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 `SGR145_R3Cons_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> EXPDTA NMR, 21 STRUCTURES > ReadCoordsPdb(): >> REMARK PdbStat -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > ReadCoordsPdb(): >> REMARK PdbStat -- PDB COORDINATES FOR TEMP_BCM_111.PDB, 20 MODEL/S TEMP_BCM_111.PDB > ReadCoordsPdb(): >> REMARK PdbStat -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > ReadCoordsPdb(): >> SEQRES 1 A 202 MET TRP ASP GLU ARG PHE SER GLN SER GLU TYR VAL TYR 1 > ReadCoordsPdb(): Counting models in file `SGR145_R3Cons_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 SGR145_R3Cons_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 62660 ATOM records read from file > ReadCoordsPdb(): --> 62660 Regular IUPAC Atoms > ReadCoordsPdb(): --> 0 Pseudo-atoms (DISMAN type) > ReadCoordsPdb(): --> 0 Lone pairs > ReadCoordsPdb(): Bye ... PdbStat> > locate_file(): file `SGR145_R3Cons_em_bcr3.hbond' opened for reading 92 NOE-distance constraints read 92 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 : 92 LONG RANGE H-BOND RESTR. (I-J)>=5 : 34 DISULFIDE CONSTRAINTS : 0 INTRA-CHAIN CONSTRAINTS : 92 INTER-CHAIN CONSTRAINTS : 0 RES # INTRA INTER seq med lng MET 1 0 0.0 0.0 0.0 0.0 TRP 2 0 0.0 0.0 0.0 0.0 ASP 3 0 0.0 0.0 0.0 0.0 GLU 4 0 0.0 0.0 0.0 0.0 ARG 5 0 0.0 0.0 0.0 0.0 PHE 6 0 0.0 0.0 0.0 0.0 SER 7 0 0.0 0.0 0.0 0.0 GLN 8 0 0.0 0.0 0.0 0.0 SER 9 0 0.0 0.0 0.0 0.0 GLU 10 0 0.0 0.0 0.0 0.0 TYR 11 0 0.0 0.0 0.0 0.0 VAL 12 0 0.0 0.0 0.0 0.0 TYR 13 0 0.0 0.0 0.0 0.0 GLY 14 0 0.0 0.0 0.0 0.0 THR 15 0 0.0 0.0 0.0 0.0 GLU 16 0 0.0 0.0 0.0 0.0 PRO 17 0 0.0 0.0 0.0 0.0 ASN 18 0 0.0 0.0 0.0 0.0 ASP 19 0 0.0 0.0 0.0 0.0 PHE 20 0 0.0 0.0 0.0 0.0 LEU 21 0 0.0 0.0 0.0 0.0 VAL 22 0 0.0 0.0 0.0 0.0 SER 23 0 0.0 0.0 0.0 0.0 VAL 24 0 0.0 0.0 0.0 0.0 ALA 25 0 0.0 0.0 0.0 0.0 ASN 26 0 0.0 0.0 0.0 0.0 GLN 27 0 0.0 0.0 0.0 0.0 ILE 28 0 0.0 0.0 0.0 0.0 PRO 29 0 0.0 0.0 0.0 0.0 GLN 30 0 0.0 0.0 0.0 0.0 GLY 31 0 0.0 0.0 0.0 0.0 LYS 32 0 0.0 0.0 0.0 0.0 ILE 33 0 0.0 0.0 0.0 0.0 LEU 34 0 0.0 0.0 0.0 0.0 CYS 35 0 0.0 0.0 0.0 0.0 LEU 36 0 0.0 0.0 0.0 0.0 ALA 37 0 0.0 