Running PDBSTAT from Linux Ayuda is on: /data/PSVS/PdbStat/PdbStat-5.1 (C) (C) Pdbstat -- A program to evaluate some statistics of macromolecules, (C) given the cartesian coordinates. (C) (C) (c) Copyright 1992-2007 Roberto Tejero and Gaetano T. Montelione (C) Center for Advanced Technology and Medicine (CABM) (C) Rutgers University (C) ** VERSION: 5.1-Exp Compiled 2008-08-07 on (europa) ** ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ===============> W E L C O M E to PDBStat <================ PDBStat has become a tool able (between other things) of: a) read and interconvert between DISMAN, DYANA, PDB, DISCOVER, IMPACT b) elaborate some info about the molecule as MW, Radius of gyration, .. c) investigate the setereochemical quality of a protein by evaluating phi, psi, chi1, impropers and chirality The sequence of acts should be: 1.- read a file (coords, constr) 2.- read a sequence file (can be free format) 3.- Follow menu (calculating, writing ...) NOTE: Be aware that if you read in a constraint file you *ALWAYS* need to read a sequence file also HAVE FUN AND ENJOY !! **** For more info type `help' or `menu' **** --> ... Reading/Loading Distances file ... 123 distance records read --> ... Reading/Loading Dihedral Library .. 799 library records read PdbStat> [rea]d [hel]p [his]tory [men]u [phi] [qui]t... PdbStat> leyendo PDB > locate_file(): file `SR213_NMR_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 23-JUN-06 2HFI > ReadCoordsPdb(): >> TITLE SOLUTION NMR STRUCTURE OF PROTEIN YPPE FROM BACILLUS > ReadCoordsPdb(): >> TITLE 2 SUBTILIS. NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET > ReadCoordsPdb(): >> TITLE 3 SR213 > ReadCoordsPdb(): >> COMPND MOL_ID: 1; 1 > ReadCoordsPdb(): Counting models in file `SR213_NMR_em_bcr3.pdb'; Model: 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 > ReadCoordsPdb(): After scanning there is(are) 20 model(s) > ReadCoordsPdb(): what model do you want [(1 to 20) or all] ?_ > ReadCoordsPdb(): Reading *all* models in file SR213_NMR_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 40620 ATOM records read from file > ReadCoordsPdb(): --> 40620 Regular IUPAC Atoms > ReadCoordsPdb(): --> 0 Pseudo-atoms (DISMAN type) > ReadCoordsPdb(): --> 0 Lone pairs > ReadCoordsPdb(): Bye ... PdbStat> > locate_file(): file `SR213_NMR_em_bcr3.hbond' opened for reading 108 NOE-distance constraints read 108 TOTAL constraints read PdbStat> -------------- SUMMARY OF CONSTRAINTS --------------- TOTAL NUMBER OF NOE CONSTRAINTS : 0 INTRA-RESIDUE CONSTRAINTS (I=J) : 0 SEQUENTIAL CONSTRAINTS (I-J)=1 : 0 BACKBONE-BACKBONE : 0 BACKBONE-SIDE CHAIN : 0 SIDE CHAIN-SIDE CHAIN : 0 MEDIUM RANGE CONSTRAINTS 1<(I-J)<5 : 0 BACKBONE-BACKBONE : 0 BACKBONE-SIDE CHAIN : 0 SIDE CHAIN-SIDE CHAIN : 0 LONG RANGE CONSTRAINTS (I-J)>=5 : 0 TOTAL HYDROGEN BOND RESTRAINTS : 108 LONG RANGE H-BOND RESTR. (I-J)>=5 : 0 DISULFIDE CONSTRAINTS : 0 INTRA-CHAIN CONSTRAINTS : 108 INTER-CHAIN CONSTRAINTS : 0 RES # INTRA INTER seq med lng MET 1 0 0.0 0.0 0.0 0.0 LEU 2 0 0.0 0.0 0.0 0.0 SER 3 0 0.0 0.0 0.0 0.0 GLN 4 0 0.0 0.0 0.0 