Dear Modeller team,
I'm trying to get the format right for a multiple alignment, I did in
HHpred server to use as input to modeller. I don't understand the error
messages. I don't know if the errors are related to the PDB file since I
have not changed anything in original PDB unless the extension. I would
appreciate very much your advice.
Thanks in advance for your help!
Maryam
***The input python script:
# Comparative modeling by the automodel class
from modeller import * # Load standard Modeller classes
from modeller.automodel import * # Load the automodel class
log.verbose() # request verbose output
env = environ() # create a new MODELLER environment to build this model in
# directories for input atom files
env.io.atom_files_directory = ['.', '../atom_files']
a = automodel(env,
alnfile = 'XPF_nuc.ali', # alignment filename
knowns = '1j23','4bxo', # codes of the templates
sequence = 'XPF') # code of the target
a.starting_model= 1 # index of the first model
a.ending_model = 1 # index of the last model
# (determines how many models to
calculate)
a.make() # do the actual comparative modeling
***The run command:
mod9.11 model_test1.py
***atom_files:
$ ls -l
total 952
-rw-r--r-- 1 mfaridou users 121905 Aug 25 23:07 1j23.atm
-rw-r--r-- 1 mfaridou users 121905 Aug 25 23:08 1j23.pdb
-rw-r--r-- 1 mfaridou users 362313 Aug 25 23:08 4bxo.atm
-rw-r--r-- 1 mfaridou users 362313 Aug 25 23:08 4bxo.pdb
*** input file XPF_nuc.ali
>P1;1j23
structurex:1j23:5:A:125:A:HEFnuclease:Pyrococcus furiosus:1.78:0.248
QEGVKVVVDSRELRSEVVKRLKLLGVKLEVKTLDVGDYIISEDVAIERKSANDLIQSIIDGGLFDQVKRLKEAYSRPIMIVEGS-LY---------GIRNVHPNAIRGAIAAVTVDF-GVPIIFSSTPEETAQYI*
>P1;4bxo
structurex:4bxo:1:A:151:A:FANCMprotein:Homo sapiens:2.15:0.255
GSGSRPHLAGTHTSLRLPQEGKGTCILVGGHEITSGLEVISSLRAIHGLQVEVCPLNGCDYIVSNRMVVERRSQSEMLNSVNKNKFIEQIQHLQSMFERICVIVEKDREKTGD------TSRMFRRTKSYDSLLTTLIGA-GIRILFSSCQEETADLL*
>P1;XPF
sequence:XPF:.:.:156:.::0.00: 0.00
RGTASADVSTDTRKAGGQEQNGTQQSIVVDMREFRSELPSLIHRRGIDIEPVTLEVGDYILTPEMCVERKSISDLIGSLNNGRLYSQCISMSRYYKRPVLLIEFDPSKPFSLTSRGALFQEISSNDISSKLTLLTLHFPRLRILWCPSPHATAELF*
***The runtime messages:
'import site' failed; use -v for traceback
Traceback (most recent call last):
File "model_test1.py", line 18, in ?
a.make() # do the actual comparative modeling
File
"/home/software/software//modeller_v9.11/modlib/modeller/automodel/automodel.py",
line 96, in make
self.homcsr(exit_stage)
File
"/home/software/software//modeller_v9.11/modlib/modeller/automodel/automodel.py",
line 423, in homcsr
self.check_alignment(aln)
File
"/home/software/software//modeller_v9.11/modlib/modeller/automodel/automodel.py",
line 405, in check_alignment
aln.check()
File
"/home/software/software//modeller_v9.11/modlib/modeller/alignment.py",
line 197, in check
self.check_structure_structure(io=io)
File
"/home/software/software//modeller_v9.11/modlib/modeller/alignment.py",
line 206, in check_structure_structure
return f(self.modpt, io.modpt, self.env.libs.modpt, eqvdst)
_modeller.SequenceMismatchError: read_te_291E> Sequence difference between
alignment and pdb :