0.0 0.0 0.0 GLU 38 0 0.0 0.0 0.0 0.0 GLY 39 0 0.0 0.0 0.0 0.0 GLU 40 0 0.0 0.0 0.0 0.0 GLY 41 0 0.0 0.0 0.0 0.0 ARG 42 0 0.0 0.0 0.0 0.0 ASN 43 0 0.0 0.0 0.0 0.0 ALA 44 0 0.0 0.0 0.0 0.0 CYS 45 0 0.0 0.0 0.0 0.0 PHE 46 0 0.0 0.0 0.0 0.0 LEU 47 0 0.0 0.0 0.0 0.0 ALA 48 0 0.0 0.0 0.0 0.0 SER 49 0 0.0 0.0 0.0 0.0 LEU 50 0 0.0 0.0 0.0 0.0 GLY 51 0 0.0 0.0 0.0 0.0 TYR 52 0 0.0 0.0 0.0 0.0 GLU 53 0 0.0 0.0 0.0 0.0 VAL 54 0 0.0 0.0 0.0 0.0 THR 55 0 0.0 0.0 0.0 0.0 ALA 56 0 0.0 0.0 0.0 0.0 VAL 57 0 0.0 0.0 0.0 0.0 ASP 58 0 0.0 0.0 0.0 0.0 GLN 59 0 0.0 0.0 0.0 0.0 SER 60 0 0.0 0.0 0.0 0.0 SER 61 0 0.0 0.0 0.0 0.0 VAL 62 0 0.0 0.0 0.0 0.0 GLY 63 0 0.0 0.0 0.0 0.0 LEU 64 0 0.0 0.0 0.0 0.0 ALA 65 0 0.0 0.0 0.0 0.0 LYS 66 0 0.0 0.0 0.0 0.0 ALA 67 0 0.0 0.0 0.0 0.0 LYS 68 0 0.0 0.0 0.0 0.0 GLN 69 0 0.0 0.0 0.0 0.0 LEU 70 0 0.0 0.0 0.0 0.0 ALA 71 0 0.0 0.0 0.0 0.0 GLN 72 0 0.0 0.0 0.0 0.0 GLU 73 0 0.0 0.0 0.0 0.0 LYS 74 0 0.0 0.0 0.0 0.0 GLY 75 0 0.0 0.0 0.0 0.0 VAL 76 0 0.0 0.0 0.0 0.0 LYS 77 0 0.0 0.0 0.0 0.0 ILE 78 0 0.0 0.0 0.0 0.0 THR 79 0 0.0 0.0 0.0 0.0 THR 80 0 0.0 0.0 0.0 0.0 VAL 81 0 0.0 0.0 0.0 0.0 GLN 82 0 0.0 0.0 0.0 0.0 SER 83 0 0.0 0.0 0.0 0.0 ASN 84 0 0.0 0.0 0.0 0.0 LEU 85 0 0.0 0.0 0.0 0.0 ALA 86 0 0.0 0.0 0.0 0.0 ASP 87 0 0.0 0.0 0.0 0.0 PHE 88 0 0.0 0.0 0.0 0.0 ASP 89 0 0.0 0.0 0.0 0.0 ILE 90 0 0.0 0.0 0.0 0.0 VAL 91 0 0.0 0.0 0.0 0.0 ALA 92 0 0.0 0.0 0.0 0.0 ASP 93 0 0.0 0.0 0.0 0.0 ALA 94 0 0.0 0.0 0.0 0.0 TRP 95 0 0.0 0.0 0.0 0.0 GLU 96 0 0.0 0.0 0.0 0.0 GLY 97 0 0.0 0.0 0.0 0.0 ILE 98 0 0.0 0.0 0.0 0.0 VAL 99 0 0.0 0.0 0.0 0.0 SER 100 0 0.0 0.0 0.0 0.0 ILE 101 0 0.0 0.0 0.0 0.0 PHE 102 0 0.0 0.0 0.0 0.0 CYS 103 0 0.0 0.0 0.0 0.0 HIS 104 0 0.0 0.0 0.0 0.0 LEU 105 0 0.0 0.0 0.0 0.0 PRO 106 0 0.0 0.0 0.0 0.0 SER 107 0 0.0 0.0 0.0 0.0 SER 108 0 0.0 0.0 0.0 0.0 LEU 109 0 0.0 0.0 0.0 0.0 ARG 110 0 0.0 0.0 0.0 0.0 GLN 111 0 0.0 0.0 0.0 0.0 GLN 112 0 0.0 0.0 0.0 0.0 LEU 113 0 0.0 0.0 0.0 0.0 TYR 114 0 0.0 0.0 0.0 0.0 PRO 115 0 0.0 0.0 0.0 0.0 LYS 116 0 0.0 0.0 0.0 0.0 VAL 117 0 0.0 0.0 0.0 0.0 TYR 118 0 0.0 0.0 0.0 0.0 GLN 119 0 0.0 0.0 0.0 0.0 GLY 120 0 0.0 0.0 0.0 0.0 LEU 121 0 0.0 0.0 0.0 0.0 LYS 