# Error while uploading a structure for refinement

**URL:** <https://ask.bioexcel.eu/t/error-while-uploading-a-structure-for-refinement/5706>\
**Category:** HADDOCK\
**Tags:** support\
**Created:** [May 28, 2025, 2:03pm UTC](https://ask.bioexcel.eu/t/error-while-uploading-a-structure-for-refinement/5706 "2025-05-28T14:03:22Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![Jana](https://avatars.discourse-cdn.com/v4/letter/j/258eb7/32.png) [@Jana](https://ask.bioexcel.eu/u/Jana)\
**Post date:** [May 28, 2025, 2:03pm UTC](https://ask.bioexcel.eu/t/error-while-uploading-a-structure-for-refinement/5706/1 "2025-05-28T14:03:23Z")

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I generated a 3D structure of the mevalonate kinase with Mg2+, ATP and mevalonate (its substrate). I then run the pdb tool to isolate each chain and then merge them again in an ensemble to make the document compatible.

Problem is I think an internal one, the page doesn’t indicate any error when I submit it but it just keeps on refreshing and I’m not able to submit to refinement the structure.  
I checked the pdb and it looks fine on ChimeraX and PyMol and works well. No error is shown, just the page is refreshing everytime I click on submit.

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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:** [May 29, 2025, 9:13am UTC](https://ask.bioexcel.eu/t/error-while-uploading-a-structure-for-refinement/5706/2 "2025-05-29T09:13:58Z")

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does the problem occurs also on a different web browser ?

And otherwise share your PDB file

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**Author:** ![Jana](https://avatars.discourse-cdn.com/v4/letter/j/258eb7/32.png) [@Jana](https://ask.bioexcel.eu/u/Jana)\
**Post date:** [May 30, 2025, 7:33am UTC](https://ask.bioexcel.eu/t/error-while-uploading-a-structure-for-refinement/5706/3 "2025-05-30T07:33:49Z")

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Morning,  
Tried with different brosers like FireFox, Safari and Chrom, nothing seems to work.

How would you like me to send you the pdb file ? Because I cannot upload anything here, maybe by e-mail if you share it with me ?

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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:** [June 5, 2025, 8:26am UTC](https://ask.bioexcel.eu/t/error-while-uploading-a-structure-for-refinement/5706/4 "2025-06-05T08:26:53Z")

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The problem with your PDB file is that you have defined multiple MODELs in it. If you want to refine your complex combining the two ligands and the magnesium they should be in the same MODEL. You probably merged those files using Chimera, which wrongly defining multiple models. See the uploaded test.pdb file - this one goes through fine in the refinement interface 🙂  
[test.pdb](https://ask.bioexcel.eu/uploads/short-url/vBqNfdvaA5BNlRuMOmxgs0f0axJ.pdb) (228.7 KB)

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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:** [June 5, 2025, 8:28am UTC](https://ask.bioexcel.eu/t/error-while-uploading-a-structure-for-refinement/5706/5 "2025-06-05T08:28:05Z")

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PS: In the way you define the chains, the HADDOCK score will be calculated from the energies between chains A and B, A and F and B and F (only interchain interactions are considered).