# iRMSD calculation - HADDOCK 2.4 web server

**URL:** <https://ask.bioexcel.eu/t/irmsd-calculation-haddock-2-4-web-server/2401>\
**Category:** HADDOCK\
**Created:** [August 16, 2020, 3:21pm UTC](https://ask.bioexcel.eu/t/irmsd-calculation-haddock-2-4-web-server/2401 "2020-08-16T15:21:31Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![bdorgna](https://avatars.discourse-cdn.com/v4/letter/b/3da27b/32.png) [@bdorgna](https://ask.bioexcel.eu/u/bdorgna)\
**Post date:** [August 16, 2020, 3:21pm UTC](https://ask.bioexcel.eu/t/irmsd-calculation-haddock-2-4-web-server/2401/1 "2020-08-16T15:21:32Z")

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Hi all,

I have a question about how the iRMSD is calculated for runs performed using the HADDOCK 2.4 web server.

All information I have found online suggests that something like a crystal structure is used as a reference for iRMSD calculation. My question is, what is the reference structure used during a server run and when no crystal structure is available? Also, can I find the reference structure in the tar file of my run?

Thanks

Ben

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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:** [August 16, 2020, 4:04pm UTC](https://ask.bioexcel.eu/t/irmsd-calculation-haddock-2-4-web-server/2401/2 "2020-08-16T16:04:38Z")

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The top ranked model is used as reference in all cases.