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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

Attachments
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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Last Post by KevinADC
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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

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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?

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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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