# Need help to number atoms sequentially **URL:** \ **Category:** HADDOCK\ **Created:** [November 24, 2025, 6:27am UTC](https://ask.bioexcel.eu/t/need-help-to-number-atoms-sequentially/5957 "2025-11-24T06:27:55Z")\ **Posts on this page:** 8\ **Page:** 1
**Author:** ![Vibes](https://avatars.discourse-cdn.com/v4/letter/v/ecb155/32.png) [@Vibes](https://ask.bioexcel.eu/u/Vibes)\ **Post date:** [November 24, 2025, 6:27am UTC](https://ask.bioexcel.eu/t/need-help-to-number-atoms-sequentially/5957/1 "2025-11-24T06:27:55Z")
The HADDOCK category is meant to discuss any HADDOCK-related issue. For general information about HADDOCK refer to [HADDOCK – Bonvin Lab](http://www.bonvinlab.org/software/haddock2.4) Hi, I want to renumber the atom sequentially like H, H1, H2 etc. I tried pdb tools function Pdb\_uniquename and pdb\_reres but it deletes almost all atoms and my ligand becomes fragmented. What should I do? I have attached the orginal pdb file and pdb file after using pdb tools. Please suggest. ![image](https://europe1.discourse-cdn.com/flex013/uploads/bioexcel/original/2X/e/ee2d30d3b8a7a992a3dc10987930b507a4d7b30a.png) ![image](https://europe1.discourse-cdn.com/flex013/uploads/bioexcel/original/2X/4/42ea4373e9978cc93a93127dacdf09364cae7b03.png) ---
**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:** [November 24, 2025, 7:59am UTC](https://ask.bioexcel.eu/t/need-help-to-number-atoms-sequentially/5957/2 "2025-11-24T07:59:33Z")
pdb\_uniquename should do the trick. No need for pdb\_reres ---
**Author:** ![Vibes](https://avatars.discourse-cdn.com/v4/letter/v/ecb155/32.png) [@Vibes](https://ask.bioexcel.eu/u/Vibes)\ **Post date:** [November 24, 2025, 9:09am UTC](https://ask.bioexcel.eu/t/need-help-to-number-atoms-sequentially/5957/3 "2025-11-24T09:09:58Z")
The pdb\_uniquename returns the pdb file by deleting all repetitive atoms. Ligand is fragmented in the output. How can I correct this? ![image](https://europe1.discourse-cdn.com/flex013/uploads/bioexcel/original/2X/4/42ea4373e9978cc93a93127dacdf09364cae7b03.png) ---
**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:** [November 24, 2025, 10:54am UTC](https://ask.bioexcel.eu/t/need-help-to-number-atoms-sequentially/5957/4 "2025-11-24T10:54:00Z")
Can you share your ligand file? Are you using the PDB-tools pdb\_uniqname tool (or some other tool called pdb\_uniq **ue** name)? I just tested pdb\_uniqname and it is working fine, not deleting atoms… ---
**Author:** ![Vibes](https://avatars.discourse-cdn.com/v4/letter/v/ecb155/32.png) [@Vibes](https://ask.bioexcel.eu/u/Vibes)\ **Post date:** [November 25, 2025, 8:22am UTC](https://ask.bioexcel.eu/t/need-help-to-number-atoms-sequentially/5957/7 "2025-11-25T08:22:52Z")
Hi, Thank you for sending through the pdb file. How did you change this? I have several ligands that I need to edit in the same way ---
**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:** [November 25, 2025, 9:22am UTC](https://ask.bioexcel.eu/t/need-help-to-number-atoms-sequentially/5957/8 "2025-11-25T09:22:20Z")
simply using a local installation of pdb-tools ([https://github.com/haddocking/pdb-tools](https://github.com/haddocking/pdb-tools)) and with as command: `pdb_uniqname NH1.pdb >NH1-renamed.pdb ` ---
**Author:** ![Vibes](https://avatars.discourse-cdn.com/v4/letter/v/ecb155/32.png) [@Vibes](https://ask.bioexcel.eu/u/Vibes)\ **Post date:** [November 26, 2025, 4:39am UTC](https://ask.bioexcel.eu/t/need-help-to-number-atoms-sequentially/5957/9 "2025-11-26T04:39:33Z")
is there any way to do this using the web based pdb tools? The installation instructions says python is required and I have no idea about it. ---
**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:** [November 26, 2025, 8:52pm UTC](https://ask.bioexcel.eu/t/need-help-to-number-atoms-sequentially/5957/10 "2025-11-26T20:52:52Z")
I just checked the server and it seems it is filtering similar atom names within one residue, which is not happening at the command line level. This is coming from biopython used in the server. I opened an issue about it, but don’t know when it will be solved. If you are going to do a lot of modelling, it is worth investing time to learn about Linux and command line