0.0 THR 5 0 0.0 0.0 0.0 0.0 LEU 6 0 0.0 0.0 0.0 0.0 LEU 7 0 0.0 0.0 0.0 0.0 GLU 8 0 0.0 0.0 0.0 0.0 MET 9 0 0.0 0.0 0.0 0.0 THR 10 0 0.0 0.0 0.0 0.0 GLU 11 0 0.0 0.0 0.0 0.0 GLN 12 0 0.0 0.0 0.0 0.0 MET 13 0 0.0 0.0 0.0 0.0 ILE 14 0 0.0 0.0 0.0 0.0 GLU 15 0 0.0 0.0 0.0 0.0 VAL 16 0 0.0 0.0 0.0 0.0 ALA 17 0 0.0 0.0 0.0 0.0 GLU 18 0 0.0 0.0 0.0 0.0 LYS 19 0 0.0 0.0 0.0 0.0 GLY 20 0 0.0 0.0 0.0 0.0 ALA 21 0 0.0 0.0 0.0 0.0 ASP 22 0 0.0 0.0 0.0 0.0 ARG 23 0 0.0 0.0 0.0 0.0 TYR 24 0 0.0 0.0 0.0 0.0 GLN 25 0 0.0 0.0 0.0 0.0 GLU 26 0 0.0 0.0 0.0 0.0 GLY 27 0 0.0 0.0 0.0 0.0 LYS 28 0 0.0 0.0 0.0 0.0 ASN 29 0 0.0 0.0 0.0 0.0 SER 30 0 0.0 0.0 0.0 0.0 ASN 31 0 0.0 0.0 0.0 0.0 HIS 32 0 0.0 0.0 0.0 0.0 SER 33 0 0.0 0.0 0.0 0.0 TYR 34 0 0.0 0.0 0.0 0.0 ASP 35 0 0.0 0.0 0.0 0.0 PHE 36 0 0.0 0.0 0.0 0.0 PHE 37 0 0.0 0.0 0.0 0.0 GLU 38 0 0.0 0.0 0.0 0.0 THR 39 0 0.0 0.0 0.0 0.0 ILE 40 0 0.0 0.0 0.0 0.0 LYS 41 0 0.0 0.0 0.0 0.0 PRO 42 0 0.0 0.0 0.0 0.0 ALA 43 0 0.0 0.0 0.0 0.0 VAL 44 0 0.0 0.0 0.0 0.0 GLU 45 0 0.0 0.0 0.0 0.0 GLU 46 0 0.0 0.0 0.0 0.0 ASN 47 0 0.0 0.0 0.0 0.0 ASP 48 0 0.0 0.0 0.0 0.0 GLU 49 0 0.0 0.0 0.0 0.0 LEU 50 0 0.0 0.0 0.0 0.0 ALA 51 0 0.0 0.0 0.0 0.0 ALA 52 0 0.0 0.0 0.0 0.0 ARG 53 0 0.0 0.0 0.0 0.0 TRP 54 0 0.0 0.0 0.0 0.0 ALA 55 0 0.0 0.0 0.0 0.0 GLU 56 0 0.0 0.0 0.0 0.0 GLY 57 0 0.0 0.0 0.0 0.0 ALA 58 0 0.0 0.0 0.0 0.0 LEU 59 0 0.0 0.0 0.0 0.0 GLU 60 0 0.0 0.0 0.0 0.0 LEU 61 0 0.0 0.0 0.0 0.0 ILE 62 0 0.0 0.0 0.0 0.0 LYS 63 0 0.0 0.0 0.0 0.0 VAL 64 0 0.0 0.0 0.0 0.0 ARG 65 0 0.0 0.0 0.0 0.0 ARG 66 0 0.0 0.0 0.0 0.0 PRO 67 0 0.0 0.0 0.0 0.0 LYS 68 0 0.0 0.0 0.0 0.0 TYR 69 0 0.0 0.0 0.0 0.0 VAL 70 0 0.0 0.0 0.0 0.0 HIS 71 0 0.0 0.0 0.0 0.0 LYS 72 0 0.0 0.0 0.0 0.0 GLU 73 0 0.0 0.0 0.0 0.0 GLN 74 0 0.0 0.0 0.0 0.0 ILE 75 0 0.0 0.0 0.0 0.0 GLU 76 0 0.0 0.0 0.0 0.0 ALA 77 0 0.0 0.0 0.0 0.0 VAL 78 0 0.0 0.0 0.0 0.0 LYS 79 0 0.0 0.0 0.0 0.0 ASP 80 0 0.0 0.0 0.0 0.0 ASN 81 0 0.0 0.0 0.0 0.0 PHE 82 0 0.0 0.0 0.0 0.0 LEU 83 0 0.0 0.0 0.0 0.0 GLU 84 0 0.0 0.0 0.0 0.0 LEU 85 0 0.0 0.0 0.0 0.0 VAL 86 0 0.0 0.0 0.0 0.0 LEU 87 0 0.0 0.0 0.0 0.0 GLN 88 0 0.0 0.0 0.0 0.0 SER 89 0 0.0 0.0 0.0 0.0 TYR 90 0 0.0 0.0 0.0 0.0 VAL 91 0 0.0 0.0 0.0 0.0 HIS 92 0 0.0 0.0 0.0 0.0 HIS 93 0 0.0 0.0 0.0 0.0 ILE 94 0 0.0 0.0 0.0 0.0 HIS 95 0 0.0 0.0 0.0 0.0 LYS 96 0 0.0 0.0 0.0 0.0 LYS 97 0 0.0 0.0 0.0 0.0 ARG 98 0 0.0 0.0 0.0 0.0 PHE 99 0 0.0 0.0 0.0 0.0 LYS 100 0 0.0 0.0 0.0 0.0 ASP 101 0 0.0 0.0 0.0 0.0 ILE 102 0 0.0 0.0 0.0 0.0 THR 103 0 0.0 0.0 0.0 0.0 GLU 104 0 0.0 0.0 0.0 0.0 SER 105 0 0.0 0.0 0.0 0.0 VAL 106 0 0.0 0.0 0.0 0.0 LEU 107 0 0.0 0.0 0.0 0.0 TYR 108 0 0.0 0.0 0.0 0.0 THR 109 0 0.0 0.0 0.0 0.0 LEU 110 0 0.0 0.0 0.0 0.0 HIS 111 0 0.0 0.0 0.0 0.0 ALA 112 0 0.0 0.0 0.0 0.0 VAL 113 0 0.0 0.0 0.0 0.0 LYS 114 0 0.0 0.0 0.0 0.0 ASP 115 0 0.0 0.0 0.0 0.0 GLU 116 0 0.0 0.0 0.0 0.0 ILE 117 0 0.0 0.0 0.0 0.0 ALA 118 0 0.0 0.0 0.0 0.0 ARG 119 0 0.0 0.0 0.0 0.0 GLU 120 0 0.0 0.0 0.0 0.0 ASP 121 0 0.0 0.0 0.0 0.0 SER 122 0 0.0 0.0 0.0 0.0 ARG 123 0 0.0 0.0 0.0 0.0 TOTAL 0 0.0 0.0 0.0 0.0 > ANALYZE_cns: Do you want a CONS.OUT file [default no] ?_