For a crystallographer, Phenix provides a very convenient tool to generate “table 1” for publication. For a NMR person, I used to manually count the NOE numbers with different categories (intra, inter, long-range..) and use PyMOL to compute the RMSD values of selected ensemble. PdbStat can do quickly generate a complete table 1 using user-loaded restraint files. Here is the example of the restraint part.

Here is the example:

# read the restraints
PdbStat> rea cons xplor NOE.tbl

It returns:
  > locate_file(): file `NOE.tbl' opened for reading 
   .. readwrite  called with  cons, xplor 
    1556 NOE-distance constraints (0 Ambiguous descriptions) read 
    1556 TOTAL constraints read 

# run analysis
PdbStat> analysis

It returns
 -------------- SUMMARY OF RESTRAINTS  --------------- 
 TOTAL NUMBER OF NOE RESTRAINTS            :  1556
      INTRA-RESIDUE RESTRAINTS   (I=J)     :   430
          BACKBONE-BACKBONE                :         7
          BACKBONE-SIDE CHAIN              :       315
          SIDE CHAIN-SIDE CHAIN            :       108
      SEQUENTIAL    RESTRAINTS   (I-J)=1   :   402
          BACKBONE-BACKBONE                :       108
          BACKBONE-SIDE CHAIN              :       234
          SIDE CHAIN-SIDE CHAIN            :        60
      MEDIUM RANGE  RESTRAINTS  1<(I-J)<5  :   248
          BACKBONE-BACKBONE                :        41
          BACKBONE-SIDE CHAIN              :       100
          SIDE CHAIN-SIDE CHAIN            :       107
      LONG  RANGE   RESTRAINTS   (I-J)>=5  :   476
          BACKBONE-BACKBONE                :        49
          BACKBONE-SIDE CHAIN              :       169
          SIDE CHAIN-SIDE CHAIN            :       258
 TOTAL HYDROGEN BOND RESTRAINTS            :     0
 DISULFIDE RESTRAINTS                      :     0
 INTRA-CHAIN RESTRAINTS                    :  1556
 INTER-CHAIN RESTRAINTS                    :     0
 AMBIGUOUS RESTRAINTS                      :     0
 ----------------------------------------------------- 
 ----------------------------------------------------- 
 ----------------------------------------------------- 

The "analysis" function also provide the detailed restraint information per residue:

RES     NUM   INTRA  INTER    SEQ     MED    LONG   INTERCHAIN
 GLY A    1      0     0.5     0.5     0.0     0.0     0.0
 SER A    2      0     1.0     1.0     0.0     0.0     0.0
 GLY A    3      1     1.5     1.5     0.0     0.0     0.0
 GLY A    4      0     1.0     1.0     0.0     0.0     0.0
 SER A    5      2     1.5     1.0     0.0     0.5     0.0
 MET A    6      6    18.5     4.5     2.0    12.0     0.0
 LYS A    7     10    16.5     6.5     0.0    10.0     0.0
 ILE A    8      6    17.5     6.0     2.0     9.5     0.0
 TYR A    9      4    25.0     6.0     0.5    18.5     0.0
 VAL A   10      7    20.5     5.5     1.0    14.0     0.0
 LYS A   11      8    17.5     5.0     1.5    11.0     0.0
 LEU A   12      6    19.5     5.0     8.5     6.0     0.0
 GLN A   13     10     5.5     3.5     1.0     1.0     0.0
 ASP A   14      3     4.5     2.5     2.0     0.0     0.0

If both NOE and dihedral angle restraints are loaded, the “analysis” will output not only NOE restraints (shown above) but also the angular restraints (below). However, the phi and psi restraints are not counted separately, if a XPLOR-NIH format is loaded. No issues to deal with CYANA format.

When using xplor-nih format:
Dihedral angle restraints:                     
Other : 140
Total : 140

When using CYANA format:
Dihedral angle restraints:                     
     PHI                                   :    70
     PSI                                   :    70
     Total                                 :   140

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