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 `HR41_NMR_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 25-JAN-08 2K07 > ReadCoordsPdb(): >> TITLE SOLUTION NMR STRUCTURE OF HUMAN E2-LIKE UBIQUITIN-FOLD > ReadCoordsPdb(): >> TITLE 2 MODIFIER CONJUGATING ENZYME 1 (UFC1). NORTHEAST STRUCTURAL > ReadCoordsPdb(): >> TITLE 3 GENOMICS CONSORTIUM TARGET HR41 > ReadCoordsPdb(): >> COMPND MOL_ID: 1; 1 > ReadCoordsPdb(): Counting models in file `HR41_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(): I'm reading file HR41_NMR_em_bcr3.pdb MODEL 1 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 2888 ATOM records read from file > ReadCoordsPdb(): --> 2888 Regular IUPAC Atoms > ReadCoordsPdb(): --> 0 Pseudo-atoms (DISMAN type) > ReadCoordsPdb(): --> 0 Lone pairs > ReadCoordsPdb(): Bye ... > =============================== INFO ================================ > INFO_mol: # atoms: 2888 (931 C, 1437 H, 256 O, 258 N, 6 S, 0 Q, 0 Metals) > INFO_mol: # residues: 175 (Avg. mol. weight: 117.3) > INFO_mol: # -- M.W. : 20532.0 g/mol. (20.53 kD) Estimated RoG : 15.66 > INFO_mol: CenterMass() -- Working PDB model 1 in file, model no. 1 > INFO_mol: CenterMass() -- Molecule `HR41_NMR_em_bcr3.pdb' model #1, TOTAL RESIDUES: 175 > INFO_mol: Radius of Gyration : 17.5449 angstroms > INFO_mol: Center of Masses: x_cm(1.849), y_cm(11.716), z_cm(19.785) > INFO_res: MADEATRRVV SEIPVLKTNA GPRDRELWVQ RLKEEYQSLI RYVENNKNAD > INFO_res: NDWFRLESNK EGTRWFGKCW YIHDLLKYEF DIEFDIPITY PTTAPEIAVP > INFO_res: ELDGKTAKMY RGGKICLTDH FKPLWARNVP KFGLAHLMAL GLGPWLAVEI > INFO_res: PDLIQKGVIQ HKEKCNQLEH HHHHH > INFO_res: > INFO_res: MET ALA ASP GLU ALA THR ARG ARG VAL VAL SER GLU > INFO_res: ILE PRO VAL LEU LYS THR ASN ALA GLY PRO ARG ASP > INFO_res: ARG GLU LEU TRP VAL GLN ARG LEU LYS GLU GLU TYR > INFO_res: GLN SER LEU ILE ARG TYR VAL GLU ASN ASN LYS ASN > INFO_res: ALA ASP ASN ASP TRP PHE ARG LEU GLU SER ASN LYS > INFO_res: GLU GLY THR ARG TRP PHE GLY LYS CYS TRP TYR ILE > INFO_res: HIS ASP LEU LEU LYS TYR GLU PHE ASP ILE GLU PHE > INFO_res: ASP ILE PRO ILE THR TYR PRO THR THR ALA PRO GLU > INFO_res: ILE ALA VAL PRO GLU LEU ASP GLY LYS THR ALA LYS > INFO_res: MET TYR ARG GLY GLY LYS ILE CYS LEU THR ASP HIS > INFO_res: PHE LYS PRO LEU TRP ALA ARG ASN VAL PRO LYS PHE > INFO_res: GLY LEU ALA HIS LEU MET ALA LEU GLY LEU GLY PRO > INFO_res: TRP