0000056: mm_bend N-Ca-C mean value is too tight

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0000056

Rosetta

[All Projects] Incorrect Results

public

2012-08-01 09:19

2012-10-09 22:48

Reporter

momeara

Assigned To

amelie

Priority

normal

Severity

major

Reproducibility

always

Status

assigned

Resolution

open

Platform

All platforms

Any

OS Version

Any

Product Version

All

Fixed in Version

Summary

0000056: mm_bend N-Ca-C mean value is too tight

Description

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.

Steps To Reproduce

Using a Rosetta script protocol like this,

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

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

Additional Information

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.

Tags

No tags attached.

Application(s) Affected

Backrub, any protocol with free N-Ca-C bond angle

Command Line Used

backrub.<platofrm>

Developer Options

Fixed in SVN Version

Attached Files

backbone_geometry_bond_angle_NCaC_by_ss_120730.pdf [^] (36,595 bytes) 2012-08-01 09:19

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Issue History
Date Modified	Username	Field	Change
2012-08-01 09:19	momeara	New Issue
2012-08-01 09:19	momeara	Status	new => assigned
2012-08-01 09:19	momeara	Assigned To	=> amelie
2012-08-01 09:19	momeara	File Added: backbone_geometry_bond_angle_NCaC_by_ss_120730.pdf
2012-10-09 22:48	amelie	Developer Options	0,1 =>
2012-10-09 22:48	amelie	Additional Information Updated	View Revisions