Closed GoogleCodeExporter closed 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
Issue 72 has been merged into this issue.
Original comment by jurge...@gmail.com
on 8 Apr 2009 at 7:18
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
Implemented.
Original comment by jurge...@gmail.com
on 27 May 2009 at 9:47
Original issue reported on code.google.com by
jurge...@gmail.com
on 6 Apr 2009 at 1:47