pdb_merge should discard MODEL/ENDMDL statements

[amjjbonvin]

pdb_mkensemble is meant to generate ensembles of models with MODEL / ENDMDL statements.

pdb_merge should in principle not do it. But the problem is that if MODEL / ENDMDL statements are present it keeps those in the output.

The question is: Should it filter it out? I would say yes.

One example: I have a dimer with chain A and B which I want to transform into a single chain PDB with shifted numbering of chain B.

If that input file has MODEL statement at the start, the resulting processed PDB file with have the two chains in different MODELs while it should be a single unit.

The following pipeline can be tested with the PDB file below.

pdb_selchain -A  dimer-test.pdb  > chainA.pdb
pdb_selchain -B  dimer-test.pdb | pdb_shiftres -500 > chainB-shifted.pdb
pdb_merge chainA.pdb chainB-shifted.pdb | pdb_chain -A | pdb_tidy > dimer-shifted.pdb

MODEL     1                                                                     
ATOM      1  N   MET A   1      11.055 -22.172  55.625  1.00 20.58           N  
ATOM      2  CA  MET A   1      11.875 -23.016  54.750  1.00 20.58           C  
ATOM      3  C   MET A   1      11.023 -23.734  53.719  1.00 20.58           C  
ATOM      4  CB  MET A   1      12.664 -24.031  55.594  1.00 20.58           C  
ATOM      5  O   MET A   1      11.531 -24.172  52.688  1.00 20.58           O  
ATOM      6  CG  MET A   1      14.102 -23.625  55.844  1.00 20.58           C  
ATOM      7  SD  MET A   1      15.023 -24.891  56.812  1.00 20.58           S  
ATOM      8  CE  MET A   1      16.625 -24.062  56.969  1.00 20.58           C  
ATOM      9  N   ASP A   2       9.797 -24.047  54.031  1.00 22.62           N  
ATOM     10  CA  ASP A   2       8.969 -25.000  53.312  1.00 22.62           C  
ATOM     11  C   ASP A   2       8.273 -24.328  52.125  1.00 22.62           C  
ATOM     12  CB  ASP A   2       7.938 -25.641  54.219  1.00 22.62           C  
ATOM     13  O   ASP A   2       7.422 -24.938  51.469  1.00 22.62           O  
ATOM     14  CG  ASP A   2       8.453 -26.891  54.906  1.00 22.62           C  
ATOM     15  OD1 ASP A   2       9.469 -27.469  54.469  1.00 22.62           O  
ATOM     16  OD2 ASP A   2       7.828 -27.312  55.906  1.00 22.62           O  
ATOM     17  N   ALA A   3       8.117 -23.016  52.125  1.00 28.78           N  
ATOM     18  CA  ALA A   3       7.055 -22.469  51.281  1.00 28.78           C  
ATOM     19  C   ALA A   3       7.398 -22.609  49.812  1.00 28.78           C  
ATOM     20  CB  ALA A   3       6.812 -21.000  51.656  1.00 28.78           C  
ATOM     21  O   ALA A   3       6.527 -22.484  48.969  1.00 28.78           O  
ATOM     22  N   LEU A   4       8.633 -22.297  49.500  1.00 32.16           N  
ATOM     23  CA  LEU A   4       8.836 -22.062  48.062  1.00 32.16           C  
ATOM     24  C   LEU A   4       8.961 -23.375  47.312  1.00 32.16           C  
ATOM     25  CB  LEU A   4      10.094 -21.203  47.844  1.00 32.16           C  
ATOM     26  O   LEU A   4      10.055 -23.734  46.875  1.00 32.16           O  
ATOM     27  CG  LEU A   4       9.914 -19.688  47.969  1.00 32.16           C  
ATOM     28  CD1 LEU A   4      11.266 -19.016  48.219  1.00 32.16           C  
ATOM     29  CD2 LEU A   4       9.234 -19.125  46.750  1.00 32.16           C  
ATOM     30  N   THR A   5       8.398 -24.500  47.812  1.00 32.47           N  
ATOM     31  CA  THR A   5       8.516 -25.734  47.031  1.00 32.47           C  
