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
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:Â A1.pdb
The simulation generated structure file looks like following:
ATOMÂ Â Â 1Â NÂ Â MET XÂ Â 1Â Â Â 43.720Â 45.860Â 63.480Â 0.00Â 0.00Â Â Â Â Â Â Â
ATOMÂ Â Â 2Â H1Â MET XÂ Â 1Â Â Â 44.460Â 45.570Â 64.150Â 0.00Â 0.00Â Â Â Â Â Â Â
ATOMÂ Â Â 3Â H2Â MET XÂ Â 1Â Â Â 42.750Â 45.730Â 63.840Â 0.00Â 0.00Â Â Â Â Â Â Â
ATOMÂ Â Â 4Â H3Â MET XÂ Â 1Â Â Â 43.890Â 45.180Â 62.720Â 0.00Â 0.00Â Â Â Â Â Â Â
ATOMÂ Â Â 5Â CAÂ MET XÂ Â 1Â Â Â 43.900Â 47.280Â 63.110Â 0.00Â 0.00Â Â Â Â Â Â Â
ATOMÂ Â Â 6Â HAÂ MET XÂ Â 1Â Â Â 43.520Â 47.850Â 63.950Â 0.00Â 0.00Â Â Â Â Â Â Â
ATOMÂ Â Â 7Â CBÂ MET XÂ Â 1Â Â Â 45.340Â 47.790Â 62.980Â 0.00Â 0.00Â Â Â Â Â Â Â
ATOMÂ Â Â 8Â HB1 MET XÂ Â 1Â Â Â 45.450Â 48.870Â 62.740Â 0.00Â 0.00Â Â Â Â Â Â Â Â Â
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