Novel_R diffraction data analysis

Relevant web site:

Reference:

Kay Diederichs & P. Andrew Karplus, Nature Str. Biol. 4 (4): 269 - 275 (1997).  Improved R-factors for diffraction data analysis in macromolecular crystallography.
 

Summary:


Uses scalepack data processed as no merge original index to generate relevant statistics, including Rmeas, Rmrgd, redundancy, and overall I/sigI.  Suggested as a more objective assessment of data quality since it factors in redundancy in calculating Rmeas.
 

Sample run:

< 32 otter /SOLVE/NOVELR> which novelr
novelr:          aliased to /max2/people/dbuckler/NOVEL_R/novel_r
< 33 otter /SOLVE/NOVELR> novelr
 SCALEPACK (1) or XDS (2)?
1
 File name for SCALEPACK no merge original ... output
../nm_smdr.sca
 Input upper and lower resolution limits (Angstroms)
1.50 40.0
 Number of sin(theta)/lamda bins (up to 100 allowed)?
10
 Random P,Q subsets(1) or based on frame ranges(2)?
1
 first, last frame number for analysis?
1 265
 Unit cell parameters (a,b,c,alf,bet,gam)
34.698 71.491 54.74 90.0 106.549 90.00
 REF #           0           0           0           2  -7.000000
  -0.1000000      -3.550000      3.6319232E-04           0
 REF #        1000           0          33          18   1102.802
    1106.920       1093.950      8.2686380E-02           0
 REF #        2000           1          12         -32   1230.788
    1329.412       1279.800      9.7635679E-02           0
 REF #        3000           1          28         -15   3921.005
    3827.047       3895.980      5.7780504E-02           0
 
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.
.


 first and last frame in file is           1         265
 NUMBER UNIQUE REFLECTIONS IN RESOL RANGE       39792
 NUMBER OBSERVED REFLECTIONS IN RESOL RANGE      212800
 NUMBER UNIQUE WITH TOO LOW RES           0
 NUMBER UNIQUE WITH TOO HIGH RES           0
< 34 otter /SOLVE/NOVELR> ls -lrt
total 6
-rw-r--r--    1 dbuckler stock       2798 Oct  5 11:48 fort.8
< 35 otter /SOLVE/NOVELR> more fort.8
Bin  Resol limit & midpoint   Ntotal (#<=0)  Nuniq (#<=0) N.ge.2 Nsingl
  1  3.23 0.155  4.07 0.123    16160 (  10)   3432 (   2)   3154    278
  2  2.56 0.195  2.82 0.177    21779 (  14)   4068 (   0)   3999     69
  3  2.24 0.223  2.38 0.210    22401 (  50)   4101 (   4)   4077     24
  4  2.04 0.246  2.13 0.235    22283 (  98)   4057 (   3)   4038     19
  5  1.89 0.265  1.96 0.255    22484 ( 172)   4108 (   7)   4102      6
  6  1.78 0.281  1.83 0.273    22360 ( 322)   4108 (  20)   4097     11
  7  1.69 0.296  1.73 0.289    22088 ( 416)   4080 (  22)   4067     13
  8  1.62 0.309  1.65 0.303    21884 ( 532)   4071 (  31)   4049     22
  9  1.55 0.322  1.58 0.316    21817 ( 787)   4094 (  57)   4076     18
 10  1.50 0.333  1.53 0.328    19544 ( 927)   3673 (  51)   3650     23
 Totals                       212800( 3328)  39792 ( 197)  39309    483

Bin  Res   Rmeas ( Rsym)    PCV         <I-over-sigma>       fract multi
     (A)    (%)    (%)      (%)   measured data  merged data  (%)
  1  4.07    7.2 (  6.3)     9.7   14.0 (14.0)   30.2 (31.6)   7.5   4.7
  2  2.82    7.0 (  6.3)    10.6   13.9 (13.9)   32.2 (32.5)  10.2   5.4
  3  2.38    7.5 (  6.8)    11.8   13.5 (13.5)   31.8 (31.9)  10.5   5.5
  4  2.13    8.1 (  7.3)    12.7   13.0 (13.0)   30.6 (30.7)  10.5   5.5
  5  1.96    8.8 (  8.0)    14.3   12.2 (12.2)   28.6 (28.6)  10.6   5.5
  6  1.83   10.4 (  9.4)    16.5   11.1 (11.1)   26.2 (26.2)  10.5   5.4
  7  1.73   12.2 ( 11.0)    50.5   10.2 (10.2)   24.1 (24.2)  10.4   5.4
  8  1.65   14.2 ( 12.9)   104.8    9.4 ( 9.4)   22.1 (22.1)  10.3   5.4
  9  1.58   15.1 ( 13.7)    24.1    8.4 ( 8.4)   19.6 (19.6)  10.3   5.3
 10  1.53   19.5 ( 17.6)   163.0    7.4 ( 7.4)   17.7 (17.7)   9.2   5.3
 Totals      8.1 (  7.3)    18.2   11.3 (11.3)   26.3 (26.5) 100.0   5.3

Bin  Res  Imrgd1   Imrgd2   Imrgd3   Fmrgd1  Fmrgd2  Fmrgd3  <Frel>
     (A)     (%)     (%)     (%)       (%)     (%)     (%)
  1  4.07    6.4     6.5     0.0       3.6     3.5     0.0  115.28
  2  2.82    5.9     6.0     0.0       3.4     3.4     0.0   86.86
  3  2.38    6.2     6.2     0.0       3.7     3.7     0.0   66.38
  4  2.13    6.7     6.9     0.0       4.1     4.2     0.0   55.57
  5  1.96    7.3     7.4     0.0       4.7     4.8     0.0   43.17
  6  1.83    8.6     9.0     0.0       5.8     6.2     0.0   32.63
  7  1.73   10.1    10.0     0.0       7.1     7.2     0.0   26.91
  8  1.65   11.7    11.2     0.0       8.2     8.5     0.0   23.58
  9  1.58   12.6    13.2     0.0      10.0    10.6     0.0   20.41
 10  1.53   16.4    15.4     0.0      12.4    12.6     0.0   17.92
 Totals      6.9     6.9     0.0       5.0     5.0     0.0   47.58

 Frames        1 to      265 from the file:
../nm_smdr.sca                         metry</font></tt>
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