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
--
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