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 `HR41_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 175 MET ALA ASP GLU ALA THR ARG ARG VAL VAL SER GLU ILE 1 > ReadCoordsPdb(): Counting models in file `HR41_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 HR41_R3Cons_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 57560 ATOM records read from file > ReadCoordsPdb(): --> 57560 Regular IUPAC Atoms > ReadCoordsPdb(): --> 0 Pseudo-atoms (DISMAN type) > ReadCoordsPdb(): --> 0 Lone pairs > ReadCoordsPdb(): Bye ... PdbStat> > locate_file(): file `HR41_R3Cons_em_bcr3.hbond' opened for reading 76 NOE-distance constraints read 76 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 : 76 LONG RANGE H-BOND RESTR. (I-J)>=5 : 16 DISULFIDE CONSTRAINTS : 0 INTRA-CHAIN CONSTRAINTS : 76 INTER-CHAIN CONSTRAINTS : 0 RES # INTRA INTER seq med lng MET 1 0 0.0 0.0 0.0 0.0 ALA 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 ALA 5 0 0.0 0.0 0.0 0.0 THR 6 0 0.0 0.0 0.0 0.0 ARG 7 0 0.0 0.0 0.0 0.0 ARG 8 0 0.0 0.0 0.0 0.0 VAL 9 0 0.0 0.0 0.0 0.0 VAL 10 0 0.0 0.0 0.0 0.0 SER 11 0 0.0 0.0 0.0 0.0 GLU 12 0 0.0 0.0 0.0 0.0 ILE 13 0 0.0 0.0 0.0 0.0 PRO 14 0 0.0 0.0 0.0 0.0 VAL 15 0 0.0 0.0 0.0 0.0 LEU 16 0 0.0 0.0 0.0 0.0 LYS 17 0 0.0 0.0 0.0 0.0 THR 18 0 0.0 0.0 0.0 0.0 ASN 19 0 0.0 0.0 0.0 0.0 ALA 20 0 0.0 0.0 0.0 0.0 GLY 21 0 0.0 0.0 0.0 0.0 PRO 22 0 0.0 0.0 0.0 0.0 ARG 23 0 0.0 0.0 0.0 0.0 ASP 24 0 0.0 0.0 0.0 0.0 ARG 25 0 0.0 0.0 0.0 0.0 GLU 26 0 0.0 0.0 0.0 0.0 LEU 27 0 0.0 0.0 0.0 0.0 TRP 28 0 0.0 0.0 0.0 0.0 VAL 29 0 0.0 0.0 0.0 0.0 GLN 30 0 0.0 0.0 0.0 0.0 ARG 31 0 0.0 0.0 0.0 0.0 LEU 32 0 0.0 0.0 0.0 0.0 LYS 33 0 0.0 0.0 0.0 0.0 GLU 34 0 0.0 0.0 0.0 0.0 GLU 35 0 0.0 0.0 0.0 0.0 TYR 36 0 0.0 0.0 0.0 0.0 GLN 37 0 0.0 0.0 0.0 0.0 SER 38 0 0.0 0.0 0.0 0.0 LEU 39 0 0.0 0.0 0.0 0.0 ILE 40 0 0.0 0.0 0.0 0.0 ARG 41 0 0.0 0.0 0.0 0.0 TYR 42 0 0.0 0.0 0.0 0.0 VAL 43 0 0.0 0.0 0.0 0.0 GLU 44 0 0.0 0.0 0.0 0.0 ASN 45 0 0.0 0.0 0.0 0.0 ASN 46 0 0.0 0.0 0.0 0.0 LYS 47 0 0.0 0.0 0.0 0.0 ASN 48 0 0.0 0.0 0.0 0.0 ALA 49 0 0.0 0.0 0.0 0.0 ASP 50 0 0.0 0.0 0.0 0.0 ASN 51 0 0.0 0.0 0.0 0.0 ASP 52 0 0.0 0.0 0.0 0.0 TRP 53 0 0.0 0.0 0.0 0.0 PHE 54 0 0.0 0.0 0.0 0.0 ARG 55 0 0.0 0.0 0.0 0.0 LEU 56 0 0.0 0.0 0.0 0.0 GLU 57 0 0.0 0.0 0.0 0.0 SER 58 0 0.0 0.0 0.0 0.0 ASN 59 0 0.0 0.0 0.0 0.0 LYS 60 0 0.0 0.0 0.0 0.0 GLU 61 0 0.0 0.0 0.0 0.0 GLY 62 0 0.0 0.0 0.0 0.0 THR 63 0 0.0 0.0 0.0 0.0 ARG 64 0 0.0 0.0 0.0 0.0 TRP 65 0 0.0 0.0 0.0 0.0 PHE 66 0 0.0 0.0 0.0 0.0 GLY 67 0 0.0 0.0 0.0 0.0 LYS 68 0 0.0 0.0 0.0 0.0 CYS 69 0 0.0 0.0 0.0 0.0 TRP 70 0 0.0 0.0 0.0 0.0 TYR 71 0 0.0 0.0 0.0 0.0 ILE 72 0 0.0 0.0 0.0 0.0 HIS 