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 enz1@pitt.edu