Running PDBSTAT from Linux Ayuda is on: /farm/software/PdbStat/PdbStat-5.7 (C) (C) Pdbstat -- A program to evaluate some statistics of macromolecules, (C) given the cartesian coordinates. (C) (C) (c) Copyright 1992-2012 Roberto Tejero and Gaetano T. Montelione (C) Center for Advanced Technology and Medicine (CABM) (C) Rutgers University (C) ** VERSION: 5.7-exp dom mar 10 23:17:04 UTC 2013 ** ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ===============> 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 ... 125 distance records read --> ... Reading/Loading Dihedral Library .. 1119 library records read PdbStat> [rea]d [hel]p [his]tory [men]u [phi] [qui]t... PdbStat> leyendo PDB > locate_file(): file `BER31_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 158 MET LYS LEU HIS THR ASP PRO ALA THR ALA LEU ASN THR 1 > ReadCoordsPdb(): Counting models in file `BER31_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(): I'm reading file BER31_R3Cons_em_bcr3.pdb MODEL 1 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 2358 ATOM records read from file > ReadCoordsPdb(): --> 2358 Regular IUPAC Atoms > ReadCoordsPdb(): --> 0 Pseudo-atoms (DISMAN type) > ReadCoordsPdb(): --> 0 Lone pairs > ReadCoordsPdb(): Bye ... > =============================== INFO ================================ > INFO_mol: # atoms: 2358 (744 C, 1170 H, 221 O, 219 N, 4 S, 0 Q, 0 Metals) > INFO_mol: # residues: 158 (Avg. mol. weight: 106.6) > INFO_mol: # -- M.W. : 16846.7 g/mol. (16.85 kD) Estimated RoG : 15.06 > INFO_mol: CenterMass() -- Working PDB model 1 in file, model no. 1 > INFO_mol: CenterMass() -- Molecule `BER31_R3Cons_em_bcr3.pdb' model #1, TOTAL RESIDUES: 158 > INFO_mol: Radius of Gyration : 15.6945 angstroms > INFO_mol: Center of Masses: x_cm(39.999), y_cm(-13.949), z_cm(4.390) > INFO_res: MKLHTDPATA LNTVTAYGDG YIEVNQVRFS HAIAFAPEGP VASWPVQRPA > INFO_res: DITASLLQQA AGLAEVVRDP LAFLDEPEAG AGARPANAPE VLLVGTGRRQ > INFO_res: HLLGPEQVRP LLAMGVGVEA MDTQAAARTY NILMAEGRRV VVALLPDGDS > INFO_res: LEHHHHHH > INFO_res: > INFO_res: MET LYS LEU HIS THR ASP PRO ALA THR ALA LEU ASN > INFO_res: THR VAL THR ALA TYR GLY ASP GLY TYR ILE GLU VAL > INFO_res: ASN GLN VAL ARG PHE SER HIS ALA ILE ALA PHE ALA > INFO_res: PRO GLU GLY PRO VAL ALA SER TRP PRO VAL GLN ARG > INFO_res: PRO ALA ASP ILE THR ALA SER