73 0 0.0 0.0 0.0 0.0 ASP 74 0 0.0 0.0 0.0 0.0 LEU 75 0 0.0 0.0 0.0 0.0 LEU 76 0 0.0 0.0 0.0 0.0 LYS 77 0 0.0 0.0 0.0 0.0 TYR 78 0 0.0 0.0 0.0 0.0 GLU 79 0 0.0 0.0 0.0 0.0 PHE 80 0 0.0 0.0 0.0 0.0 ASP 81 0 0.0 0.0 0.0 0.0 ILE 82 0 0.0 0.0 0.0 0.0 GLU 83 0 0.0 0.0 0.0 0.0 PHE 84 0 0.0 0.0 0.0 0.0 ASP 85 0 0.0 0.0 0.0 0.0 ILE 86 0 0.0 0.0 0.0 0.0 PRO 87 0 0.0 0.0 0.0 0.0 ILE 88 0 0.0 0.0 0.0 0.0 THR 89 0 0.0 0.0 0.0 0.0 TYR 90 0 0.0 0.0 0.0 0.0 PRO 91 0 0.0 0.0 0.0 0.0 THR 92 0 0.0 0.0 0.0 0.0 THR 93 0 0.0 0.0 0.0 0.0 ALA 94 0 0.0 0.0 0.0 0.0 PRO 95 0 0.0 0.0 0.0 0.0 GLU 96 0 0.0 0.0 0.0 0.0 ILE 97 0 0.0 0.0 0.0 0.0 ALA 98 0 0.0 0.0 0.0 0.0 VAL 99 0 0.0 0.0 0.0 0.0 PRO 100 0 0.0 0.0 0.0 0.0 GLU 101 0 0.0 0.0 0.0 0.0 LEU 102 0 0.0 0.0 0.0 0.0 ASP 103 0 0.0 0.0 0.0 0.0 GLY 104 0 0.0 0.0 0.0 0.0 LYS 105 0 0.0 0.0 0.0 0.0 THR 106 0 0.0 0.0 0.0 0.0 ALA 107 0 0.0 0.0 0.0 0.0 LYS 108 0 0.0 0.0 0.0 0.0 MET 109 0 0.0 0.0 0.0 0.0 TYR 110 0 0.0 0.0 0.0 0.0 ARG 111 0 0.0 0.0 0.0 0.0 GLY 112 0 0.0 0.0 0.0 0.0 GLY 113 0 0.0 0.0 0.0 0.0 LYS 114 0 0.0 0.0 0.0 0.0 ILE 115 0 0.0 0.0 0.0 0.0 CYS 116 0 0.0 0.0 0.0 0.0 LEU 117 0 0.0 0.0 0.0 0.0 THR 118 0 0.0 0.0 0.0 0.0 ASP 119 0 0.0 0.0 0.0 0.0 HIS 120 0 0.0 0.0 0.0 0.0 PHE 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 LEU 124 0 0.0 0.0 0.0 0.0 TRP 125 0 0.0 0.0 0.0 0.0 ALA 126 0 0.0 0.0 0.0 0.0 ARG 127 0 0.0 0.0 0.0 0.0 ASN 128 0 0.0 0.0 0.0 0.0 VAL 129 0 0.0 0.0 0.0 0.0 PRO 130 0 0.0 0.0 0.0 0.0 LYS 131 0 0.0 0.0 0.0 0.0 PHE 132 0 0.0 0.0 0.0 0.0 GLY 133 0 0.0 0.0 0.0 0.0 LEU 134 0 0.0 0.0 0.0 0.0 ALA 135 0 0.0 0.0 0.0 0.0 HIS 136 0 0.0 0.0 0.0 0.0 LEU 137 0 0.0 0.0 0.0 0.0 MET 138 0 0.0 0.0 0.0 0.0 ALA 139 0 0.0 0.0 0.0 0.0 LEU 140 0 0.0 0.0 0.0 0.0 GLY 141 0 0.0 0.0 0.0 0.0 LEU 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 TRP 145 0 0.0 0.0 0.0 0.0 LEU 146 0 0.0 0.0 0.0 0.0 ALA 147 0 0.0 0.0 0.0 0.0 VAL 148 0 0.0 0.0 0.0 0.0 GLU 149 0 0.0 0.0 0.0 0.0 ILE 150 0 0.0 0.0 0.0 0.0 PRO 151 0 0.0 0.0 0.0 0.0 ASP 152 0 0.0 0.0 0.0 0.0 LEU 153 0 0.0 0.0 0.0 0.0 ILE 154 0 0.0 0.0 0.0 0.0 GLN 155 0 0.0 0.0 0.0 0.0 LYS 156 0 0.0 0.0 0.0 0.0 GLY 157 0 0.0 0.0 0.0 0.0 VAL 158 0 0.0 0.0 0.0 0.0 ILE 159 0 0.0 0.0 0.0 0.0 GLN 160 0 0.0 0.0 0.0 0.0 HIS 161 0 0.0 0.0 0.0 0.0 LYS 162 0 0.0 0.0 0.0 0.0 GLU 163 0 0.0 0.0 0.0 0.0 LYS 164 0 0.0 0.0 0.0 0.0 CYS 165 0 0.0 0.0 0.0 0.0 ASN 166 0 0.0 0.0 0.0 0.0 GLN 167 0 0.0 0.0 0.0 0.0 LEU 168 0 0.0 0.0 0.0 0.0 GLU 169 0 0.0 0.0 0.0 0.0 HIS 170 0 0.0 0.0 0.0 0.0 HIS 171 0 0.0 0.0 0.0 0.0 HIS 172 0 0.0 0.0 0.0 0.0 HIS 173 0 0.0 0.0 0.0 0.0 HIS 174 0 0.0 0.0 0.0 0.0 HIS 175 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] ?_