Tôi có một tập tin lớn (một cơ sở dữ liệu hóa học), và tôi cần phải hiển thị hồ sơ chỉ tiêu đề, được định nghĩa là dòng mà không bắt đầu với: ATOM, CONNECT, HETATM, TER, hoặc END. Tôi phải sử dụng grepđể làm điều này. Đây là một mẫu của tệp (toàn bộ tệp ở đây ):
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
Bây giờ, một trong những suy nghĩ của tôi là grep -v ATOM 4HKD và điều đó sẽ in ra tất cả các dòng không có nguyên tử.
—
Fernando Martinez
Toàn bộ tập tin có nguyên tử con hetam ter hoặc end.
—
Fernando Martinez
Vâng, đó sẽ là greP -wv ATOM 4HKD để hiển thị các dòng không có nguyên tử, sau đó grep -wv TER 4HKD để hiển thị các dòng mà không cần ter. Và vv cho các mẫu khác ví dụ kết nối. Nhưng bí ẩn là làm thế nào để bạn làm cho nó một tiêu đề. Hoặc là loại bỏ chúng khỏi tập tin đủ. Một tập tin ubfox x.
—
Fernando Martinez