9

I have a large file (a chemical database), and I need to display only header records, which are defined as lines that don't start with: ATOM, CONNECT, HETATM, TER, or END. I'm supposed to use grep to do this. Here's a sample of the file (the entire file is here):

HEADER    TRANSFERASE                             15-OCT-12   4HKD              
TITLE     CRYSTAL STRUCTURE OF HUMAN MST2 SARAH DOMAIN                          
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: SERINE/THREONINE-PROTEIN KINASE 3;                         
COMPND   3 CHAIN: A, B, C, D;                                                   
COMPND   4 FRAGMENT: SARAH DOMAIN, UNP RESIDUES 436-484;                        
COMPND   5 SYNONYM: MAMMALIAN STE20-LIKE PROTEIN KINASE 2, MST-2, STE20-LIKE    
COMPND   6 KINASE MST2, SERINE/THREONINE-PROTEIN KINASE KRS-1, SERINE/THREONINE-
COMPND   7 PROTEIN KINASE 3 36KDA SUBUNIT, MST2/N, SERINE/THREONINE-PROTEIN     
COMPND   8 KINASE 3 20KDA SUBUNIT, MST2/C;                                      
COMPND   9 EC: 2.7.11.1;                                                        
COMPND  10 ENGINEERED: YES                                                      
SOURCE    MOL_ID: 1;                                                            
SOURCE   2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;                                   
SOURCE   3 ORGANISM_COMMON: HUMAN;                                              
SOURCE   4 ORGANISM_TAXID: 9606;                                                
SOURCE   5 GENE: STK3, KRS1, MST2;                                              
SOURCE   6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;                                 
SOURCE   7 EXPRESSION_SYSTEM_TAXID: 562;                                        
SOURCE   8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3) CODON PLUS;                     
SOURCE   9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;                              
SOURCE  10 EXPRESSION_SYSTEM_PLASMID: HT-PET28A                                 
KEYWDS    HOMODIMERIZATION, HETERODOMERIZATION, SAV1, NEK2, RASSF, TRANSFERASE  
EXPDTA    X-RAY DIFFRACTION                                                     
AUTHOR    G.G.LIU,Z.B.SHI,Z.C.ZHOU                                              
REVDAT   1   04-SEP-13 4HKD    0                                                
JRNL        AUTH   G.G.LIU,Z.B.SHI,Z.C.ZHOU                                     
JRNL        TITL   CRYSTAL STRUCTURE OF HUMAN MST2 SARAH DOMAIN                 
JRNL        REF    TO BE PUBLISHED                                              
JRNL        REFN                                                                
REMARK   2                                                                      
REMARK   2 RESOLUTION.    1.50 ANGSTROMS.                                       
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : PHENIX (PHENIX.REFINE: 1.8_1069)                     
REMARK   3   AUTHORS     : PAUL ADAMS,PAVEL AFONINE,VICENT CHEN,IAN             
REMARK   3               : DAVIS,KRESHNA GOPAL,RALF GROSSE-                     
REMARK   3               : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO,              
REMARK   3               : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL            
REMARK   3               : MORIARTY,REETAL PAI,RANDY READ,JANE                  
REMARK   3               : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM             
REMARK   3               : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH,             
REMARK   3               : LAURENT STORONI,TOM TERWILLIGER,PETER                
REMARK   3               : ZWART                                                
REMARK   3                                                                      
REMARK   3    REFINEMENT TARGET : ML                                            
REMARK   3                                                                      
REMARK   3  DATA USED IN REFINEMENT.                                            
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50                           
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 34.86                          
REMARK   3   MIN(FOBS/SIGMA_FOBS)              : 1.380                          
REMARK   3   COMPLETENESS FOR RANGE        (%) : 91.9                           
REMARK   3   NUMBER OF REFLECTIONS             : 29481                          
REMARK   3                                                                      
REMARK   3  FIT TO DATA USED IN REFINEMENT.                                     
REMARK   3   R VALUE     (WORKING + TEST SET) : 0.197                           
REMARK   3   R VALUE            (WORKING SET) : 0.195                           
REMARK   3   FREE R VALUE                     : 0.231                           
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 5.080                           
REMARK   3   FREE R VALUE TEST SET COUNT      : 1497                            
REMARK   3                                                                      
REMARK   3  FIT TO DATA USED IN REFINEMENT (IN BINS).                           
REMARK   3   BIN  RESOLUTION RANGE  COMPL.    NWORK NFREE   RWORK  RFREE        
REMARK   3     1 34.8685 -  3.3427    0.97     2878   149  0.1998 0.2322        
REMARK   3     2  3.3427 -  2.6535    0.98     2711   175  0.2033 0.2452        
REMARK   3     3  2.6535 -  2.3182    0.96     2660   155  0.1968 0.2148        
REMARK   3     4  2.3182 -  2.1063    0.94     2620   114  0.1875 0.2318        
REMARK   3     5  2.1063 -  1.9553    0.91     2533   113  0.1909 0.2295        
REMARK   3     6  1.9553 -  1.8400    0.91     2476   143  0.1883 0.2137        
REMARK   3     7  1.8400 -  1.7479    0.90     2465   128  0.1840 0.2029        
REMARK   3     8  1.7479 -  1.6718    0.90     2446   130  0.1783 0.2144        
REMARK   3     9  1.6718 -  1.6074    0.90     2419   129  0.1864 0.2400        
REMARK   3    10  1.6074 -  1.5520    0.90     2487   120  0.1938 0.2588        
REMARK   3    11  1.5520 -  1.5030    0.85     2289   141  0.1993 0.2471        
REMARK   3                                                                      
REMARK   3  BULK SOLVENT MODELLING.                                             
REMARK   3   METHOD USED        : FLAT BULK SOLVENT MODEL                       
REMARK   3   SOLVENT RADIUS     : 1.11                                          
REMARK   3   SHRINKAGE RADIUS   : 0.90                                          
REMARK   3   K_SOL              : NULL                                          
REMARK   3   B_SOL              : NULL                                          
REMARK   3                                                                      