LEU ALA VAL GLU ILE PRO ASP LEU ILE GLN LYS > INFO_res: GLY VAL ILE GLN HIS LYS GLU LYS CYS ASN GLN LEU > INFO_res: GLU HIS HIS HIS HIS HIS HIS > INFO_res: > INFO_res: 11 ALA 10 ARG 8 ASN 10 ASP 3 CYS 5 GLN > INFO_res: 15 GLU 10 GLY 10 HIS 11 ILE 17 LEU 14 LYS > INFO_res: 3 MET 6 PHE 10 PRO 3 SER 8 THR 6 TYR > INFO_res: 6 TRP 9 VAL > INFO_res: DISULFIDE: ** NO INFO FOR DISULFIDES IN FILE > ===================================================================== > ReadCoordsPdb(): *** monomer, 1 [1] chains *** PdbStat> > locate_file(): file `HR41_NMR_em_bcr3.upl' opened for reading 0 SANI-RDC constraints read 3491 NOE-distance constraints (0 Ambiguous NOE/s) read 3491 TOTAL constraints read PdbStat> -------------- SUMMARY OF RESTRAINTS --------------- TOTAL NUMBER OF NOE RESTRAINTS : 3491 INTRA-RESIDUE RESTRAINTS (I=J) : 668 SEQUENTIAL RESTRAINTS (I-J)=1 : 916 BACKBONE-BACKBONE : 200 BACKBONE-SIDE CHAIN : 89 SIDE CHAIN-SIDE CHAIN : 627 MEDIUM RANGE RESTRAINTS 1<(I-J)<5 : 808 BACKBONE-BACKBONE : 204 BACKBONE-SIDE CHAIN : 182 SIDE CHAIN-SIDE CHAIN : 422 LONG RANGE RESTRAINTS (I-J)>=5 : 1099 TOTAL HYDROGEN BOND RESTRAINTS : 0 LONG RANGE H-BOND RESTR. (I-J)>=5 : 0 DISULFIDE RESTRAINTS : 0 INTRA-CHAIN RESTRAINTS : 3491 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 ALA A 2 0 0.0 0.0 0.0 0.0 0.0 ASP A 3 0 2.5 1.0 1.5 0.0 0.0 GLU A 4 1 7.0 2.5 4.5 0.0 0.0 ALA A 5 1 6.5 2.5 4.0 0.0 0.0 THR A 6 3 16.0 3.5 8.5 4.0 0.0 ARG A 7 5 12.0 4.0 8.0 0.0 0.0 ARG A 8 2 13.0 5.5 7.5 0.0 0.0 VAL A 9 4 17.0 6.0 9.5 1.5 0.0 VAL A 10 4 22.5 7.0 11.0 4.5 0.0 SER A 11 0 11.0 7.0 4.0 0.0 0.0 GLU A 12 8 14.0 7.5 3.0 3.5 0.0 ILE A 13 8 30.0 7.5 6.0 16.5 0.0 PRO A 14 0 6.5 5.0 0.0 1.5 0.0 VAL A 15 4 25.0 7.0 0.0 18.0 0.0 LEU A 16 8 32.0 8.5 2.0 21.5 0.0 LYS A 17 5 7.0 7.0 0.0 0.0 0.0 THR A 18 1 15.0 5.0 2.5 7.5 0.0 ASN A 19 3 12.0 4.5 0.0 7.5 0.0 ALA A 20 0 14.5 3.0 3.0 8.5 0.0 GLY A 21 0 6.0 2.0 3.0 1.0 0.0 PRO A 22 0 21.0 3.5 1.0 16.5 0.0 ARG A 23 10 12.0 7.0 1.0 4.0 0.0 ASP A 24 3 22.5 6.5 16.0 0.0 0.0 ARG A 25 10 9.5 5.0 4.5 0.0 0.0 GLU A 26 2 14.0 7.0 7.0 0.0 0.0 LEU A 27 9 30.0 8.5 16.5 5.0 0.0 TRP A 28 7 49.5 9.0 17.5 23.0 0.0 VAL A 29 4 20.0 6.5 13.5 0.0 0.0 GLN A 30 5 23.5 3.5 17.5 2.5 0.0 ARG A 31 3 15.5 4.5 7.0 4.0 0.0 LEU A 32 9 37.5 7.5 20.0 10.0 0.0 LYS A 33 10 23.0 9.0 14.0 0.0 0.0 GLU A 34 8 20.5 7.5 7.5 5.5 0.0 GLU A 35 4 