Hi! Sorry for the very basic question, but again I'm facing issues with MODELLER.
When I run MODELLER I got the following error:
"*_modeller.ModellerError: read_al_373E> Protein specified in ALIGN_CODES(i) was not found in the alignment file; ALIGN_CODES( 1) = 6KG7.pdb*"
But my structure file is present in my directory:
*(base) [medfpo@uol-pc-301925 hPIEZO2_structure]$ ls -l 6KG7.pdb -rw-r--r--. 1 medfpo Domain Users 1177728 Mar 31 13:25 6KG7.pdb*
I don't have any idea what's the problem. I didn't misspell any name and the structure file is present. I included one line: *env.io.atom_files_directory = ['.'], *but It didn't change the output error. I included below my script file and alignment file. Thank you in advance.
This is my script below:
*from modeller import *from modeller.automodel import *import syslog.verbose()env = environ()aln = alignment(env)aln.append(file='align.pir', align_codes=('target', 'template1'))# directories for input atom filesenv.io.atom_files_directory = ['.']*
*a = automodel(env, alnfile = 'align.pir', # alignment filename knowns = ('6KG7.pdb'), # codes of the templates sequence = 'target', assess_methods = (assess.DOPE, assess.GA341))a.starting_model = 1 a.ending_model = 5 a.make()# RANK MODELS ACCORDING DOPE score # Get a list of all successfully built models from a.outputs ok_models = [x for x in a.outputs if x['failure'] is None]# Rank the models by DOPE score key = 'DOPE score'if sys.version_info[:2] == (2,3): # Python 2.3's sort doesn't have a key argument ok_models.sort(lambda a,b: cmp(a[key], b[key])) else: ok_models.sort(key=lambda a: a[key])# Get top model m = ok_models[0]print("Top model: %s (DOPE score %.3f)" % (m['name'], m[key]))*
and the first 5 lines of my alignment file:
(
*base) [medfpo@uol-pc-301925 hPIEZO2_structure]$ head -5 align.pir >P1;template1structure:6KG7.pdb:8:A:2822:A:::-1.00:-1.00-------GLIFRLLLPICLAVACAFRYNGLSFVYLIYLLLIPLFSEPTKATMQGHTGRLLQSLCITSLSFLLLHIIFHI------------------------------------------VFVPDIGMFIASLTIWLVCRT----------------------------------------------------------LRRFASVASKLKEFIGNMITTAGKV*