# Small error in the Tutorial for local HADDOCK2.4

**URL:** <https://ask.bioexcel.eu/t/small-error-in-the-tutorial-for-local-haddock2-4/2909>\
**Category:** HADDOCK\
**Created:** [May 6, 2021, 12:40pm UTC](https://ask.bioexcel.eu/t/small-error-in-the-tutorial-for-local-haddock2-4/2909 "2021-05-06T12:40:25Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![jbibbe](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/jbibbe/32/432_2.png) [@jbibbe](https://ask.bioexcel.eu/u/jbibbe)\
**Post date:** [May 6, 2021, 12:40pm UTC](https://ask.bioexcel.eu/t/small-error-in-the-tutorial-for-local-haddock2-4/2909/1 "2021-05-06T12:40:25Z")

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I am doing the “[Tutorial describing the use of a local version of HADDOCK2.4](https://www.bonvinlab.org/education/HADDOCK24/HADDOCK24-local-tutorial/#defining-restraints-for-docking)” and I think there’s a small error in the description of how to filter residues on their solvent accessibility. The text says that the HADDOCK server uses a 15% solvent accessibility as a cutoff (see below), but when you use FreeSASA and awk to filter residues, there seems to be a 40% cutoff. This 40% cutoff agrees with the explanation in the [support manual](https://www.bonvinlab.org/software/haddock2.2/generate_air_help/).

This is the text that says that the HADDOCK webserver uses a 15% cutoff:

> An important aspect is to filter both the active (the residues identified from your mapping experiment) and passive residues by their solvent accessibility. **Our webserver uses a default relative accessibility of 15% as cutoff**. This is not a hard limit. You might consider including even more buried residues if some important chemical group seems solvent accessible from a visual inspection.

This is what the text in the tutorial says, and I think the 15% is wrong here:

> The following command will return all residues with a relative SASA for either the backbone or the side-chain \> 15%:
> 
> ```
> awk '{if (NF==13 && $5>40) print $0; if (NF==14 && $6>40) print $0}' e2a_1F3G.rsa
> 
> ```

**Do I understand it correctly that 40% should be used?**

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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 6, 2021, 12:54pm UTC](https://ask.bioexcel.eu/t/small-error-in-the-tutorial-for-local-haddock2-4/2909/2 "2021-05-06T12:54:12Z")

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The server does filter the user input at 15% and defines automatically passive residues around those at the same cutoff.

There is no right or wrong value. We have indeed used 40% in the past when doing manual setup / definition of active residues.

The more restraints you define at the end the longer will the computations become.

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<div class="post-metadata">

**Author:** ![jbibbe](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/jbibbe/32/432_2.png) [@jbibbe](https://ask.bioexcel.eu/u/jbibbe)\
**Post date:** [May 6, 2021, 3:07pm UTC](https://ask.bioexcel.eu/t/small-error-in-the-tutorial-for-local-haddock2-4/2909/3 "2021-05-06T15:07:15Z")

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Thank you for your answer! I will try some cutoffs and see how long it takes.

The awk line does filter for \>40% and not 15% though, right?

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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 6, 2021, 3:26pm UTC](https://ask.bioexcel.eu/t/small-error-in-the-tutorial-for-local-haddock2-4/2909/4 "2021-05-06T15:26:22Z")

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> The awk line does filter for \>40% and not 15% though, right?

Yes

Also, always look at what you are selecting when working on your own system. Always good to visualise things first.