Dear Modeller users!
I've followed 1st modeller tutorial making alignment of my target against 1 template (with the inclusion of hetatm from the template). As the result I've obtained the below alignment
>P1;2rh1A
structureX:2rh1.pdb: 29 :A:+283 :A:::-1.00:-1.00
---------DEVWVVGMGIVMS----------LIVLAIVFGNVLVITAIAKFERLQTVTNYFITSLACADLVMGL
AVVPFGAAHILMKMWTFGNFWCEFWTSIDVLCVTASIETLCVIAVDRYFAITSPFKYQSLLTKNKARVIILMVWI
VSGLTSFLPIQ-MH--WYRATHQE-----AINCYAEETCCDFFTNQAYAIASSIVSFYVPLVIMVFVYSRVFQEA
KRQLKFCLKEHKALKTLGIIMGTFTLCWLPFFIVNIVHVIQDNLIRKEVYILLNWIGYVNSGFNPLIYC-RSPDF
RIAFQELLCL------.*
>P1;od_r
sequence:od_r: : : : ::: 0.00: 0.00
MEGKNLTSISECFLLGFSEQLEEQKPLFGSFLFMYLVTVAGNLLIILVIITDTQLHTPMYFFLANLSLADACFVS
TTVPKMLANIQIQSQAISYSGCLLQLYFFMLFVMLEAFLLAVMAYDCYVAICHPLHYILIMSPGLCIFLVSASWI
MNALHSLLHTLLMNSLSFCANHEIPHFFCDINPLLSLSCTDPFTNELVIFITGGLTGLICVLCLIISYTNVFSTI
LKIPSA-QGKRKAFSTCSSHLSVVSLFFGTSFCVDFSSPSTHSAQKDTVASVMYTV--VTPMLNPFIYSLRNQEI
KSSLRKLIWVRKIHSP-*
where Od_r is the modeled protein and 2rh1 is the template consisted of ligand ('.' in aliugn file)
now I'm running script for making models (where ligand should be included from the template and obtain error about atom mismatches
from modeller import *
from modeller.automodel import *
# Read in HETATM records from template PDBs
env.io.hetatm = True
env.io.hydrogen= True
# directories for input atom files
env.io.atom_files_directory = ['.', './results']
env = environ()
a = automodel(env, alnfile='result.ali',
knowns='2rh1A', sequence='od_r',
assess_methods=(assess.DOPE,
assess.GA341))
a.starting_model = 1
a.ending_model = 10
a.make()
return f(self.modpt, io.modpt, self.env.libs.modpt, eqvdst)
_modeller.ModellerError: read_te_290E> Number of residues in the alignment and pdb files are different: 283 282 For alignment entry: 1 2rh1A
how it could be fixed and obtain models with the ligands in the positions identical to the templates ?