Dear Users
Hello
I am trying to build a model of a protein sequence where I have structures of two domains of the same 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 ATOM 9 HB2 MET X 1 45.800 47.630 63.980 0.00 0.00 ATOM 10 CG MET X 1 46.250 47.060 61.990 0.00 0.00 ATOM 11 HG1 MET X 1 47.240 47.350 62.410 0.00 0.00 ATOM 12 HG2 MET X 1 46.180 45.950 62.040 0.00 0.00 ATOM 13 SD MET X 1 46.260 47.620 60.260 0.00 0.00 ATOM 14 CE MET X 1 47.960 47.000 60.080 0.00 0.00 ATOM 15 HE1 MET X 1 47.960 45.900 60.270 0.00 0.00 ATOM 16 HE2 MET X 1 48.350 47.180 59.060 0.00 0.00 ATOM 17 HE3 MET X 1 48.640 47.540 60.770 0.00 0.00 ATOM 18 C MET X 1 43.020 47.620 61.960 0.00 0.00 ATOM 19 O MET X 1 42.650 46.780 61.140 0.00 0.00 ATOM 20 N ALA X 2 42.710 48.920 61.800 0.00 0.00 ATOM 21 HN ALA X 2 43.190 49.580 62.370 0.00 0.00 ATOM 22 CA ALA X 2 42.060 49.460 60.650 0.00 0.00 ATOM 23 HA ALA X 2 41.530 48.650 60.160 0.00 0.00 ATOM 24 CB ALA X 2 41.310 50.730 61.090 0.00 0.00 ATOM 25 HB1 ALA X 2 41.940 51.410 61.700 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