# Pdb\_validate & pdb\_tidy

**URL:** <https://ask.bioexcel.eu/t/pdb-validate-pdb-tidy/5274>\
**Category:** PDB-tools\
**Created:** [September 27, 2024, 2:26pm UTC](https://ask.bioexcel.eu/t/pdb-validate-pdb-tidy/5274 "2024-09-27T14:26:08Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![Beril](https://avatars.discourse-cdn.com/v4/letter/b/6de8d8/32.png) [@Beril](https://ask.bioexcel.eu/u/Beril)\
**Post date:** [September 27, 2024, 2:26pm UTC](https://ask.bioexcel.eu/t/pdb-validate-pdb-tidy/5274/1 "2024-09-27T14:26:08Z")

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Hello,

I have a small question regarding pdb\_tidy. I want my pdb file to comply with the required numbers of white spaces. I guess I only need to use pdb\_validate and pdb\_tidy. I am loading my pdb file to PDBTools, and adding only pdb\_validate from the main tool selection for the pipeline. Although I tried adding pre- and post-processing tools that would end up with the same result (pdb\_splitchain, pdb\_validate, pdb\_merge), I could not utilize pdb\_validate and pdb\_tidy. I could not figure out what I am doing wrong.

Thank you for your time and consideration!

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**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:** [October 2, 2024, 3:05pm UTC](https://ask.bioexcel.eu/t/pdb-validate-pdb-tidy/5274/2 "2024-10-02T15:05:06Z")

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If pdb\_tidy does not work, you could try reading it in e.g. Pymol or Chimera and exporting it again as a PDB format.

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**Author:** ![Beril](https://avatars.discourse-cdn.com/v4/letter/b/6de8d8/32.png) [@Beril](https://ask.bioexcel.eu/u/Beril)\
**Post date:** [October 5, 2024, 11:35am UTC](https://ask.bioexcel.eu/t/pdb-validate-pdb-tidy/5274/3 "2024-10-05T11:35:38Z")

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Hello Professor,

Thank you so much for your reply! I edited manually according to the following link: [PDB format - Plouf](https://cupnet.net/pdb-format/) This was presented in another reply ([Ligand Formatting - #2 by VGPReys](https://ask.bioexcel.eu/t/ligand-formatting/5275/2)) . I edited my ligands accordingly, and now the docking jobs were queued on HADDOCK server successfully. I went back and tried to use PDB-Tools Web once more to check whether I can use validate tool for ligands I generated. I uploaded my pdb and used only pdb\_validate, checked Tidy mark, and clicked Run. I got the following error: " **Last tool output is not PDB format and tidy cannot be applied**" . Then, I used the tool without marking Tidy and got the result. Thank you so much for your time and help!