Hello

I am trying to build a model of a protein sequence where I have structure of two domains of the protein as an input. One structure is collected from PDB. another is simulation generated. I got the following error:

Traceback (most recent call last):
  File "align1.py", line 7, in <module>
    mdl = Model(env, file=pdb, model_segment=('FIRST:A', 'LAST:A'))
  File "/usr/lib/python3.8/dist-packages/modeller/model.py", line 101, in __init__
    self.read(**vars)
  File "/usr/lib/python3.8/dist-packages/modeller/model.py", line 151, in read
    return _modeller.mod_model_read2(self.modpt, io.modpt,
_modeller.ModellerError: rdpdb___303E> No atoms were read from the specified input PDB file, since the starting residue number and/or chain id in MODEL_SEGMENT (or the alignment file header) was not found; requested starting position: residue number " FIRST", chain " A"; atom file name:  A1.pdb

The simulation generated structure file looks like following:

ATOM      1  N   MET X   1      43.720  45.860  63.480  0.00  0.00            

ATOM      2  H1  MET X   1      44.460  45.570  64.150  0.00  0.00            

ATOM      3  H2  MET X   1      42.750  45.730  63.840  0.00  0.00            

ATOM      4  H3  MET X   1      43.890  45.180  62.720  0.00  0.00            

ATOM      5  CA  MET X   1      43.900  47.280  63.110  0.00  0.00            

ATOM      6  HA  MET X   1      43.520  47.850  63.950  0.00  0.00            

ATOM      7  CB  MET X   1      45.340  47.790  62.980  0.00  0.00            

ATOM      8  HB1 MET X   1      45.450  48.870  62.740  0.00  0.00                 

The code used is the following:

from modeller import *

env = environ()
aln = alignment(env)
env.io.hetatm = True
for (pdb, chain) in (('UP1', 'A'), ('A1', 'X')):
    mdl = Model(env, file=pdb, model_segment=('FIRST:A', 'LAST:X'))
    aln.append_model(mdl, atom_files=pdb, align_codes=pdb)
aln.append(file='query1.ali', align_codes='query')
aln.malign()
aln.write(file='querytemplate_new.ali', alignment_format='PIR')
aln.write(file='querytemplate_new.pap', alignment_format='PAP')

Any help regarding how to solve this error will be great.

Thanks

Ira