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
prashant.jnu 0 Newbie Poster
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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
KevinADC 192 Practically a Posting Shark
Do you know any perl at all?
prashant.jnu 0 Newbie Poster
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
katharnakh 7 Posting Whiz in Training
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?
ithelp 757 Posting Virtuoso Banned
How about converting the text file into a database and then use perl?
KevinADC 192 Practically a Posting Shark
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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