# Point Mutaion on 4-chain protein

**URL:** <https://ask.bioexcel.eu/t/point-mutaion-on-4-chain-protein/3432>\
**Category:** HADDOCK\
**Created:** [January 25, 2022, 3:28pm UTC](https://ask.bioexcel.eu/t/point-mutaion-on-4-chain-protein/3432 "2022-01-25T15:28:41Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![Deniz](https://avatars.discourse-cdn.com/v4/letter/d/3da27b/32.png) [@Deniz](https://ask.bioexcel.eu/u/Deniz)\
**Post date:** [January 25, 2022, 3:28pm UTC](https://ask.bioexcel.eu/t/point-mutaion-on-4-chain-protein/3432/1 "2022-01-25T15:28:41Z")

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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)

Dear Haddoc Users, Hi,

I am new here. I want to make point mutation on my 4-chain protein. I have already run the “ _pdb\_mutate.py_ ” script for each chain separately and obtained the four pdb files.

How can I proceed from here? Specifically, how can my system recover the missing atoms?

If I use the link below (and enter the # of molecules 4), the program asks me about the active residues.

[https://wenmr.science.uu.nl/haddock2.4/submit/1](https://wenmr.science.uu.nl/haddock2.4/submit/1)

If you could help me, I would appreciate.  
Best regards,  
Deniz

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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:** [January 25, 2022, 3:56pm UTC](https://ask.bioexcel.eu/t/point-mutaion-on-4-chain-protein/3432/2 "2022-01-25T15:56:20Z")

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Do you just want to use haddock to generate the mutations?

Then simply use the refinement interface of the server:

[https://wenmr.science.uu.nl/haddock2.4/refinement/1](https://wenmr.science.uu.nl/haddock2.4/refinement/1)

Submit your mutated model and haddock will generate all missing atoms and refine the model

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**Author:** ![Deniz](https://avatars.discourse-cdn.com/v4/letter/d/3da27b/32.png) [@Deniz](https://ask.bioexcel.eu/u/Deniz)\
**Post date:** [January 26, 2022, 9:00am UTC](https://ask.bioexcel.eu/t/point-mutaion-on-4-chain-protein/3432/3 "2022-01-26T09:00:11Z")

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Dear Prof. Bonvin,  
Thanks for your quick reply.  
Yes, I just want to use haddock to generate the point mutation at each chain.  
I uploaded the mutated model to the link you sent, then I chose the “Water Refinement” protocol.  
Haddock generated 4 models; however, the z score of the cluster-1 is zero. Would this be a problem?  
Best regards,

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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:** [January 26, 2022, 10:16am UTC](https://ask.bioexcel.eu/t/point-mutaion-on-4-chain-protein/3432/4 "2022-01-26T10:16:08Z")

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By definition the z-score will be zero if you have only one point (cluster)

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**Author:** ![Deniz](https://avatars.discourse-cdn.com/v4/letter/d/3da27b/32.png) [@Deniz](https://ask.bioexcel.eu/u/Deniz)\
**Post date:** [January 26, 2022, 10:37am UTC](https://ask.bioexcel.eu/t/point-mutaion-on-4-chain-protein/3432/5 "2022-01-26T10:37:30Z")

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Thank you.  
Sincerely,  
Deniz