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