[modeller_usage] Re: 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
To:
Subject: [modeller_usage] Re: 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
From: Irawati Roy <>
Date: Sat, 11 Feb 2023 13:22:40 +0530
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 <
> 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
> --
> https://salilab.org/modeller/
> Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage
>
Hi Ben
I have tried the one you suggested:
for (pdb, chain) in (('UP1', 'A'), ('A1', 'X')): Â Â Â mdl = Model(env, file=pdb, Â Â Â Â Â Â Â 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: Â 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 Â Â Â 1 Â N Â LYS A Â 8 Â Â Â -1.918 Â 8.681 -21.146 Â 1.00 50.51 Â Â Â Â Â N Â ATOM Â Â Â 2 Â CA Â LYS A Â 8 Â Â Â -0.507 Â 8.878 -21.478 Â 1.00 48.22 Â Â Â Â Â C Â ATOM Â Â Â 3 Â C Â LYS A Â 8 Â Â Â 0.404 Â 8.527 -20.296 Â 1.00 47.11 Â Â Â Â Â C Â ATOM Â Â Â 4 Â O Â LYS A Â 8 Â Â Â 0.000 Â 8.625 -19.134 Â 1.00 48.46 Â Â Â Â Â O Â ATOM Â Â Â 5 Â CB Â LYS A Â 8 Â Â Â -0.247 Â 10.291 -22.004 Â 1.00 49.66 Â Â Â Â Â C Â ATOM Â Â Â 6 Â CG Â LYS A Â 8 Â Â Â 0.608 Â 10.308 -23.253 Â 1.00 51.85 Â Â Â Â Â C Â ATOM Â Â Â 7 Â CD Â LYS A Â 8 Â Â Â 0.814 Â 11.719 -23.780 Â 1.00 56.64 Â Â Â Â Â C Â ATOM Â Â Â 8 Â CE Â LYS A Â 8 Â Â Â 2.244 Â 11.918 -24.207 Â 1.00 58.15 Â Â Â Â Â C Â ATOM Â Â Â 9 Â NZ Â LYS A Â 8 Â Â Â 2.506 Â 13.325 -24.593 Â 1.00 62.88 Â Â Â Â Â N Â ATOM Â Â 10 Â N Â GLU A Â 9 Â Â Â 1.603 Â 8.032 -20.605 Â 1.00 37.26 Â Â Â Â Â N Â ATOM Â Â 11 Â CA Â GLU A Â 9 Â Â Â 2.583 Â 7.593 -19.614 Â 1.00 34.59 Â Â Â Â Â C Â ATOM Â Â 12 Â C Â GLU A Â 9 Â Â Â 3.103 Â 8.809 -18.815 Â 1.00 33.40 Â Â Â Â Â C Â ATOM Â Â 13 Â O Â GLU A Â 9 Â Â Â 3.270 Â 9.871 -19.423 Â 1.00 31.28 Â Â Â Â Â O Â ATOM Â Â 14 Â CB Â GLU A Â 9 Â Â Â 3.757 Â 6.847 -20.320 Â 1.00 35.61 Â Â Â Â Â C Â ATOM Â Â 15 Â CG Â GLU A Â 9 Â Â Â 3.337 Â 5.522 -20.971 Â 1.00 47.83 Â Â Â Â Â C Â ATOM Â Â 16 Â CD Â GLU A Â 9 Â Â Â 3.947 Â 5.111 -22.308 Â 1.00 66.95 Â Â Â Â Â C Â
A1.pdb
ATOM Â Â Â 1 Â N Â MET X Â 1 Â Â Â 43.720 Â 45.860 Â 63.480 Â 0.00 Â 0.00 Â Â Â Â Â Â ATOM Â Â Â 2 Â H1 Â MET X Â 1 Â Â Â 44.460 Â 45.570 Â 64.150 Â 0.00 Â 0.00 Â Â Â Â Â Â ATOM Â Â Â 3 Â H2 Â MET X Â 1 Â Â Â 42.750 Â 45.730 Â 63.840 Â 0.00 Â 0.00 Â Â Â Â Â Â ATOM Â Â Â 4 Â H3 Â MET X Â 1 Â Â Â 43.890 Â 45.180 Â 62.720 Â 0.00 Â 0.00 Â Â Â Â Â Â ATOM Â Â Â 5 Â CA Â MET X Â 1 Â Â Â 43.900 Â 47.280 Â 63.110 Â 0.00 Â 0.00 Â Â Â Â Â Â ATOM Â Â Â 6 Â HA Â MET X Â 1 Â Â Â 43.520 Â 47.850 Â 63.950 Â 0.00 Â 0.00 Â Â Â Â Â Â ATOM Â Â Â 7 Â CB Â MET X Â 1 Â Â Â 45.340 Â 47.790 Â 62.980 Â 0.00 Â 0.00 Â Â Â Â Â Â ATOM Â Â Â 8 Â HB1 MET X Â 1 Â Â Â 45.450 Â 48.870 Â 62.740 Â 0.00 Â 0.00 Â Â Â Â Â Â ATOM Â Â Â 9 Â HB2 MET X Â 1 Â Â Â 45.800 Â 47.630 Â 63.980 Â 0.00 Â 0.00 Â Â Â Â Â Â ATOM Â Â 10 Â CG Â MET X Â 1 Â Â Â 46.250 Â 47.060 Â 61.990 Â 0.00 Â 0.00 Â Â Â Â Â Â ATOM Â Â 11 Â HG1 MET X Â 1 Â Â Â 47.240 Â 47.350 Â 62.410 Â 0.00 Â 0.00 Â Â Â Â Â Â ATOM Â Â 12 Â HG2 MET X Â 1 Â Â Â 46.180 Â 45.950 Â 62.040 Â 0.00 Â 0.00 Â Â Â Â Â Â ATOM Â Â 13 Â SD Â MET X Â 1 Â Â Â 46.260 Â 47.620 Â 60.260 Â 0.00 Â 0.00 Â Â Â Â Â Â ATOM Â Â 14 Â CE Â MET X Â 1 Â Â Â 47.960 Â 47.000 Â 60.080 Â 0.00 Â 0.00 Â Â Â Â Â Â ATOM Â Â 15 Â HE1 MET X Â 1 Â Â Â 47.960 Â 45.900 Â 60.270 Â 0.00 Â 0.00 Â Â Â Â Â Â ATOM Â Â 16 Â HE2 MET X Â 1 Â Â Â 48.350 Â 47.180 Â 59.060 Â 0.00 Â 0.00 Â Â Â Â Â Â ATOM Â Â 17 Â HE3 MET X Â 1 Â Â Â 48.640 Â 47.540 Â 60.770 Â 0.00 Â 0.00 Â Â Â Â Â Â ATOM Â Â 18 Â C Â MET X Â 1 Â Â Â 43.020 Â 47.620 Â 61.960 Â 0.00 Â 0.00 Â Â Â Â Â Â ATOM Â Â 19 Â O Â MET X Â 1 Â Â Â 42.650 Â 46.780 Â 61.140 Â 0.00 Â 0.00 Â Â Â Â Â Â ATOM Â Â 20 Â N Â ALA X Â 2 Â Â Â 42.710 Â 48.920 Â 61.800 Â 0.00 Â 0.00Â Â Â Â
Thanks
Ira
On Sat, Feb 11, 2023 at 12:59 PM Modeller Caretaker <">> 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: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 0.00
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')):
>Â Â Â Â 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))