ATOM     32  C   THR A   5       7.887 -25.578  45.656  1.00 32.47           C  
ATOM     33  CB  THR A   5       7.844 -26.906  47.781  1.00 32.47           C  
ATOM     34  O   THR A   5       6.688 -25.312  45.531  1.00 32.47           O  
ATOM     35  CG2 THR A   5       8.734 -27.438  48.906  1.00 32.47           C  
ATOM     36  OG1 THR A   5       6.605 -26.453  48.344  1.00 32.47           O  
TER                                            
ATOM   2959  N   MET B   1      19.234 -25.625  52.031  1.00 20.58           N  
ATOM   2960  CA  MET B   1      18.266 -24.609  52.406  1.00 20.58           C  
ATOM   2961  C   MET B   1      18.688 -23.234  51.906  1.00 20.58           C  
ATOM   2962  CB  MET B   1      18.125 -24.562  53.938  1.00 20.58           C  
ATOM   2963  O   MET B   1      17.859 -22.328  51.812  1.00 20.58           O  
ATOM   2964  CG  MET B   1      16.938 -25.359  54.469  1.00 20.58           C  
ATOM   2965  SD  MET B   1      16.766 -25.250  56.281  1.00 20.58           S  
ATOM   2966  CE  MET B   1      15.359 -26.359  56.562  1.00 20.58           C  
ATOM   2967  N   ASP B   2      19.953 -23.000  51.719  1.00 22.56           N  
ATOM   2968  CA  ASP B   2      20.531 -21.672  51.594  1.00 22.56           C  
ATOM   2969  C   ASP B   2      20.469 -21.203  50.156  1.00 22.56           C  
ATOM   2970  CB  ASP B   2      21.969 -21.656  52.094  1.00 22.56           C  
ATOM   2971  O   ASP B   2      21.047 -20.156  49.812  1.00 22.56           O  
ATOM   2972  CG  ASP B   2      22.078 -21.359  53.594  1.00 22.56           C  
ATOM   2973  OD1 ASP B   2      21.094 -20.859  54.188  1.00 22.56           O  
ATOM   2974  OD2 ASP B   2      23.156 -21.625  54.156  1.00 22.56           O  
ATOM   2975  N   ALA B   3      20.359 -22.094  49.219  1.00 29.11           N  
ATOM   2976  CA  ALA B   3      20.781 -21.719  47.844  1.00 29.11           C  
ATOM   2977  C   ALA B   3      19.844 -20.688  47.250  1.00 29.11           C  
ATOM   2978  CB  ALA B   3      20.859 -22.953  46.969  1.00 29.11           C  
ATOM   2979  O   ALA B   3      20.172 -20.078  46.219  1.00 29.11           O  
ATOM   2980  N   LEU B   4      18.578 -20.891  47.500  1.00 32.12           N  
ATOM   2981  CA  LEU B   4      17.656 -20.109  46.656  1.00 32.12           C  
ATOM   2982  C   LEU B   4      17.547 -18.688  47.188  1.00 32.12           C  
ATOM   2983  CB  LEU B   4      16.281 -20.766  46.625  1.00 32.12           C  
ATOM   2984  O   LEU B   4      16.484 -18.281  47.688  1.00 32.12           O  
ATOM   2985  CG  LEU B   4      16.094 -21.891  45.594  1.00 32.12           C  
ATOM   2986  CD1 LEU B   4      14.906 -22.766  45.969  1.00 32.12           C  
ATOM   2987  CD2 LEU B   4      15.922 -21.312  44.188  1.00 32.12           C  
ATOM   2988  N   THR B   5      18.500 -18.156  47.969  1.00 32.59           N  
ATOM   2989  CA  THR B   5      18.328 -16.781  48.438  1.00 32.59           C  
ATOM   2990  C   THR B   5      18.250 -15.820  47.250  1.00 32.59           C  
ATOM   2991  CB  THR B   5      19.500 -16.375  49.344  1.00 32.59           C  
ATOM   2992  O   THR B   5      19.188 -15.695  46.469  1.00 32.59           O  
ATOM   2993  CG2 THR B   5      19.312 -16.938  50.750  1.00 32.59           C  
ATOM   2994  OG1 THR B   5      20.719 -16.859  48.812  1.00 32.59           O  
TER                                                   
ENDMDL                                                                          
END