LEU LEU GLN GLN ALA > INFO_res: ALA GLY LEU ALA GLU VAL VAL ARG ASP PRO LEU ALA > INFO_res: PHE LEU ASP GLU PRO GLU ALA GLY ALA GLY ALA ARG > INFO_res: PRO ALA ASN ALA PRO GLU VAL LEU LEU VAL GLY THR > INFO_res: GLY ARG ARG GLN HIS LEU LEU GLY PRO GLU GLN VAL > INFO_res: ARG PRO LEU LEU ALA MET GLY VAL GLY VAL GLU ALA > INFO_res: MET ASP THR GLN ALA ALA ALA ARG THR TYR ASN ILE > INFO_res: LEU MET ALA GLU GLY ARG ARG VAL VAL VAL ALA LEU > INFO_res: LEU PRO ASP GLY ASP SER LEU GLU HIS HIS HIS HIS > INFO_res: HIS HIS > INFO_res: > INFO_res: 25 ALA 10 ARG 4 ASN 8 ASP 7 GLN 10 GLU > INFO_res: 13 GLY 9 HIS 4 ILE 17 LEU 1 LYS 4 MET > INFO_res: 3 PHE 12 PRO 4 SER 8 THR 3 TYR 1 TRP > INFO_res: 15 VAL > INFO_res: DISULFIDE: ** NO INFO FOR DISULFIDES IN FILE > ===================================================================== > ReadCoordsPdb(): *** monomer, 1 [1] chains *** PdbStat> > locate_file(): file `BER31_R3Cons_em_bcr3.upl' opened for reading 0 SANI-RDC constraints read 1059 NOE-distance constraints (0 Ambiguous NOE/s) read 1059 TOTAL constraints read PdbStat> -------------- SUMMARY OF RESTRAINTS --------------- TOTAL NUMBER OF NOE RESTRAINTS : 1059 INTRA-RESIDUE RESTRAINTS (I=J) : 164 SEQUENTIAL RESTRAINTS (I-J)=1 : 237 BACKBONE-BACKBONE : 96 BACKBONE-SIDE CHAIN : 7 SIDE CHAIN-SIDE CHAIN : 134 MEDIUM RANGE RESTRAINTS 1<(I-J)<5 : 200 BACKBONE-BACKBONE : 32 BACKBONE-SIDE CHAIN : 47 SIDE CHAIN-SIDE CHAIN : 121 LONG RANGE RESTRAINTS (I-J)>=5 : 458 TOTAL HYDROGEN BOND RESTRAINTS : 0 LONG RANGE H-BOND RESTR. (I-J)>=5 : 0 DISULFIDE RESTRAINTS : 0 INTRA-CHAIN RESTRAINTS : 1059 INTER-CHAIN RESTRAINTS : 0 AMBIGUOUS RESTRAINTS : 0 ----------------------------------------------------- ----------------------------------------------------- ----------------------------------------------------- RES # INTRA INTER seq med lng InterChain MET A 1 0 0.0 0.0 0.0 0.0 0.0 LYS A 2 0 0.0 0.0 0.0 0.0 0.0 LEU A 3 0 0.0 0.0 0.0 0.0 0.0 HIS A 4 0 0.0 0.0 0.0 0.0 0.0 THR A 5 0 0.0 0.0 0.0 0.0 0.0 ASP A 6 0 0.0 0.0 0.0 0.0 0.0 PRO A 7 0 0.0 0.0 0.0 0.0 0.0 ALA A 8 0 0.0 0.0 0.0 0.0 0.0 THR A 9 0 0.0 0.0 0.0 0.0 0.0 ALA A 10 0 0.0 0.0 0.0 0.0 0.0 LEU A 11 4 6.0 2.0 0.0 4.0 0.0 ASN A 12 0 3.0 2.5 0.0 0.5 0.0 THR A 13 1 6.5 2.0 2.0 2.5 0.0 VAL A 14 2 14.0 3.0 3.0 8.0 0.0 THR A 15 1 7.0 2.5 2.0 2.5 0.0 ALA A 