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 `CTR107_R3_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> EXPDTA NMR, 21 STRUCTURES > ReadCoordsPdb(): >> REMARK PdbStat -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > ReadCoordsPdb(): >> REMARK PdbStat -- PDB COORDINATES FOR TEMP.PDB, 20 MODEL/S TEMP.PDB > ReadCoordsPdb(): >> REMARK PdbStat -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > ReadCoordsPdb(): >> SEQRES 1 A 166 MET ASP PHE GLU CYS GLN PHE VAL CYS GLU LEU LYS GLU 1 > ReadCoordsPdb(): Counting models in file `CTR107_R3_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 CTR107_R3_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 49740 ATOM records read from file > ReadCoordsPdb(): --> 49740 Regular IUPAC Atoms > ReadCoordsPdb(): --> 0 Pseudo-atoms (DISMAN type) > ReadCoordsPdb(): --> 0 Lone pairs > ReadCoordsPdb(): Bye ... PdbStat> > locate_file(): file `CTR107_R3_em_bcr3.hbond' opened for reading 44 NOE-distance constraints read 44 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 : 44 LONG RANGE H-BOND RESTR. (I-J)>=5 : 40 DISULFIDE CONSTRAINTS : 0 INTRA-CHAIN CONSTRAINTS : 44 INTER-CHAIN CONSTRAINTS : 0 RES # INTRA INTER seq med lng MET 1 0 0.0 0.0 0.0 0.0 ASP 2 0 0.0 0.0 0.0 0.0 PHE 3 0 0.0 0.0 0.0 0.0 GLU 4 0 0.0 0.0 0.0 0.0 CYS 5 0 0.0 0.0 0.0 0.0 GLN 6 0 0.0 0.0 0.0 0.0 PHE 7 0 0.0 0.0 0.0 0.0 VAL 8 0 0.0 0.0 0.0 0.0 CYS 9 0 0.0 0.0 0.0 0.0 GLU 10 0 0.0 0.0 0.0 0.0 LEU 11 0 0.0 0.0 0.0 0.0 LYS 12 0 0.0 0.0 0.0 0.0 GLU 13 0 0.0 0.0 0.0 0.0 LEU 14 0 0.0 0.0 0.0 0.0 ALA 15 0 0.0 0.0 0.0 0.0 PRO 16 0 0.0 0.0 0.0 0.0 VAL 17 0 0.0 0.0 0.0 0.0 PRO 18 0 0.0 0.0 0.0 0.0 ALA 19 0 0.0 0.0 0.0 0.0 LEU 20 0 0.0 0.0 0.0 0.0 LEU 21 0 0.0 0.0 0.0 0.0 ILE 22 0 0.0 0.0 0.0 0.0 ARG 23 0 0.0 0.0 0.0 0.0 THR 24 0 0.0 0.0 0.0 0.0 GLN 25 0 0.0 0.0 0.0 0.0 THR 26 0 0.0 0.0 0.0 0.0 ALA 27 0 0.0 0.0 0.0 0.0 MET 28 0 0.0 0.0 0.0 0.0 SER 29 0 0.0 0.0 0.0 0.0 GLU 30 0 0.0 0.0 0.0 0.0 LEU 31 0 0.0 0.0 0.0 0.0 GLY 32 0 0.0 0.0 0.0 0.0 SER 33 0 0.0 0.0 0.0 0.0 LEU 34 0 0.0 0.0 0.0 0.0 PHE 35 0 0.0 0.0 0.0 0.0 GLU 36 0 0.0 0.0 0.0 0.0 ALA 37 0 0.0 0.0 0.0 0.0 GLY 38 0 0.0 0.0 0.0 0.0 TYR 39 0 0.0 0.0 0.0 0.0 HIS 40 0 0.0 0.0 0.0 0.0 ASP 41 0 0.0 0.0 0.0 0.0 ILE 42 0 0.0 0.0 0.0 0.0 LEU 43 0 0.0 0.0 0.0 0.0 GLN 44 0 0.0 0.0 0.0 0.0 LEU 45 0 0.0 0.0 0.0 0.0 LEU 46 0 0.0 0.0 0.0 0.0 ALA 47 0 0.0 0.0 0.0 0.0 GLY 48 0 0.0 0.0 0.0 0.0 GLN 49 0 0.0 0.0 0.0 0.0 GLY 50 0 0.0 0.0 0.0 0.0 LYS 51 0 0.0 0.0 0.0 0.0 SER 52 0 0.0 0.0 0.0 0.0 PRO 53 0 0.0 0.0 0.0 0.0 SER 54 0 0.0 0.0 0.0 0.0 GLY 55 0 0.0 0.0 0.0 0.0 PRO 56 0 0.0 0.0 0.0 0.0 PRO 57 0 0.0 0.0 0.0 0.0 PHE 58 0 0.0 0.0 0.0 0.0 ALA 59 0 0.0 0.0 0.0 0.0 ARG 60 0 0.0 0.0 0.0 0.0 TYR 61 0 0.0 0.0 0.0 0.0 PHE 62 