Member Avatar for prashant.jnu

Dear All,
Well I am not very much new in perl but some time i write codes according to my need . Actually I am working in computational chemistry field . I have a protein data bank file and it had many columns like create a text file having different columns . If i want to delete some to columns from that file using perl script so how can i do that . Another thing related to one column having no 1-99 and 1-99 in one serines followd by another series on a no like UOE 1--1 and UOE 2--2 it represent to atom no actually . I want to change it is 1 to no of total atom. Can anybody help me out .I have also attached a sample file.
Thanks and regards
Prashant

HEADER    ASPARTYL PROTEASE                       13-OCT-97   1AXA              
TITLE     ACTIVE-SITE MOBILITY IN HUMAN IMMUNODEFICIENCY VIRUS TYPE 1           
TITLE    2 PROTEASE AS DEMONSTRATED BY CRYSTAL STRUCTURE OF A28S                
TITLE    3 MUTANT                                                               
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: HIV-1 PROTEASE;                                            
COMPND   3 CHAIN: A, B;                                                         
COMPND   4 EC: 3.4.23.16;                                                       
COMPND   5 ENGINEERED: YES;                                                     
COMPND   6 MUTATION: YES                                                        
SOURCE    MOL_ID: 1;                                                            
SOURCE   2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1;                 
SOURCE   3 ORGANISM_COMMON: HIV-1;                                              
SOURCE   4 EXPRESSION_SYSTEM: ESCHERICHIA COLI;                                 
SOURCE   5 EXPRESSION_SYSTEM_STRAIN: BL21                                       
KEYWDS    HIV PROTEASE, MUTANT, X-RAY, ASPARTIC PROTEASE, HYDROLASE,            
KEYWDS   2 ACID PROTEINASE, ASPARTYL PROTEASE                                   
EXPDTA    X-RAY DIFFRACTION                                                     
AUTHOR    L.HONG,J.A.HARTSUCK,S.FOUNDLING,J.ERMOLIEFF,J.TANG                    
REVDAT   1   15-APR-98 1AXA    0                                                
JRNL        AUTH   L.HONG,J.A.HARTSUCK,S.FOUNDLING,J.ERMOLIEFF,J.TANG           
JRNL        TITL   ACTIVE-SITE MOBILITY IN HUMAN IMMUNODEFICIENCY               
JRNL        TITL 2 VIRUS, TYPE 1, PROTEASE AS DEMONSTRATED BY CRYSTAL           
JRNL        TITL 3 STRUCTURE OF A28S MUTANT.                                    
JRNL        REF    PROTEIN SCI.                  V.   7   300 1998              
JRNL        REFN   ASTM PRCIEI  US ISSN 0961-8368                               
REMARK   1                                                                      
REMARK   2                                                                      
REMARK   2 RESOLUTION. 2.00 ANGSTROMS.                                          
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : TNT V. 5-E                                           
REMARK   3   AUTHORS     : TRONRUD,TEN EYCK,MATTHEWS                            
REMARK   3                                                                      
REMARK   3  DATA USED IN REFINEMENT.                                            
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00                           
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 20.00                          
REMARK   3   DATA CUTOFF            (SIGMA(F)) : 0.000                          
REMARK   3   COMPLETENESS FOR RANGE        (%) : 92.6                           
REMARK   3   NUMBER OF REFLECTIONS             : 11025                          
REMARK   3                                                                      
REMARK   3  USING DATA ABOVE SIGMA CUTOFF.                                      
REMARK   3   CROSS-VALIDATION METHOD          :NULL                             
REMARK   3   FREE R VALUE TEST SET SELECTION  :NULL                             
REMARK   3   R VALUE     (WORKING + TEST SET) :NULL                             
REMARK   3   R VALUE            (WORKING SET) :0.194                            
REMARK   3   FREE R VALUE                     :NULL                             
REMARK   3   FREE R VALUE TEST SET SIZE   (%) :NULL                             
REMARK   3   FREE R VALUE TEST SET COUNT      :NULL                             
REMARK   3                                                                      
REMARK   3  USING ALL DATA, NO SIGMA CUTOFF.                                    
REMARK   3   R VALUE   (WORKING + TEST SET, NO CUTOFF) : NULL                   
REMARK   3   R VALUE          (WORKING SET, NO CUTOFF) : 0.1940                 
REMARK   3   FREE R VALUE                  (NO CUTOFF) : NULL                   
REMARK   3   FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL                   
REMARK   3   FREE R VALUE TEST SET COUNT   (NO CUTOFF) : NULL                   
REMARK   3   TOTAL NUMBER OF REFLECTIONS   (NO CUTOFF) : 11025                  
REMARK   3                                                                      
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.                    
REMARK   3   PROTEIN ATOMS            : 1524                                    
REMARK   3   NUCLEIC ACID ATOMS       : 0                                       
REMARK   3   HETEROGEN ATOMS          : 84                                      
REMARK   3   SOLVENT ATOMS            : 63                                      
REMARK   3                                                                      
REMARK   3  WILSON B VALUE (FROM FCALC, A**2) : NULL                            
REMARK   3                                                                      