16 0 4.5 1.5 1.0 2.0 0.0 TYR A 17 2 5.5 1.0 2.0 2.5 0.0 GLY A 18 0 1.0 1.0 0.0 0.0 0.0 ASP A 19 2 2.0 1.5 0.5 0.0 0.0 GLY A 20 0 1.5 1.5 0.0 0.0 0.0 TYR A 21 4 4.0 1.5 1.0 1.5 0.0 ILE A 22 3 14.0 2.5 0.5 11.0 0.0 GLU A 23 2 10.5 4.0 2.0 4.5 0.0 VAL A 24 1 14.0 3.5 1.0 9.5 0.0 ASN A 25 0 2.5 1.5 0.0 1.0 0.0 GLN A 26 1 2.5 0.5 1.0 1.0 0.0 VAL A 27 3 4.0 1.5 2.5 0.0 0.0 ARG A 28 0 4.5 2.0 0.0 2.5 0.0 PHE A 29 2 13.0 1.5 5.0 6.5 0.0 SER A 30 0 2.0 1.5 0.0 0.5 0.0 HIS A 31 0 4.5 2.5 1.5 0.5 0.0 ALA A 32 0 11.5 3.0 0.0 8.5 0.0 ILE A 33 3 16.5 3.0 4.0 9.5 0.0 ALA A 34 0 9.5 2.5 0.0 7.0 0.0 PHE A 35 1 14.0 2.5 1.0 10.5 0.0 ALA A 36 0 8.0 2.0 1.5 4.5 0.0 PRO A 37 0 3.5 0.5 0.0 3.0 0.0 GLU A 38 1 4.5 3.0 1.5 0.0 0.0 GLY A 39 0 3.0 3.0 0.0 0.0 0.0 PRO A 40 0 2.0 2.0 0.0 0.0 0.0 VAL A 41 4 10.5 3.0 0.0 7.5 0.0 ALA A 42 0 5.0 2.0 0.0 3.0 0.0 SER A 43 0 2.5 0.5 0.0 2.0 0.0 TRP A 44 2 19.0 0.5 3.0 15.5 0.0 PRO A 45 0 1.5 1.0 0.0 0.5 0.0 VAL A 46 3 18.0 2.5 4.5 11.0 0.0 GLN A 47 1 4.5 3.5 0.0 1.0 0.0 ARG A 48 2 6.0 1.5 3.0 1.5 0.0 PRO A 49 0 6.0 1.0 2.0 3.0 0.0 ALA A 50 0 3.0 1.5 1.5 0.0 0.0 ASP A 51 0 4.5 1.0 1.0 2.5 0.0 ILE A 52 3 16.5 2.0 4.5 10.0 0.0 THR A 53 1 8.5 2.5 5.5 0.5 0.0 ALA A 54 0 6.5 1.5 2.0 3.0 0.0 SER A 55 2 6.5 2.5 4.0 0.0 0.0 LEU A 56 5 15.5 3.0 8.0 4.5 0.0 LEU A 57 4 10.0 1.5 2.5 6.0 0.0 GLN A 58 3 9.5 2.0 2.5 5.0 0.0 GLN A 59 2 7.0 3.0 3.0 1.0 0.0 ALA A 60 0 6.0 2.0 0.5 3.5 0.0 ALA A 61 0 10.0 0.5 2.0 7.5 0.0 GLY A 62 0 1.0 0.5 0.5 0.0 0.0 LEU A 63 4 7.5 3.0 1.0 3.5 0.0 ALA A 64 0 3.0 2.5 0.0 0.5 0.0 GLU A 65 0 0.0 0.0 0.0 0.0 0.0 VAL A 66 0 0.0 0.0 0.0 0.0 0.0 VAL A 67 0 0.0 0.0 0.0 0.0 0.0 ARG A 68 0 0.0 0.0 0.0 0.0 0.0 ASP A 69 0 0.0 0.0 0.0 0.0 0.0 PRO A 70 0 0.0 0.0 0.0 0.0 0.0 LEU A 71 0 0.0 0.0 0.0 0.0 0.0 ALA A 72 0 0.0 0.0 0.0 0.0 0.0 PHE A 73 0 0.0 0.0 0.0 0.0 0.0 LEU A 74 0 0.0 0.0 0.0 0.0 0.0 ASP A 75 0 0.0 0.0 0.0 0.0 0.0 GLU A 76 0 0.0 0.0 0.0 0.0 0.0 PRO A 77 0 0.0 0.0 0.0 0.0 0.0 GLU A 78 0 0.0 0.0 0.0 0.0 0.0 ALA A 79 0 0.0 0.0 0.0 0.0 0.0 GLY A 80 0 0.0 0.0 0.0 0.0 0.0 ALA A 81 0 0.0 0.0 0.0 0.0 0.0 GLY A 82 0 0.0 0.0 0.0 0.0 0.0 ALA A 83 0 0.0 0.0 0.0 0.0 0.0 ARG A 84 0 0.0 0.0 0.0 0.0 0.0 PRO A 85 0 0.0 0.0 0.0 0.0 0.0 ALA A 86 0 1.0 0.5 0.5 0.0 0.0 ASN A 87 0 1.5 1.5 0.0 0.0 0.0 ALA A 88 0 5.0 1.5 0.5 3.0 0.0 PRO A 89 0 9.0 1.0 0.5 7.5 0.0 GLU A 90 