122 0 0.0 0.0 0.0 0.0 PRO 123 0 0.0 0.0 0.0 0.0 GLY 124 0 0.0 0.0 0.0 0.0 GLY 125 0 0.0 0.0 0.0 0.0 VAL 126 0 0.0 0.0 0.0 0.0 PHE 127 0 0.0 0.0 0.0 0.0 ILE 128 0 0.0 0.0 0.0 0.0 LEU 129 0 0.0 0.0 0.0 0.0 GLU 130 0 0.0 0.0 0.0 0.0 GLY 131 0 0.0 0.0 0.0 0.0 PHE 132 0 0.0 0.0 0.0 0.0 ALA 133 0 0.0 0.0 0.0 0.0 PRO 134 0 0.0 0.0 0.0 0.0 GLU 135 0 0.0 0.0 0.0 0.0 GLN 136 0 0.0 0.0 0.0 0.0 LEU 137 0 0.0 0.0 0.0 0.0 GLN 138 0 0.0 0.0 0.0 0.0 TYR 139 0 0.0 0.0 0.0 0.0 ASN 140 0 0.0 0.0 0.0 0.0 THR 141 0 0.0 0.0 0.0 0.0 GLY 142 0 0.0 0.0 0.0 0.0 GLY 143 0 0.0 0.0 0.0 0.0 PRO 144 0 0.0 0.0 0.0 0.0 LYS 145 0 0.0 0.0 0.0 0.0 ASP 146 0 0.0 0.0 0.0 0.0 LEU 147 0 0.0 0.0 0.0 0.0 ASP 148 0 0.0 0.0 0.0 0.0 LEU 149 0 0.0 0.0 0.0 0.0 LEU 150 0 0.0 0.0 0.0 0.0 PRO 151 0 0.0 0.0 0.0 0.0 LYS 152 0 0.0 0.0 0.0 0.0 LEU 153 0 0.0 0.0 0.0 0.0 GLU 154 0 0.0 0.0 0.0 0.0 THR 155 0 0.0 0.0 0.0 0.0 LEU 156 0 0.0 0.0 0.0 0.0 GLN 157 0 0.0 0.0 0.0 0.0 SER 158 0 0.0 0.0 0.0 0.0 GLU 159 0 0.0 0.0 0.0 0.0 LEU 160 0 0.0 0.0 0.0 0.0 PRO 161 0 0.0 0.0 0.0 0.0 SER 162 0 0.0 0.0 0.0 0.0 LEU 163 0 0.0 0.0 0.0 0.0 ASN 164 0 0.0 0.0 0.0 0.0 TRP 165 0 0.0 0.0 0.0 0.0 LEU 166 0 0.0 0.0 0.0 0.0 ILE 167 0 0.0 0.0 0.0 0.0 ALA 168 0 0.0 0.0 0.0 0.0 ASN 169 0 0.0 0.0 0.0 0.0 ASN 170 0 0.0 0.0 0.0 0.0 LEU 171 0 0.0 0.0 0.0 0.0 GLU 172 0 0.0 0.0 0.0 0.0 ARG 173 0 0.0 0.0 0.0 0.0 ASN 174 0 0.0 0.0 0.0 0.0 LEU 175 0 0.0 0.0 0.0 0.0 ASP 176 0 0.0 0.0 0.0 0.0 GLU 177 0 0.0 0.0 0.0 0.0 GLY 178 0 0.0 0.0 0.0 0.0 ALA 179 0 0.0 0.0 0.0 0.0 TYR 180 0 0.0 0.0 0.0 0.0 HIS 181 0 0.0 0.0 0.0 0.0 GLN 182 0 0.0 0.0 0.0 0.0 GLY 183 0 0.0 0.0 0.0 0.0 LYS 184 0 0.0 0.0 0.0 0.0 ALA 185 0 0.0 0.0 0.0 0.0 ALA 186 0 0.0 0.0 0.0 0.0 LEU 187 0 0.0 0.0 0.0 0.0 ILE 188 0 0.0 0.0 0.0 0.0 GLN 189 0 0.0 0.0 0.0 0.0 LEU 190 0 0.0 0.0 0.0 0.0 LEU 191 0 0.0 0.0 0.0 0.0 GLY 192 0 0.0 0.0 0.0 0.0 GLN 193 0 0.0 0.0 0.0 0.0 LYS 194 0 0.0 0.0 0.0 0.0 LEU 195 0 0.0 0.0 0.0 0.0 GLU 196 0 0.0 0.0 0.0 0.0 HIS 197 0 0.0 0.0 0.0 0.0 HIS 198 0 0.0 0.0 0.0 0.0 HIS 199 0 0.0 0.0 0.0 0.0 HIS 200 0 0.0 0.0 0.0 0.0 HIS 201 0 0.0 0.0 0.0 0.0 HIS 202 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] ?_