REMARK   3  ERROR ESTIMATES.                                                    
REMARK   3   COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED)     : 0.130            
REMARK   3   PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.520           
REMARK   3                                                                      
REMARK   3  B VALUES.                                                           
REMARK   3   FROM WILSON PLOT           (A**2) : NULL                           
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : NULL                           
REMARK   3   OVERALL ANISOTROPIC B VALUE.                                       
REMARK   3    B11 (A**2) : NULL                                                 
REMARK   3    B22 (A**2) : NULL                                                 
REMARK   3    B33 (A**2) : NULL                                                 
REMARK   3    B12 (A**2) : NULL                                                 
REMARK   3    B13 (A**2) : NULL                                                 
REMARK   3    B23 (A**2) : NULL                                                 
REMARK   3                                                                      
REMARK   3  TWINNING INFORMATION.                                               
REMARK   3   FRACTION: NULL                                                     
REMARK   3   OPERATOR: NULL                                                     
REMARK   3                                                                      
REMARK   3  DEVIATIONS FROM IDEAL VALUES.                                       
REMARK   3                 RMSD          COUNT                                  
REMARK   3   BOND      :  0.007           1771                                  
REMARK   3   ANGLE     :  1.179           2367                                  
REMARK   3   CHIRALITY :  0.083            255                                  
REMARK   3   PLANARITY :  0.006            317                                  
REMARK   3   DIHEDRAL  : 14.379            737                                  
REMARK   3                                                                      
REMARK   3  TLS DETAILS                                                         
REMARK   3   NUMBER OF TLS GROUPS  : NULL                                       
REMARK   3                                                                      
REMARK   3  NCS DETAILS                                                         
REMARK   3   NUMBER OF NCS GROUPS : NULL                                        
REMARK   3                                                                      
REMARK   3  OTHER REFINEMENT REMARKS: NULL                                      
REMARK   4                                                                      
REMARK   4 4HKD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-OCT-12.                  
REMARK 100 THE RCSB ID CODE IS RCSB075574.                                      
REMARK 200                                                                      
REMARK 200 EXPERIMENTAL DETAILS                                                 
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION                  
REMARK 200  DATE OF DATA COLLECTION        : 16-APR-12                          
REMARK 200  TEMPERATURE           (KELVIN) : 100                                
REMARK 200  PH                             : 4.6                                
REMARK 200  NUMBER OF CRYSTALS USED        : 1                                  
REMARK 200                                                                      
REMARK 200  SYNCHROTRON              (Y/N) : Y                                  
REMARK 200  RADIATION SOURCE               : SSRF                               
REMARK 200  BEAMLINE                       : BL17U                              
REMARK 200  X-RAY GENERATOR MODEL          : NULL                               
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M                                  
REMARK 200  WAVELENGTH OR RANGE        (A) : 0.97915                            
REMARK 200  MONOCHROMATOR                  : SI 111 CHANNEL                     
REMARK 200  OPTICS                         : NULL                               
REMARK 200                                                                      
REMARK 200  DETECTOR TYPE                  : CCD                                
REMARK 200  DETECTOR MANUFACTURER          : ADSC QUANTUM 315                   
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : HKL-2000                           
REMARK 200  DATA SCALING SOFTWARE          : HKL-2000                           
REMARK 200                                                                      
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 29548                              
REMARK 200  RESOLUTION RANGE HIGH      (A) : 1.500                              
REMARK 200  RESOLUTION RANGE LOW       (A) : 50.000                             
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : 2.000                              
REMARK 200                                                                      
REMARK 200 OVERALL.                                                             
REMARK 200  COMPLETENESS FOR RANGE     (%) : 92.3                               
REMARK 200  DATA REDUNDANCY                : 5.300                              
REMARK 200  R MERGE                    (I) : NULL                               
REMARK 200  R SYM                      (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR THE DATA SET  : 17.1000   
  • NOw one of my thought is grep -v ATOM 4HKD and that will print out all the lines without atom. – Fernando Martinez Sep 14 '14 at 20:25
  • The entire file has atom conect hetam ter or end . – Fernando Martinez Sep 14 '14 at 21:00
  • Well it would be greP -wv ATOM 4HKD to display the lines without atom, then grep -wv TER 4HKD to display the lines without ter. And etc for the other pattern for example connect. But the mystery is how do you make it a header. Or is removing them from the file enough. An ubuntu x file. – Fernando Martinez Sep 14 '14 at 21:17
16

Your comment is the right approach; if you have to use grep you should probably use -v. Then you just need to match all lines that start with the keywords you mentioned.

$ grep -Ev '^(ATOM|CONECT|HETATM|TER|END)' /path/to/your/file

-E is to use extended regular expressions. ^ matches the beginning of the line, and (a|b|c) means "a or b or c". I suspect "CONNECT" in your question was a typo since it doesn't appear in the file, so I changed it to CONECT here

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