MantisBT - Rosetta
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0000056Rosetta[All Projects] Incorrect Resultspublic2012-08-01 09:192012-10-09 22:48
All platformsAnyAny
Backrub, any protocol with free N-Ca-C bond angle
0000056: mm_bend N-Ca-C mean value is too tight
The mean value of the mm_bend term N-Ca-C is set by the 107 in the CHARMM parameter set,

NH1 CT1 C 50.000 107.0000 ! ALLOW PEP POL ARO ALI

line 960, in rosetta_database/chemical/mm_atom_type_sets/fa_standard/par_all27_prot_na.prm

The mean observed value in the top8000 set from the pdb is at about 111.2. The mean value with the mm_bend term set to a weight of 1 has a mean value of about 110.1.

Consider using the ideal bond angles like the cart_bonded term.

There is logic to warn in the mm_bend term is turned on. This should also allow the use of the cart_bonded_term.
Using a Rosetta script protocol like this,

    <s weights=score12_full> <Reweight scoretype=mm_bend weight=1/> </s>
    <RestrictToRepacking name=rtrp/> <PreserveCBeta name=preserve_cb/>
     <MetropolisHastings name=mc scorefxn=s trials=10000>
  <Backrub sampling_weight=.75/>
  <Sidechain sampling_weight=0.25 task_operations=rtrp,preserve_cb/>
    <Add mover_name=mc/>

leads wrong distributions when doing a features analysis using the rosetta_tests/features/scripts/anslysis/plots/backbone_geometry/bond_angles.R analysis script

This was shown in the features analysis tutorial at RosettaCon 2012, so where ever the tutorials be come available look for the presentation there.

(Mantis gives an error if the feature request field is set to false, so I set it to true)

Note that this bug only affects the _last structures, not the lowest-energy ones. The latter are the default output of the backrub application and have native-like bond angles.
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pdf backbone_geometry_bond_angle_NCaC_by_ss_120730.pdf (36,595) 2012-08-01 09:19
Issue History
2012-08-01 09:19momearaNew Issue
2012-08-01 09:19momearaStatusnew => assigned
2012-08-01 09:19momearaAssigned To => amelie
2012-08-01 09:19momearaFile Added: backbone_geometry_bond_angle_NCaC_by_ss_120730.pdf
2012-10-09 22:48amelieDeveloper Options0,1 =>
2012-10-09 22:48amelieAdditional Information Updatedbug_revision_view_page.php?rev_id=37#r37

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