# Different violation results in ana\_noe\_viol\_all.list and ana\_noe\_viol\_ambig.lis

**URL:** <https://ask.bioexcel.eu/t/different-violation-results-in-ana-noe-viol-all-list-and-ana-noe-viol-ambig-lis/293>\
**Category:** HADDOCK\
**Created:** [February 9, 2017, 8:35am UTC](https://ask.bioexcel.eu/t/different-violation-results-in-ana-noe-viol-all-list-and-ana-noe-viol-ambig-lis/293 "2017-02-09T08:35:32Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![greatea](https://avatars.discourse-cdn.com/v4/letter/g/c0e974/32.png) [@greatea](https://ask.bioexcel.eu/u/greatea)\
**Post date:** [February 9, 2017, 8:35am UTC](https://ask.bioexcel.eu/t/different-violation-results-in-ana-noe-viol-all-list-and-ana-noe-viol-ambig-lis/293/1 "2017-02-09T08:35:32Z")

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Dear all,

I defined 6 active residues for Haddock2.2, so I have 6 ambiguous restraints and NO unambiguous restraint or Hbond restraint.

After docking, in the it1/water/analysis fold, there are two files:

ana\_noe\_viol\_all.lis is for the violations of ambiguous restraints and unambiguous restraints.

ana\_noe\_viol\_ambig.lis is for the violations of ambiguous restraints.

Because I only defined 6 ambiguous restraints, these two files should be the same. But the files gave me different Rave and violations, and only part of the ambiguous restraints is present in ana\_noe\_viol\_ambig.lis, while all of 6 ambiguous restraints is present in ana\_noe\_viol\_all.lis.

For ana\_noe\_viol\_all.lis,  
Rexp= 2.000 Rave= 2.916 Viol= -0.916 #viol= 275 ( A 102  
Rexp= 2.000 Rave= 2.352 Viol= -0.352 #viol= 335 ( A 12  
Rexp= 2.000 Rave= 2.309 Viol= -0.309 #viol= 244 ( B 272  
Rexp= 2.000 Rave= 2.284 Viol= -0.284 #viol= 159 ( A 103  
Rexp= 2.000 Rave= 2.096 Viol= -0.096 #viol= 128 ( B 106  
Rexp= 2.000 Rave= 2.094 Viol= -0.094 #viol= 15 ( B 273

For ana\_noe\_viol\_ambig.lis  
Rexp= 2.000 Rave= 3.099 Viol= -1.099 #viol= 75 ( A 102  
Rexp= 2.000 Rave= 3.002 Viol= -1.002 #viol= 26 ( A 12  
Rexp= 2.000 Rave= 2.715 Viol= -0.715 #viol= 18 ( B 272  
Rexp= 2.000 Rave= 2.343 Viol= -0.343 #viol= 47 ( A 103

Why?

Thanks a lot for your help!

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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:** [February 9, 2017, 4:34pm UTC](https://ask.bioexcel.eu/t/different-violation-results-in-ana-noe-viol-all-list-and-ana-noe-viol-ambig-lis/293/2 "2017-02-09T16:34:42Z")

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For the first analysis with all restraints the cutoff for printing violations is set to 0.025 to have a long list while it is 0.3A for the individuals sets…

I would not worry about a violation of 0.1A 🙂

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**Author:** ![greatea](https://avatars.discourse-cdn.com/v4/letter/g/c0e974/32.png) [@greatea](https://ask.bioexcel.eu/u/greatea)\
**Post date:** [February 10, 2017, 4:55am UTC](https://ask.bioexcel.eu/t/different-violation-results-in-ana-noe-viol-all-list-and-ana-noe-viol-ambig-lis/293/3 "2017-02-10T04:55:20Z")

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Thanks for your reply!

There are fewer (only 4) restraints in ana\_noe\_viol\_ambig.lis, because the #violations of the other 2 restraints is 0, which will not be list in the file?

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<div class="post-metadata">

**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:** [February 10, 2017, 10:51am UTC](https://ask.bioexcel.eu/t/different-violation-results-in-ana-noe-viol-all-list-and-ana-noe-viol-ambig-lis/293/4 "2017-02-10T10:51:31Z")

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for the ana\_noe\_viol\_ambig.lis, only violation \> 0.3A are listed, which is why the others are not showing.