PDB tools pdb_fixinsert seems to delete residues from PDB files with insertion codes

PDB-tools
1

I am running into problems using PDB-Tools on an antibody structure, 1HZH, that uses insertion codes and has missing residues (no diffraction).

The final PDB generated by the pipeline is missing residues. The first missing residue is P54 which is before any of the insertion codes.

Here is my pipeline:
{
“pipeline”: [
{
“id”: “pdb_fixinsert_1”,
“tool”: “pdb_fixinsert”,
“args”: [
{
“field”: “selection_1_text”,
“value”: “”
}
]
},
{
“id”: “pdb_selchain_2”,
“tool”: “pdb_selchain”,
“args”: [
{
“field”: “chain_ids_2_text”,
“value”: “H”
}
]
},
{
“id”: “pdb_fixinsert_3”,
“tool”: “pdb_fixinsert”,
“args”: [
{
“field”: “selection_3_text”,
“value”: “”
}
]
},
{
“id”: “pdb_reres_5”,
“tool”: “pdb_reres”,
“args”: [
{
“field”: “starting_5_text”,
“value”: “1”
}
]
}
]
}

1HZH_H_original_sequence
QVQLVQSGAEVKKPGASVKVSCQASGYRFSNFVIHWVRQAPGQRFEWMGWINPYNGNKEFSAKFQDRVTFTADTSANTAYMELRSLRSADTAVYYCARVGPYSWDDSPQDNYYMDVWGKGTTVIVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKAEPKSCDKTHTCPPCPAPELLGGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQPREPQVYTLPPSRDELTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSPGK
1HZH_H_PDB_Tools_after_pipeline
QVQLVQSGAEVKKPGASVKVSCQASGYRFSNFVIHWVRQAPGQRFEWMGWINYNGNKEFSAKFQDRVTFTADTSANTAYMELSRSADTAVYYCARVGPYSWDPDYMDVWGKGTTVIVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKAEPKSCDKTHTCPPCPAPELLGGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQPREPQVYTLPPSRDELTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQ QGNVFSCSVMHEALHNHYTQKSLSLSPGK

2

Thanks David - we will look into this.

A local install of pdb-tools does not seem to give this problem.
We need to check our server installation.

3

Hi,
Could you please share with us the url of the job from the PDB-Tools web server?

4

Brian:

I had to re-run it:

https://wenmr.science.uu.nl/pdbtools/run/3Io8Ovut

–David

5

Hi @dweis1 ,

Thanks for your feedback. We are currently looking on what is happening with 1HZH. Insertion codes are tricky and not all PDBs follow the conventions. We need to finish some deadlines this week, but we will address your issue during the next few days. Stay tuned, and sorry for the delays.

Meanwhile, I see in your first example you define chain H. But on the last link you selected chain K. Could you help us clarify? Maybe there are issues with both chains we need to review nonetheless.

Thanks and Cheers,

6

Both chains yielded the same results.

Thanks for looking into this.