# PDB tools pdb\_fixinsert seems to delete residues from PDB files with insertion codes

**URL:** <https://ask.bioexcel.eu/t/pdb-tools-pdb-fixinsert-seems-to-delete-residues-from-pdb-files-with-insertion-codes/3120>\
**Category:** PDB-tools\
**Created:** [June 18, 2021, 10:05pm UTC](https://ask.bioexcel.eu/t/pdb-tools-pdb-fixinsert-seems-to-delete-residues-from-pdb-files-with-insertion-codes/3120 "2021-06-18T22:05:51Z")\
**Posts on this page:** 6\
**Page:** 1

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**Author:** ![dweis1](https://avatars.discourse-cdn.com/v4/letter/d/e9a140/32.png) [@dweis1](https://ask.bioexcel.eu/u/dweis1)\
**Post date:** [June 18, 2021, 10:05pm UTC](https://ask.bioexcel.eu/t/pdb-tools-pdb-fixinsert-seems-to-delete-residues-from-pdb-files-with-insertion-codes/3120/1 "2021-06-18T22:05:51Z")

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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

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<div class="post-metadata">

**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\
**Post date:** [June 19, 2021, 12:01pm UTC](https://ask.bioexcel.eu/t/pdb-tools-pdb-fixinsert-seems-to-delete-residues-from-pdb-files-with-insertion-codes/3120/2 "2021-06-19T12:01:40Z")

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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.

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**Author:** ![bjimenez](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/bjimenez/32/195_2.png) [@bjimenez](https://ask.bioexcel.eu/u/bjimenez)\
**Post date:** [June 21, 2021, 7:19am UTC](https://ask.bioexcel.eu/t/pdb-tools-pdb-fixinsert-seems-to-delete-residues-from-pdb-files-with-insertion-codes/3120/3 "2021-06-21T07:19:57Z")

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

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<div class="post-metadata">

**Author:** ![dweis1](https://avatars.discourse-cdn.com/v4/letter/d/e9a140/32.png) [@dweis1](https://ask.bioexcel.eu/u/dweis1)\
**Post date:** [June 22, 2021, 2:19pm UTC](https://ask.bioexcel.eu/t/pdb-tools-pdb-fixinsert-seems-to-delete-residues-from-pdb-files-with-insertion-codes/3120/4 "2021-06-22T14:19:43Z")

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Brian:

I had to re-run it:

[https://wenmr.science.uu.nl/pdbtools/run/3Io8Ovut](https://wenmr.science.uu.nl/pdbtools/run/3Io8Ovut)

–David

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**Author:** ![joaomcteixeira](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/joaomcteixeira/32/480_2.png) [@joaomcteixeira](https://ask.bioexcel.eu/u/joaomcteixeira)\
**Post date:** [June 25, 2021, 10:15am UTC](https://ask.bioexcel.eu/t/pdb-tools-pdb-fixinsert-seems-to-delete-residues-from-pdb-files-with-insertion-codes/3120/5 "2021-06-25T10:15:39Z")

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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,

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<div class="post-metadata">

**Author:** ![dweis1](https://avatars.discourse-cdn.com/v4/letter/d/e9a140/32.png) [@dweis1](https://ask.bioexcel.eu/u/dweis1)\
**Post date:** [June 25, 2021, 12:00pm UTC](https://ask.bioexcel.eu/t/pdb-tools-pdb-fixinsert-seems-to-delete-residues-from-pdb-files-with-insertion-codes/3120/6 "2021-06-25T12:00:28Z")

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Both chains yielded the same results.

Thanks for looking into this.