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Full Discussion: how I can add a constant to a field without changing the file format
Top Forums Shell Programming and Scripting how I can add a constant to a field without changing the file format Post 302424887 by bio_ on Wednesday 26th of May 2010 01:32:03 PM
Old 05-26-2010
how I can add a constant to a field without changing the file format
Hi, I need to edit a file Protein Data Bank (pdb) and then open that file with the program VMD but when I edit the file with awk, it changes pdb format and the VMD program can not read it.
I need to subtract 34 to field 6 ($ 6).
this is a pdb file :
Code:
ATOM    918  N   GLY B 103     -11.855   8.675 -11.404  1.00  0.00           N  
ATOM    919  CA  GLY B 103     -13.297   8.831 -11.189  1.00  0.00           C  
ATOM    920  C   GLY B 103     -13.977   7.468 -11.253  1.00  0.00           C  
ATOM    921  O   GLY B 103     -14.817   7.213 -12.116  1.00  0.00           O  
ATOM    922  H   GLY B 103     -11.342   7.827 -11.132  1.00  0.00           H  
ATOM    923  HA2 GLY B 103     -13.483   9.303 -10.207  1.00  0.00           H  
ATOM    924  HA3 GLY B 103     -13.734   9.500 -11.952  1.00  0.00           H  
ATOM    925  N   MET B 104     -13.601   6.588 -10.332  1.00  0.00           N  
ATOM    926  CA  MET B 104     -14.127   5.222 -10.341  1.00  0.00           C  
ATOM    927  C   MET B 104     -15.232   5.094  -9.286  1.00  0.00           C  
ATOM    928  O   MET B 104     -16.396   4.872  -9.620  1.00  0.00           O  
ATOM    929  CB  MET B 104     -12.929   4.298 -10.093  1.00  0.00           C  
ATOM    930  CG  MET B 104     -13.316   2.824 -10.092  1.00  0.00           C  
ATOM    931  SD  MET B 104     -14.028   2.373 -11.684  1.00  0.00           S  
ATOM    932  CE  MET B 104     -14.384   0.636 -11.368  1.00  0.00           C  
ATOM    933  H   MET B 104     -12.859   6.880  -9.688  1.00  0.00           H  
ATOM    934  HA  MET B 104     -14.557   4.991 -11.333  1.00  0.00           H  
ATOM    935  HB2 MET B 104     -12.161   4.469 -10.870  1.00  0.00           H  
ATOM    936  HB3 MET B 104     -12.447   4.551  -9.131  1.00  0.00           H  
ATOM    937  HG2 MET B 104     -12.421   2.209  -9.894  1.00  0.00           H  
ATOM    938  HG3 MET B 104     -14.041   2.627  -9.283  1.00  0.00           H  
ATOM    939  HE1 MET B 104     -15.076   0.527 -10.513  1.00  0.00           H  
ATOM    940  HE2 MET B 104     -14.852   0.168 -12.252  1.00  0.00           H  
ATOM    941  HE3 MET B 104     -13.456   0.082 -11.135  1.00  0.00           H

when I try with this script:
Code:
#!/bin/bash

awk  '$6= $6 - 34'  > pba10.

I get this

Code:
ATOM 918 N GLY B 69 -11.855 8.675 -11.404 1.00 0.00 N
ATOM 919 CA GLY B 69 -13.297 8.831 -11.189 1.00 0.00 C
ATOM 920 C GLY B 69 -13.977 7.468 -11.253 1.00 0.00 C
ATOM 921 O GLY B 69 -14.817 7.213 -12.116 1.00 0.00 O
ATOM 922 H GLY B 69 -11.342 7.827 -11.132 1.00 0.00 H
ATOM 923 HA2 GLY B 69 -13.483 9.303 -10.207 1.00 0.00 H
ATOM 924 HA3 GLY B 69 -13.734 9.500 -11.952 1.00 0.00 H
ATOM 925 N MET B 70 -13.601 6.588 -10.332 1.00 0.00 N
ATOM 926 CA MET B 70 -14.127 5.222 -10.341 1.00 0.00 C
ATOM 927 C MET B 70 -15.232 5.094 -9.286 1.00 0.00 C
ATOM 928 O MET B 70 -16.396 4.872 -9.620 1.00 0.00 O
ATOM 929 CB MET B 70 -12.929 4.298 -10.093 1.00 0.00 C
ATOM 930 CG MET B 70 -13.316 2.824 -10.092 1.00 0.00 C
ATOM 931 SD MET B 70 -14.028 2.373 -11.684 1.00 0.00 S
ATOM 932 CE MET B 70 -14.384 0.636 -11.368 1.00 0.00 C
ATOM 933 H MET B 70 -12.859 6.880 -9.688 1.00 0.00 H
ATOM 934 HA MET B 70 -14.557 4.991 -11.333 1.00 0.00 H
ATOM 935 HB2 MET B 70 -12.161 4.469 -10.870 1.00 0.00 H
ATOM 936 HB3 MET B 70 -12.447 4.551 -9.131 1.00 0.00 H
ATOM 937 HG2 MET B 70 -12.421 2.209 -9.894 1.00 0.00 H
ATOM 938 HG3 MET B 70 -14.041 2.627 -9.283 1.00 0.00 H
ATOM 939 HE1 MET B 70 -15.076 0.527 -10.513 1.00 0.00 H
ATOM 940 HE2 MET B 70 -14.852 0.168 -12.252 1.00 0.00 H
ATOM 941 HE3 MET B 70 -13.456 0.082 -11.135 1.00 0.00 H

and thist pdb file can not read by VMD, i have tried replacing the spaces with a "\t" but the result is not good
 

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