0 2.5 2.0 0.0 0.5 0.0 VAL A 91 3 15.5 3.5 3.0 9.0 0.0 LEU A 92 2 20.5 3.5 0.5 16.5 0.0 LEU A 93 5 22.5 3.5 2.5 16.5 0.0 VAL A 94 2 16.5 3.0 1.5 12.0 0.0 GLY A 95 0 4.5 1.0 0.0 3.5 0.0 THR A 96 1 10.0 0.5 2.5 7.0 0.0 GLY A 97 0 3.0 0.5 0.5 2.0 0.0 ARG A 98 0 3.0 2.0 0.5 0.5 0.0 ARG A 99 0 4.5 3.5 1.0 0.0 0.0 GLN A 100 3 3.5 2.5 0.5 0.5 0.0 HIS A 101 0 6.0 1.5 1.0 3.5 0.0 LEU A 102 0 1.5 1.0 0.0 0.5 0.0 LEU A 103 5 9.5 2.5 1.5 5.5 0.0 GLY A 104 0 2.0 2.0 0.0 0.0 0.0 PRO A 105 0 3.0 1.0 2.0 0.0 0.0 GLU A 106 2 3.5 2.5 1.0 0.0 0.0 GLN A 107 2 4.5 2.5 0.5 1.5 0.0 VAL A 108 2 9.0 2.5 4.5 2.0 0.0 ARG A 109 2 4.5 2.0 2.0 0.5 0.0 PRO A 110 0 7.0 2.0 3.0 2.0 0.0 LEU A 111 4 17.0 3.0 4.5 9.5 0.0 LEU A 112 4 7.0 3.0 3.0 1.0 0.0 ALA A 113 0 4.0 2.0 2.0 0.0 0.0 MET A 114 6 11.5 1.0 6.5 4.0 0.0 GLY A 115 0 1.5 1.0 0.5 0.0 0.0 VAL A 116 3 13.5 2.5 3.0 8.0 0.0 GLY A 117 0 6.5 3.0 0.0 3.5 0.0 VAL A 118 3 9.5 3.0 1.0 5.5 0.0 GLU A 119 1 12.5 4.0 1.0 7.5 0.0 ALA A 120 0 10.5 2.5 1.0 7.0 0.0 MET A 121 7 12.5 2.0 3.0 7.5 0.0 ASP A 122 0 4.5 3.0 1.5 0.0 0.0 THR A 123 1 9.5 3.0 1.0 5.5 0.0 GLN A 124 2 5.0 3.0 1.5 0.5 0.0 ALA A 125 0 6.0 2.0 4.0 0.0 0.0 ALA A 126 0 10.0 1.0 2.5 6.5 0.0 ALA A 127 0 11.0 1.0 3.5 6.5 0.0 ARG A 128 0 5.0 2.0 3.0 0.0 0.0 THR A 129 1 10.5 3.0 5.0 2.5 0.0 TYR A 130 0 13.0 3.0 4.0 6.0 0.0 ASN A 131 0 5.5 2.0 3.0 0.5 0.0 ILE A 132 7 7.5 2.5 5.0 0.0 0.0 LEU A 133 5 10.5 2.5 6.0 2.0 0.0 MET A 134 5 12.5 1.5 3.5 7.5 0.0 ALA A 135 0 3.5 1.0 2.0 0.5 0.0 GLU A 136 2 5.5 1.0 4.5 0.0 0.0 GLY A 137 0 2.0 1.5 0.5 0.0 0.0 ARG A 138 2 3.0 1.5 1.0 0.5 0.0 ARG A 139 2 3.5 2.0 0.0 1.5 0.0 VAL A 140 2 15.5 3.5 1.5 10.5 0.0 VAL A 141 2 21.0 4.0 1.0 16.0 0.0 VAL A 142 2 14.5 3.0 3.0 8.5 0.0 ALA A 143 0 12.0 1.5 1.0 9.5 0.0 LEU A 144 4 12.0 0.0 2.0 10.0 0.0 LEU A 145 1 15.5 0.0 0.0 15.5 0.0 PRO A 146 0 6.0 1.5 0.0 4.5 0.0 ASP A 147 0 3.0 2.5 0.5 0.0 0.0 GLY A 148 0 1.0 1.0 0.0 0.0 0.0 ASP A 149 0 0.5 0.0 0.5 0.0 0.0 SER A 150 0 0.0 0.0 0.0 0.0 0.0 LEU A 151 0 0.0 0.0 0.0 0.0 0.0 GLU A 152 0 0.0 0.0 0.0 0.0 0.0 HIS A 153 0 0.0 0.0 0.0 0.0 0.0 HIS A 154 0 0.0 0.0 0.0 0.0 0.0 HIS A 155 0 0.0 0.0 0.0 0.0 0.0 HIS A 156 0 0.0 0.0 0.0 0.0 0.0 HIS A 157 0 0.0 0.0 0.0 0.0 0.0 HIS A 158 0 0.0 0.0 0.0 0.0 0.0 TOTAL 164 895.0 237.0 200.0 458.0 0.0 > ANALYZE_cns: Do you want a CONS.OUT file [default no] ?_