REMARK   3  RMS DEVIATIONS FROM IDEAL VALUES.    RMS    WEIGHT  COUNT           
REMARK   3   BOND LENGTHS                 (A) : 0.019 ; 0.800 ; 1632            
REMARK   3   BOND ANGLES            (DEGREES) : 3.200 ; 1.300 ; 2193            
REMARK   3   TORSION ANGLES         (DEGREES) : 28.500; 0.000 ; 941             
REMARK   3   PSEUDOROTATION ANGLES  (DEGREES) : NULL  ; NULL  ; NULL            
REMARK   3   TRIGONAL CARBON PLANES       (A) : 0.015 ; 2.000 ; 35              
REMARK   3   GENERAL PLANES               (A) : 0.016 ; 5.000 ; 230             
REMARK   3   ISOTROPIC THERMAL FACTORS (A**2) : 2.200 ; 8.000 ; 1632            
REMARK   3   NON-BONDED CONTACTS          (A) : 0.080 ; 5.000 ; 563             
REMARK   3                                                                      
REMARK   3  INCORRECT CHIRAL-CENTERS (COUNT) : NULL                             
REMARK   3                                                                      
REMARK   3  BULK SOLVENT MODELING.                                              
REMARK   3   METHOD USED : BABINET                                              
REMARK   3   KSOL        : 0.82                                                 
REMARK   3   BSOL        : 266.20                                               
REMARK   3                                                                      
REMARK   3  RESTRAINT LIBRARIES.                                                
REMARK   3   STEREOCHEMISTRY : TNT PROTGEO                                      
REMARK   3   ISOTROPIC THERMAL FACTOR RESTRAINTS : TNT BCORREL                  
REMARK   3                                                                      
REMARK   3  OTHER REFINEMENT REMARKS: NULL                                      
REMARK   4                                                                      
REMARK   4 1AXA COMPLIES WITH FORMAT V. 3.0, 1-DEC-2006                         
REMARK   4                                                                      
REMARK   4 THIS IS THE REMEDIATED VERSION OF THIS PDB ENTRY.                    
REMARK   4 REMEDIATED DATA FILE REVISION 3.101 (2007-05-29)                     
REMARK 200                                                                      
REMARK 200 EXPERIMENTAL DETAILS                                                 
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION                  
REMARK 200  DATE OF DATA COLLECTION        : MAY-1996                           
REMARK 200  TEMPERATURE           (KELVIN) : 293.0                              
REMARK 200  PH                             : 6.80                               
REMARK 200  NUMBER OF CRYSTALS USED        : 1                                  
REMARK 200                                                                      
REMARK 200  SYNCHROTRON              (Y/N) : N                                  
REMARK 200  RADIATION SOURCE               : NULL                               
REMARK 200  BEAMLINE                       : NULL                               
REMARK 200  X-RAY GENERATOR MODEL          : NULL                               
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M                                  
REMARK 200  WAVELENGTH OR RANGE        (A) : 1.5418                             
REMARK 200  MONOCHROMATOR                  : CRYSTAL                            
REMARK 200  OPTICS                         : NULL                               
REMARK 200                                                                      
REMARK 200  DETECTOR TYPE                  : MULTIWIRE AREA DETECTOR            
REMARK 200  DETECTOR MANUFACTURER          : SIEMENS                            
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : SAINT                              
REMARK 200  DATA SCALING SOFTWARE          : SAINT                              
REMARK 200                                                                      
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 11025                              
REMARK 200  RESOLUTION RANGE HIGH      (A) : 2.000                              
REMARK 200  RESOLUTION RANGE LOW       (A) : 34.000                             
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : 2.000                              
REMARK 200                                                                      
REMARK 200 OVERALL.                                                             
REMARK 200  COMPLETENESS FOR RANGE     (%) : 93.0                               
REMARK 200  DATA REDUNDANCY                : 4.900                              
REMARK 200  R MERGE                    (I) : NULL                               
REMARK 200  R SYM                      (I) : 0.06400                            
REMARK 200  <I/SIGMA(I)> FOR THE DATA SET  : 15.0000                            
REMARK 200
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Member Avatar for KevinADC

Do you know any perl at all?

Member Avatar for prashant.jnu

Yes I do , I do only write small script like automation of program actually my requirement is very specific , i usually some time need the perl . So if help in this issue it will be very grateful for me

Member Avatar for katharnakh

Yes I do , I do only write small script like automation of program actually my requirement is very specific , i usually some time need the perl . So if help in this issue it will be very grateful for me

what have you done so far, with perl with respect to your question above?

Member Avatar for ithelp

How about converting the text file into a database and then use perl?

Member Avatar for KevinADC

I will be glad to help, but I don't know where to start. All you have done so far is post a very general and somewhat vague idea of what you want to do. If you can be more specific maybe I can help.

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