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Add criteria for Omega dihedral #154

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
Just like DR criteria use a fraction and a cutoff.

Original issue reported on code.google.com by jurge...@gmail.com on 6 Apr 2009 at 1:47

GoogleCodeExporter commented 9 years ago 
Actually modified the current criteria to a criteria on RMS instead of MAX.

# CING note that since revision 546 the criteria are checked against the rms 
average viol but renaming has been postponed.
# Will be named OMEGA_RMSALL_XXXX in the future. Average/S.d. from hi-res 
structures is 179.6 +/- 4.7 degrees.
# Wilson et al. Who checks the checkers? Four validation tools applied to eight 
atomic resolution structures. J Mol Biol (1998) vol. 276 pp. 417-436 
#Defaults: 15,20 before. Now the defaults are reduced to: 2 and 3 times s.d.: 
9.4 and 14.1.
OMEGA_MAXALL_POOR = 9.4
OMEGA_MAXALL_BAD  = 14.1

Results for omega between residue 20 and 21:
NB in CING the omega is assigned to residue 20 and not 21 such as IUPAC 
recommends and Procheck does! I would say this is a violation of conventions.

DEBUG: found residue <Residue GLUH20> model 0 omega to violate from square 
trans/cis:    7.953 (omega:  171.647)
DEBUG: found residue <Residue GLUH20> model 1 omega to violate from square 
trans/cis:    0.202 (omega:  179.802)
DEBUG: found residue <Residue GLUH20> model 2 omega to violate from square 
trans/cis:    1.117 (omega:  178.483)
DEBUG: found residue <Residue GLUH20> model 3 omega to violate from square 
trans/cis:   12.311 (omega:  167.289)
DEBUG: found residue <Residue GLUH20> model 4 omega to violate from square 
trans/cis:    2.963 (omega:  176.637)
DEBUG: found residue <Residue GLUH20> model 5 omega to violate from square 
trans/cis:    6.544 (omega:  173.056)
DEBUG: found residue <Residue GLUH20> model 6 omega to violate from square 
trans/cis:   11.157 (omega:  168.443)
DEBUG: found residue <Residue GLUH20> model 7 omega to violate from square 
trans/cis:    1.077 (omega:  180.677)
DEBUG: found residue <Residue GLUH20> model 8 omega to violate from square 
trans/cis:    4.278 (omega:  175.322)
DEBUG: found residue <Residue GLUH20> model 9 omega to violate from square 
trans/cis:    9.584 (omega:  170.016)
DEBUG: found residue <Residue GLUH20> model 10 omega to violate from square 
trans/cis:    4.880 (omega:  174.720)
DEBUG: found residue <Residue GLUH20> model 11 omega to violate from square 
trans/cis:    5.604 (omega:  173.996)
DEBUG: found residue <Residue GLUH20> model 12 omega to violate from square 
trans/cis:   12.972 (omega:  166.628)
DEBUG: found residue <Residue GLUH20> model 13 omega to violate from square 
trans/cis:    7.795 (omega:  171.805)
DEBUG: found residue <Residue GLUH20> model 14 omega to violate from square 
trans/cis:    3.444 (omega:  176.156)
DEBUG: found residue <Residue GLUH20> model 15 omega to violate from square 
trans/cis:    1.911 (omega:  177.689)
DEBUG: found residue <Residue GLUH20> model 16 omega to violate from square 
trans/cis:    2.551 (omega:  177.049)
DEBUG: found residue <Residue GLUH20> model 17 omega to violate from square 
trans/cis:    9.225 (omega:  170.375)
DEBUG: found residue <Residue GLUH20> model 18 omega to violate from square 
trans/cis:    4.931 (omega:  174.669)
DEBUG: found residue <Residue GLUH20> model 19 omega to violate from square 
trans/cis:    5.113 (omega:  174.487)
DEBUG: found rmsViol:    6.875
DEBUG: found residue <Residue LYSx21> model 0 omega to violate from square 
trans/cis:   22.915 (omega:  156.685)
DEBUG: found residue <Residue LYSx21> model 1 omega to violate from square 
trans/cis:   11.374 (omega:  168.226)
DEBUG: found residue <Residue LYSx21> model 2 omega to violate from square 
trans/cis:   10.920 (omega:  168.680)
DEBUG: found residue <Residue LYSx21> model 3 omega to violate from square 
trans/cis:    7.522 (omega:  172.078)
DEBUG: found residue <Residue LYSx21> model 4 omega to violate from square 
trans/cis:   24.218 (omega:  155.382)
DEBUG: found residue <Residue LYSx21> model 5 omega to violate from square 
trans/cis:    9.071 (omega:  170.529)
DEBUG: found residue <Residue LYSx21> model 6 omega to violate from square 
trans/cis:   14.149 (omega:  165.451)
DEBUG: found residue <Residue LYSx21> model 7 omega to violate from square 
trans/cis:   12.450 (omega:  167.150)
DEBUG: found residue <Residue LYSx21> model 8 omega to violate from square 
trans/cis:   16.920 (omega:  162.680)
DEBUG: found residue <Residue LYSx21> model 9 omega to violate from square 
trans/cis:   17.630 (omega:  161.970)
DEBUG: found residue <Residue LYSx21> model 10 omega to violate from square 
trans/cis:    9.653 (omega:  169.947)
DEBUG: found residue <Residue LYSx21> model 11 omega to violate from square 
trans/cis:   15.467 (omega:  164.133)
DEBUG: found residue <Residue LYSx21> model 12 omega to violate from square 
trans/cis:    9.657 (omega:  169.943)
DEBUG: found residue <Residue LYSx21> model 13 omega to violate from square 
trans/cis:   12.347 (omega:  167.253)
DEBUG: found residue <Residue LYSx21> model 14 omega to violate from square 
trans/cis:   13.481 (omega:  166.119)
DEBUG: found residue <Residue LYSx21> model 15 omega to violate from square 
trans/cis:   11.712 (omega:  167.888)
DEBUG: found residue <Residue LYSx21> model 16 omega to violate from square 
trans/cis:   10.574 (omega:  169.026)
DEBUG: found residue <Residue LYSx21> model 17 omega to violate from square 
trans/cis:    9.515 (omega:  170.085)
DEBUG: found residue <Residue LYSx21> model 18 omega to violate from square 
trans/cis:   14.495 (omega:  165.105)
DEBUG: found residue <Residue LYSx21> model 19 omega to violate from square 
trans/cis:    9.407 (omega:  170.193)
DEBUG: found rmsViol:   13.873

