Re: [modeller_usage] Mismatch between residues of alignment and pdb
To: Sunidhi <>,
Subject: Re: [modeller_usage] Mismatch between residues of alignment and pdb
From: Modeller Caretaker <>
Date: Fri, 30 Oct 2020 12:24:47 -0700
On 10/30/20 1:01 AM, Sunidhi wrote:
I downloaded the pdb_95.pir files, updated on May 14th 2020, from here
<https://salilab.org/modeller/downloads/pdb_95.pir.gz>. I used the
tutorial <https://salilab.org/modeller/tutorial/basic.html> to model one
chain of a protein. I downloaded the pdb structure from RCSB-PDB. No
changes done from my side in either files. Firstly, I was receiving an
error " 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 " 1", chain " "; atom file name: 1r42A.pdb".
I can't see how this could be possible because pdb_95.pir contains the
following header for 1r42A:
This will instruct Modeller to read ATOM/HETATM records from the 1r42
structure file, starting at residue 19 in chain A and ending at residue
615 in chain A. The error message you show could only happen if the
header were modified to read something like
The alignment section of stated structure -
>P1;1r42A
structure:1r42A: 19:A: 596: :::-1.00:-1.00
This is also not what's in the original file. It tells Modeller to read
residues starting at 19 in chain A, and ending at residue 596 in a chain
with no ID. Since there is no such residue, it will continue to the end
of the file, reading the B through E chains, and that won't match your
alignment sequence, of course.