0 0.0 0.0 0.0 0.0 GLY 63 0 0.0 0.0 0.0 0.0 MET 64 0 0.0 0.0 0.0 0.0 SER 65 0 0.0 0.0 0.0 0.0 ALA 66 0 0.0 0.0 0.0 0.0 GLY 67 0 0.0 0.0 0.0 0.0 THR 68 0 0.0 0.0 0.0 0.0 PHE 69 0 0.0 0.0 0.0 0.0 GLU 70 0 0.0 0.0 0.0 0.0 VAL 71 0 0.0 0.0 0.0 0.0 GLU 72 0 0.0 0.0 0.0 0.0 PHE 73 0 0.0 0.0 0.0 0.0 GLY 74 0 0.0 0.0 0.0 0.0 PHE 75 0 0.0 0.0 0.0 0.0 PRO 76 0 0.0 0.0 0.0 0.0 VAL 77 0 0.0 0.0 0.0 0.0 GLU 78 0 0.0 0.0 0.0 0.0 GLY 79 0 0.0 0.0 0.0 0.0 GLY 80 0 0.0 0.0 0.0 0.0 VAL 81 0 0.0 0.0 0.0 0.0 GLU 82 0 0.0 0.0 0.0 0.0 GLY 83 0 0.0 0.0 0.0 0.0 SER 84 0 0.0 0.0 0.0 0.0 GLY 85 0 0.0 0.0 0.0 0.0 ARG 86 0 0.0 0.0 0.0 0.0 VAL 87 0 0.0 0.0 0.0 0.0 VAL 88 0 0.0 0.0 0.0 0.0 THR 89 0 0.0 0.0 0.0 0.0 GLY 90 0 0.0 0.0 0.0 0.0 LEU 91 0 0.0 0.0 0.0 0.0 THR 92 0 0.0 0.0 0.0 0.0 PRO 93 0 0.0 0.0 0.0 0.0 SER 94 0 0.0 0.0 0.0 0.0 GLY 95 0 0.0 0.0 0.0 0.0 LYS 96 0 0.0 0.0 0.0 0.0 ALA 97 0 0.0 0.0 0.0 0.0 ALA 98 0 0.0 0.0 0.0 0.0 SER 99 0 0.0 0.0 0.0 0.0 SER 100 0 0.0 0.0 0.0 0.0 LEU 101 0 0.0 0.0 0.0 0.0 TYR 102 0 0.0 0.0 0.0 0.0 ILE 103 0 0.0 0.0 0.0 0.0 GLY 104 0 0.0 0.0 0.0 0.0 PRO 105 0 0.0 0.0 0.0 0.0 TYR 106 0 0.0 0.0 0.0 0.0 GLY 107 0 0.0 0.0 0.0 0.0 GLU 108 0 0.0 0.0 0.0 0.0 ILE 109 0 0.0 0.0 0.0 0.0 GLU 110 0 0.0 0.0 0.0 0.0 ALA 111 0 0.0 0.0 0.0 0.0 VAL 112 0 0.0 0.0 0.0 0.0 TYR 113 0 0.0 0.0 0.0 0.0 ASP 114 0 0.0 0.0 0.0 0.0 ALA 115 0 0.0 0.0 0.0 0.0 LEU 116 0 0.0 0.0 0.0 0.0 MET 117 0 0.0 0.0 0.0 0.0 LYS 118 0 0.0 0.0 0.0 0.0 TRP 119 0 0.0 0.0 0.0 0.0 VAL 120 0 0.0 0.0 0.0 0.0 ASP 121 0 0.0 0.0 0.0 0.0 ASP 122 0 0.0 0.0 0.0 0.0 ASN 123 0 0.0 0.0 0.0 0.0 GLY 124 0 0.0 0.0 0.0 0.0 PHE 125 0 0.0 0.0 0.0 0.0 ASP 126 0 0.0 0.0 0.0 0.0 LEU 127 0 0.0 0.0 0.0 0.0 SER 128 0 0.0 0.0 0.0 0.0 GLY 129 0 0.0 0.0 0.0 0.0 GLU 130 0 0.0 0.0 0.0 0.0 ALA 131 0 0.0 0.0 0.0 0.0 TYR 132 0 0.0 0.0 0.0 0.0 GLU 133 0 0.0 0.0 0.0 0.0 ILE 134 0 0.0 0.0 0.0 0.0 TYR 135 0 0.0 0.0 0.0 0.0 LEU 136 0 0.0 0.0 0.0 0.0 ASP 137 0 0.0 0.0 0.0 0.0 ASN 138 0 0.0 0.0 0.0 0.0 PRO 139 0 0.0 0.0 0.0 0.0 ALA 140 0 0.0 0.0 0.0 0.0 GLU 141 0 0.0 0.0 0.0 0.0 THR 142 0 0.0 0.0 0.0 0.0 ALA 143 0 0.0 0.0 0.0 0.0 PRO 144 0 0.0 0.0 0.0 0.0 ASP 145 0 0.0 0.0 0.0 0.0 GLN 146 0 0.0 0.0 0.0 0.0 LEU 147 0 0.0 0.0 0.0 0.0 ARG 148 0 0.0 0.0 0.0 0.0 THR 149 0 0.0 0.0 0.0 0.0 ARG 150 0 0.0 0.0 0.0 0.0 VAL 151 0 0.0 0.0 0.0 0.0 SER 152 0 0.0 0.0 0.0 0.0 LEU 153 0 0.0 0.0 0.0 0.0 MET 154 0 0.0 0.0 0.0 0.0 LEU 155 0 0.0 0.0 0.0 0.0 HIS 156 0 0.0 0.0 0.0 0.0 GLU 157 0 0.0 0.0 0.0 0.0 SER 158 0 0.0 0.0 0.0 0.0 LEU 159 0 0.0 0.0 0.0 0.0 GLU 160 0 0.0 0.0 0.0 0.0 HIS 161 0 0.0 0.0 0.0 0.0 HIS 162 0 0.0 0.0 0.0 0.0 HIS 163 0 0.0 0.0 0.0 0.0 HIS 164 0 0.0 0.0 0.0 0.0 HIS 165 0 0.0 0.0 0.0 0.0 HIS 166 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] ?_