15.5 6.5 5.5 3.5 0.0 TYR A 36 3 25.0 7.0 16.5 1.5 0.0 GLN A 37 13 18.5 6.5 11.5 0.5 0.0 SER A 38 1 17.0 4.0 6.0 7.0 0.0 LEU A 39 9 23.5 4.0 8.5 11.0 0.0 ILE A 40 10 24.5 7.5 17.0 0.0 0.0 ARG A 41 9 21.0 7.5 11.5 2.0 0.0 TYR A 42 0 25.0 6.5 8.5 10.0 0.0 VAL A 43 3 22.5 8.0 13.5 1.0 0.0 GLU A 44 8 22.5 8.5 14.0 0.0 0.0 ASN A 45 10 19.0 6.0 9.0 4.0 0.0 ASN A 46 2 18.5 3.0 8.5 7.0 0.0 LYS A 47 9 18.5 3.5 10.5 4.5 0.0 ASN A 48 4 12.0 4.5 7.5 0.0 0.0 ALA A 49 1 13.0 5.5 7.5 0.0 0.0 ASP A 50 4 8.0 6.5 1.5 0.0 0.0 ASN A 51 8 16.0 5.5 7.5 3.0 0.0 ASP A 52 3 10.5 5.0 0.5 5.0 0.0 TRP A 53 1 25.5 3.0 1.5 21.0 0.0 PHE A 54 0 13.0 3.0 3.0 7.0 0.0 ARG A 55 2 10.5 5.5 0.0 5.0 0.0 LEU A 56 8 38.5 7.0 3.0 28.5 0.0 GLU A 57 8 14.5 7.5 0.0 7.0 0.0 SER A 58 1 15.5 6.0 5.5 4.0 0.0 ASN A 59 3 15.5 4.5 3.0 8.0 0.0 LYS A 60 3 10.5 9.5 1.0 0.0 0.0 GLU A 61 7 21.5 10.5 7.5 3.5 0.0 GLY A 62 0 18.0 4.0 9.5 4.5 0.0 THR A 63 2 19.0 2.5 7.0 9.5 0.0 ARG A 64 14 23.5 7.0 6.5 10.0 0.0 TRP A 65 6 50.0 7.5 2.5 40.0 0.0 PHE A 66 3 25.0 5.0 5.0 15.0 0.0 GLY A 67 0 20.5 6.0 0.0 14.5 0.0 LYS A 68 10 16.0 7.0 2.0 7.0 0.0 CYS A 69 0 19.5 6.5 0.0 13.0 0.0 TRP A 70 2 25.0 5.5 3.5 16.0 0.0 TYR A 71 0 24.5 6.5 2.5 15.5 0.0 ILE A 72 5 23.5 7.5 3.0 13.0 0.0 HIS A 73 0 16.0 7.5 4.0 4.5 0.0 ASP A 74 0 8.5 5.5 2.0 1.0 0.0 LEU A 75 5 7.0 5.5 1.5 0.0 0.0 LEU A 76 6 22.5 7.0 6.5 9.0 0.0 LYS A 77 18 24.0 7.0 0.5 16.5 0.0 TYR A 78 2 25.0 6.0 4.5 14.5 0.0 GLU A 79 1 7.5 4.0 0.0 3.5 0.0 PHE A 80 0 31.5 4.0 2.5 25.0 0.0 ASP A 81 2 10.0 5.5 0.5 4.0 0.0 ILE A 82 4 31.0 7.0 3.0 21.0 0.0 GLU A 83 2 22.0 7.0 0.5 14.5 0.0 PHE A 84 1 32.0 6.5 2.5 23.0 0.0 ASP A 85 2 10.0 6.0 0.0 4.0 0.0 ILE A 86 7 37.0 5.0 4.0 28.0 0.0 PRO A 87 0 19.0 7.0 7.0 5.0 0.0 ILE A 88 8 17.5 9.5 1.5 6.5 0.0 THR A 89 2 12.0 7.0 5.0 0.0 0.0 TYR A 90 6 26.5 5.5 10.0 11.0 0.0 PRO A 91 0 13.0 3.5 0.5 9.0 0.0 THR A 92 2 7.0 1.5 0.5 5.0 0.0 THR A 93 2 14.0 5.0 3.0 6.0 0.0 ALA A 94 1 18.0 5.5 1.5 11.0 0.0 PRO A 95 0 25.5 4.0 0.0 21.5 0.0 GLU A 96 7 7.5 5.0 0.0 2.5 0.0 ILE A 97 5 30.0 7.5 0.0 22.5 0.0 ALA A 98 1 18.0 6.0 3.5 8.5 0.0 VAL A 99 0 32.0 6.0 8.0 18.0 0.0 PRO A 100 0 14.5 7.5 4.0 3.0 0.0 GLU A 101 3 12.0 7.0 3.0 2.0 0.0 LEU A 102 3 26.5 6.0 9.5 11.0 0.0 ASP A 103 3 8.0 4.0 3.0 1.0 0.0 GLY A 104 0 3.0 2.5 0.0 0.5 0.0 LYS A 105 12 12.0 3.5 4.5 4.0 0.0 THR A 106 1 13.0 6.0 2.0 5.0 0.0 ALA A 107 0 4.0 4.0 0.0 