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[modeller_usage] ALIGN_CODES(i) error, Again

Hello Modeller people,

I realize this error has been posted repeatedly and I have tried to check for all possible solutions mentioned but I still can't do it right.
My alignment filename is   2nwx_ASCT.ali   and my pdb filename is   2nwx_A.pdb   so the names and letter cases match exactly.

The error I'm getting is:
ModellerError: read_al_373E> Protein specified in ALIGN_CODES(i) was not found in the alignment file; ALIGN_CODES(       2) =  ASCT

The script and alignment files are below.

Thank you in advance for the help

Elia Zumot


The script I use with modeller version 9.10 on Linux is:

from modeller import *
from modeller.automodel import *

env = environ()

def do_align():
	a = automodel(env, alnfile='2nwx_ASCT.ali',
              knowns='2nwx_A', sequence='ASCT',
              assess_methods=(assess.DOPE, assess.GA341))
	a.starting_model = 1
	a.ending_model = 5
	a.make()

do_align()


and my alignment file (2nwx_ASCT.ali) is:

>P1;2nwx_A
structure:2nwx_A.pdb:4:A:416:A::::
EYPVLQKILIGLILGAIVGLILGHYGYAHAVHTYVKPFGDLFVRLLKMLVMPIVFASLVVGAASISPAR-
LGRVGVKIVVYYLLTSAFAVTLGIIMARLFNPGAGIHLAVGG---------QQFQPHQAPPLVHILLDIV
PTNPFGALANG----------------------------------------------------QVLPTIF
FAIILGIAITYLMNSENEKVRKSAETLLDAINGLAEAMYKIVNGVMQYAPIGVFALIAYVMAEQG--VHV
VGELAKVTAAVYVGLTLQILLVYFVLLKIY-GIDPISFIKHAKDAMLTAFVTRSSSGTLPVTMRVAKE-M
GISEGIYSFTLPLGATINMDGTALYQGVCTFFIANALGSHLTVGQQLTIVLTAVLASIGTAGVPGAGAIM
LAMVLHSVGLPLTDPNVAAAYAMILGIDAILDMGRTMVNVTGDLTGTAIVAKTE*


>P2;ASCT
sequence:ASCT:4:::::::
RNAFVLLTVTAVIVGTILGFTLRPYRMSYREVKYFSFPGELLMRMLQMLVLPLIISSLVTGMAAL-DSKA
SGKMGMRAVVYYMTTTIIAVVIGIIIVIIIHPGKGTKENMH-------REGKIVRVTAADAFLDLIRNMF
PPNLVEASFKQFKTNYEKRSFKVPIQANETLVGAVINNVSEAMETLTRITEELVPVPGSVNGVNALGLVV
FSMAFGFVIGNMK--------EQGQALREFFDSLNEAIMRLVAVIMWYAPVGILFLIAGKIVEMEDMGVI
GGQLAMYTVTVIVGLLIHAVIVLPLLYFLVTRKNPWVFIGGLLQALITALGTSSSSATLPITFKGLEENN
GVDKRVTRFVLPVGATINMDGTALYEALAAIFIAQVNNFELNFGQIITISITATAASIGAAGIPQAGLVT
MVIVLTSVGLPTDD------ITLIIAVDWFLDRLRTTTNVLGDSLGAGILHHLN*








Elia Zomot, PhD
Computational and Systems Biology Department
School of Medicine, University of Pittsburgh
3089 BST3, 3501 Fifth Ave, Pittsburgh, PA 15213
Voice: 412 624 8699 - Fax: 412 648 3163