In short, I think it is ok now. The next omega e.g. should still be flagged as 
it is now:
ORANGE: [OMEGA] value 13.873 > 9.400 (3.0 times known s.d. of 4.7 degrees)

Committed in revision 547.

Original comment by jurge...@gmail.com on 7 Apr 2009 at 12:52

GoogleCodeExporter commented 9 years ago 
Issue 72 has been merged into this issue.

Original comment by jurge...@gmail.com on 8 Apr 2009 at 7:18

GoogleCodeExporter commented 9 years ago 
Considering our discussion yesterday I propose to do this criteria the same as 
the other checks from What If. 
Calculate a per residue per model Z-score (number of 
times the known sd) and average over the models. The average Z-score is then 
compared to the thresholds. 
Consider the below thresholds for the other What If 
criteria:

WI_RAMCHK_POOR =  -1.0
WI_RAMCHK_BAD  =  -1.3

WI_C12CHK_POOR =  -0.9
WI_C12CHK_BAD  =  -1.2

Then most likely the omega cutoff will be similar, ok? 1brv values for first 
model below.

What If report on omega follows:

------------------------------------------------------------------------
Omega average and std. deviation= 176.935 7.524
Significant deviations from expected 5.5!!!
------------------------------------------------------------------------
# 58 # Warning: Omega angle restraints not strong enough
========================================================
The omega angles for trans-peptide bonds in a structure is
expected to give a gaussian distribution with the average around
+178 degrees, and a standard deviation around 5.5. In the current
structure the standard deviation of this distribution is above 7.0,
which indicates that the omega values have been under-constrained.

 Standard deviation of omega values : 1.368
------------------------------------------------------------------------

ID        : model_000.pdb
CheckID   : RAMCHK
 Program  : WHAT IF
 Version  : 6.0 (20080412-0930)
 Text     : Ramachandran check
 DocURL   : http://swift.cmbi.ru.nl/whatif/
 Date     : 2009-02-11
  Level   : RESIDUE   
   LText  : The following list contains per-residue Z-scores describing
   LText  : how well each residue fits into the allowed areas of the
   LText  : Ramachandran plot.
   Type   : FLOAT     
   Poor   : <   -3.00
   Bad    : <   -4.00
   Name   : A- 172-PRO
    Value : -0.547
   Name   : A- 173-CYS
    Value : -0.061
   Name   : A- 174-SER
    Value : -0.879
   Name   : A- 175-THR
    Value : -1.106
   Name   : A- 176-CYS
    Value :  0.180
   Name   : A- 177-GLU
    Value : -0.748
   Name   : A- 178-GLY
    Value : -0.005
   Name   : A- 179-ASN
    Value : -0.348
   Name   : A- 180-LEU
    Value : -0.941
   Name   : A- 181-ALA
    Value : -1.019
   Name   : A- 182-CYS
    Value : -0.410
   Name   : A- 183-LEU
    Value : -0.588
   Name   : A- 184-SER
    Value :  0.184
   Name   : A- 185-LEU
    Value : -1.080
   Name   : A- 186-CYS
    Value :  0.099
   Name   : A- 187-HIS
    Value : -0.489
   Name   : A- 188-ILE
    Value : -0.131

ID        : model_000.pdb
CheckID   : C12CHK
 Program  : WHAT IF
 Version  : 6.0 (20080412-0930)
 Text     : Chi-1/chi-2 rotamer normality check
 DocURL   : http://swift.cmbi.ru.nl/whatif/
 Date     : 2009-02-11
  Level   : RESIDUE   
   LText  : The following list contains per-residue Z-scores describing
   LText  : how well each rotamer fits into the common areas of the
   LText  : chi-2/chi-2 correlation plot.
   Type   : FLOAT     
   Poor   : <   -3.00
   Bad    : <   -4.00
   Name   : A- 171-VAL
    Value : -0.932
   Name   : A- 173-CYS
    Value : -0.871
   Name   : A- 174-SER
    Value : -0.598
   Name   : A- 175-THR
    Value : -0.807
   Name   : A- 176-CYS
    Value : -0.516
   Name   : A- 177-GLU
    Value :  0.552
   Name   : A- 179-ASN
    Value : -0.928
   Name   : A- 180-LEU
    Value : -1.289
   Name   : A- 182-CYS
    Value : -0.815
   Name   : A- 183-LEU
    Value : -0.636
   Name   : A- 184-SER
    Value : -0.465
   Name   : A- 185-LEU
    Value : -1.251
   Name   : A- 186-CYS
    Value : -0.793
   Name   : A- 187-HIS
    Value : -0.789
   Name   : A- 188-ILE
    Value : -0.184
   Name   : A- 189-GLU
    Value : -0.977

Original comment by jurge...@gmail.com on 8 Apr 2009 at 7:33

GoogleCodeExporter commented 9 years ago 
Implemented.

Original comment by jurge...@gmail.com on 27 May 2009 at 9:47