0.0 0.0 LYS A 108 0 1.5 1.0 0.5 0.0 0.0 MET A 109 0 11.5 0.0 1.5 10.0 0.0 TYR A 110 0 6.0 1.5 2.0 2.5 0.0 ARG A 111 1 5.0 5.0 0.0 0.0 0.0 GLY A 112 0 4.0 4.0 0.0 0.0 0.0 GLY A 113 0 1.5 1.0 0.5 0.0 0.0 LYS A 114 11 12.5 5.0 2.0 5.5 0.0 ILE A 115 6 30.5 7.0 2.0 21.5 0.0 CYS A 116 2 5.5 4.5 0.0 1.0 0.0 LEU A 117 7 22.0 6.0 6.0 10.0 0.0 THR A 118 2 10.0 6.0 4.0 0.0 0.0 ASP A 119 2 5.0 2.5 2.5 0.0 0.0 HIS A 120 0 5.5 1.0 4.5 0.0 0.0 PHE A 121 2 27.0 5.5 13.5 8.0 0.0 LYS A 122 18 18.0 12.0 5.5 0.5 0.0 PRO A 123 0 15.5 10.0 5.5 0.0 0.0 LEU A 124 8 30.0 8.5 17.5 4.0 0.0 TRP A 125 6 35.0 9.0 7.5 18.5 0.0 ALA A 126 1 12.0 4.5 7.5 0.0 0.0 ARG A 127 10 18.5 10.0 8.5 0.0 0.0 ASN A 128 4 20.0 11.5 8.5 0.0 0.0 VAL A 129 2 23.0 5.0 8.5 9.5 0.0 PRO A 130 0 5.5 2.5 0.5 2.5 0.0 LYS A 131 17 18.5 2.5 1.5 14.5 0.0 PHE A 132 2 20.5 5.0 4.5 11.0 0.0 GLY A 133 0 10.5 3.5 3.5 3.5 0.0 LEU A 134 3 26.5 3.5 5.5 17.5 0.0 ALA A 135 0 19.0 3.5 4.5 11.0 0.0 HIS A 136 4 26.0 3.0 11.5 11.5 0.0 LEU A 137 6 37.5 5.5 9.0 23.0 0.0 MET A 138 2 10.5 6.0 3.5 1.0 0.0 ALA A 139 1 15.5 4.5 5.0 6.0 0.0 LEU A 140 6 18.5 5.0 3.5 10.0 0.0 GLY A 141 0 10.5 4.0 3.5 3.0 0.0 LEU A 142 9 26.5 4.5 8.5 13.5 0.0 GLY A 143 1 11.0 5.5 3.5 2.0 0.0 PRO A 144 0 6.0 4.0 2.0 0.0 0.0 TRP A 145 4 34.5 8.5 12.0 14.0 0.0 LEU A 146 6 27.5 10.0 6.0 11.5 0.0 ALA A 147 1 10.0 4.0 4.5 1.5 0.0 VAL A 148 5 7.5 3.0 4.5 0.0 0.0 GLU A 149 6 7.0 5.0 2.0 0.0 0.0 ILE A 150 4 28.5 5.0 10.0 13.5 0.0 PRO A 151 0 10.0 2.5 5.0 2.5 0.0 ASP A 152 0 5.5 1.5 4.0 0.0 0.0 LEU A 153 7 17.5 4.5 7.0 6.0 0.0 ILE A 154 10 27.5 7.5 8.0 12.0 0.0 GLN A 155 1 7.5 6.0 1.5 0.0 0.0 LYS A 156 21 12.5 4.5 8.0 0.0 0.0 GLY A 157 0 4.0 3.5 0.5 0.0 0.0 VAL A 158 2 13.0 2.5 5.5 5.0 0.0 ILE A 159 6 19.5 6.0 0.0 13.5 0.0 GLN A 160 7 7.5 7.5 0.0 0.0 0.0 HIS A 161 0 8.0 6.0 0.0 2.0 0.0 LYS A 162 4 4.5 4.5 0.0 0.0 0.0 GLU A 163 3 6.5 4.5 0.5 1.5 0.0 LYS A 164 13 11.5 6.5 0.0 5.0 0.0 CYS A 165 0 6.5 5.5 0.5 0.5 0.0 ASN A 166 0 3.0 3.0 0.0 0.0 0.0 GLN A 167 4 4.5 4.5 0.0 0.0 0.0 LEU A 168 9 7.5 7.5 0.0 0.0 0.0 GLU A 169 3 4.5 4.5 0.0 0.0 0.0 HIS A 170 0 0.0 0.0 0.0 0.0 0.0 HIS A 171 0 0.0 0.0 0.0 0.0 0.0 HIS A 172 0 0.0 0.0 0.0 0.0 0.0 HIS A 173 0 0.0 0.0 0.0 0.0 0.0 HIS A 174 0 0.0 0.0 0.0 0.0 0.0 HIS A 175 0 0.0 0.0 0.0 0.0 0.0 TOTAL 668 2823.0 916.0 808.0 1099.0 0.0 > ANALYZE_cns: Do you want a CONS.OUT file [default no] ?_