodel``iTasser``Model evaluation`
``` ```