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
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
On 2/10/23 10:10 PM, Irawati Roy via modeller_usage wrote: > 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: ... > _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
You have asked Modeller to read residues from chain 'A', but your PDB file only has atoms in chain 'X'.
> for (pdb, chain) in (('UP1', 'A'), ('A1', 'X')): > mdl = Model(env, file=pdb, model_segment=('FIRST:A', 'LAST:X'))
This will read atoms from each PDB file starting at the first residue in chain A and continuing until it reaches the last residue in chain X. This is probably not what you meant. Perhaps you meant something like the following instead:
for (pdb, chain) in (('UP1', 'A'), ('A1', 'X')): mdl = Model(env, file=pdb, model_segment=('FIRST:'+chain, 'LAST:'+chain))
Ben Webb, Modeller Caretaker
Hi Ben
I have tried the one you suggested:
for (pdb, chain) in (('UP1', 'A'), ('A1', 'X')): mdl = Model(env, file=pdb, model_segment=('FIRST:'+chain, 'LAST:'+chain))
I have got a similar error but with the first .pdb file now.
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 " +chain"; atom file name: UP1.pdb
The UP1.pdb file has A chain and A1.pdb file has X chain. How can I make the modeller read these two at one go? For convenience, I am attaching excerpts from both the .pdb files.
*UP1.pdb* ATOM 1 N LYS A 8 -1.918 8.681 -21.146 1.00 50.51 N ATOM 2 CA LYS A 8 -0.507 8.878 -21.478 1.00 48.22 C ATOM 3 C LYS A 8 0.404 8.527 -20.296 1.00 47.11 C ATOM 4 O LYS A 8 0.000 8.625 -19.134 1.00 48.46 O ATOM 5 CB LYS A 8 -0.247 10.291 -22.004 1.00 49.66 C ATOM 6 CG LYS A 8 0.608 10.308 -23.253 1.00 51.85 C ATOM 7 CD LYS A 8 0.814 11.719 -23.780 1.00 56.64 C ATOM 8 CE LYS A 8 2.244 11.918 -24.207 1.00 58.15 C ATOM 9 NZ LYS A 8 2.506 13.325 -24.593 1.00 62.88 N ATOM 10 N GLU A 9 1.603 8.032 -20.605 1.00 37.26 N ATOM 11 CA GLU A 9 2.583 7.593 -19.614 1.00 34.59 C ATOM 12 C GLU A 9 3.103 8.809 -18.815 1.00 33.40 C ATOM 13 O GLU A 9 3.270 9.871 -19.423 1.00 31.28 O ATOM 14 CB GLU A 9 3.757 6.847 -20.320 1.00 35.61 C ATOM 15 CG GLU A 9 3.337 5.522 -20.971 1.00 47.83 C ATOM 16 CD GLU A 9 3.947 5.111 -22.308 1.00 66.95 C
*A1.pdb* 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
Thanks Ira
On Sat, Feb 11, 2023 at 12:59 PM Modeller Caretaker < modeller-care@salilab.org> wrote:
> On 2/10/23 10:10 PM, Irawati Roy via modeller_usage wrote: > > 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: > ... > > _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 > > You have asked Modeller to read residues from chain 'A', but your PDB > file only has atoms in chain 'X'. > > > for (pdb, chain) in (('UP1', 'A'), ('A1', 'X')): > > mdl = Model(env, file=pdb, model_segment=('FIRST:A', 'LAST:X')) > > This will read atoms from each PDB file starting at the first residue in > chain A and continuing until it reaches the last residue in chain X. > This is probably not what you meant. Perhaps you meant something like > the following instead: > > for (pdb, chain) in (('UP1', 'A'), ('A1', 'X')): > mdl = Model(env, file=pdb, > model_segment=('FIRST:'+chain, 'LAST:'+chain)) > > Ben Webb, Modeller Caretaker > -- > modeller-care@salilab.org https://salilab.org/modeller/ > Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage >
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Irawati Roy -
Modeller Caretaker