Re: [modeller_usage] Mismatch between residues of alignment and pdb

[Modeller Caretaker <modeller-care@ucsf.edu>]

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:

>P1;1r42A
structureX:1r42:19:A:615:A:[long name]:[long source]: 2.20: 0.23

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

>P1;1r42A
structureX:1r42A:1::[res]:[chain]:[long name]:[long source]: 2.20: 0.23

That won't match of course because there is no residue 1 in a chain with 
no ID in that file.

> Ideally the pdb_95.pir file should have the same info as pdbs

It does - in fact it is generated from the PDB files. You can even run 
the scripts yourself; see
https://salilab.org/modeller/wiki/Rebuilding%20sequence%20databases

> 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.

	Ben Webb, Modeller Caretaker
--
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