[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

[Modeller Caretaker <>]

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/
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