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remove spaces in between file

 
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# 1  
Old 10-19-2011
remove spaces in between file
hey,
I have this file:

Code:
ATOM   2510 HG12 VAL   160       8.462  15.861   1.637
ATOM   2511 HG13 VAL   160       9.152  14.510   0.725
ATOM   2512 CG2  VAL   160       6.506  16.579  -0.088
ATOM   2513 HG21 VAL   160       5.499  16.421  -0.478
ATOM   2514 HG22 VAL   160       6.417  16.984   0.920
ATOM   2515 HG23 VAL   160       7.032  17.294  -0.721
ATOM   2516 C    VAL   160       7.872  13.131  -1.419
ATOM   2517 O    VAL   160       8.337  12.679  -2.487
ATOM   2518 OXT  VAL   160       7.646  12.461  -0.386
TER 
ATOM   2519 N    VAL   161     -14.431   5.789 -25.371
ATOM   2520 H1   VAL   161     -15.336   5.698 -25.811
ATOM   2521 H2   VAL   161     -13.730   5.341 -25.946
ATOM   2522 H3   VAL   161     -14.202   6.769 -25.271
ATOM   2523 CA   VAL   161     -14.460   5.150 -24.037
ATOM   2524 HA   VAL   161     -13.436   4.844 -23.821
ATOM   2525 CB   VAL   161     -14.865   6.136 -22.897
ATOM   2526 HB   VAL   161     -15.820   5.852 -22.458
ATOM   2527 CG1  VAL   161     -13.804   6.048 -21.790


I have to remove "TER" and make the next line continous. Like this:
Code:
ATOM   2510 HG12 VAL   160       8.462  15.861   1.637
ATOM   2511 HG13 VAL   160       9.152  14.510   0.725
ATOM   2512 CG2  VAL   160       6.506  16.579  -0.088
ATOM   2513 HG21 VAL   160       5.499  16.421  -0.478
ATOM   2514 HG22 VAL   160       6.417  16.984   0.920
ATOM   2515 HG23 VAL   160       7.032  17.294  -0.721
ATOM   2516 C    VAL   160       7.872  13.131  -1.419
ATOM   2517 O    VAL   160       8.337  12.679  -2.487
ATOM   2518 OXT  VAL   160       7.646  12.461  -0.386
ATOM   2519 N    VAL   161     -14.431   5.789 -25.371
ATOM   2520 H1   VAL   161     -15.336   5.698 -25.811
ATOM   2521 H2   VAL   161     -13.730   5.341 -25.946
ATOM   2522 H3   VAL   161     -14.202   6.769 -25.271
ATOM   2523 CA   VAL   161     -14.460   5.150 -24.037
ATOM   2524 HA   VAL   161     -13.436   4.844 -23.821
ATOM   2525 CB   VAL   161     -14.865   6.136 -22.897
ATOM   2526 HB   VAL   161     -15.820   5.852 -22.458
ATOM   2527 CG1  VAL   161     -13.804   6.048 -21.790

sed can replace ter with a space but how to remove that space Smiliethen?...thanks

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Last edited by radoulov; 10-19-2011 at 08:12 AM..
# 2  
Old 10-19-2011
Code:
 
grep -v "^TER" inputfile > outputfile

# 3  
Old 10-19-2011
Code:
grep -v '^TER' file > newfile
#or
sed '/^TER/d' file > newfile

# 4  
Old 10-19-2011
This doesnot work...Space is still there
# 5  
Old 10-19-2011
This means ?
 
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