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 `DRR147D_NMR_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 31-DEC-08 2KCZ > ReadCoordsPdb(): >> TITLE SOLUTION NMR STRUCTURE OF THE C-TERMINAL DOMAIN OF PROTEIN > ReadCoordsPdb(): >> TITLE 2 DR_A0006 FROM DEINOCOCCUS RADIODURANS. NORTHEAST > ReadCoordsPdb(): >> TITLE 3 STRUCTURAL GENOMICS CONSORTIUM TARGET DRR147D > ReadCoordsPdb(): >> COMPND MOL_ID: 1; 1 > ReadCoordsPdb(): Counting models in file `DRR147D_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 DRR147D_NMR_em_bcr3.pdb MODEL 1 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 2446 ATOM records read from file > ReadCoordsPdb(): --> 2446 Regular IUPAC Atoms > ReadCoordsPdb(): --> 0 Pseudo-atoms (DISMAN type) > ReadCoordsPdb(): --> 0 Lone pairs > ReadCoordsPdb(): Bye ... > =============================== INFO ================================ > INFO_mol: # atoms: 2446 (767 C, 1222 H, 221 O, 232 N, 4 S, 0 Q, 0 Metals) > INFO_mol: # residues: 155 (Avg. mol. weight: 112.0) > INFO_mol: # -- M.W. : 17357.4 g/mol. (17.36 kD) Estimated RoG : 14.95 > INFO_mol: CenterMass() -- Working PDB model 1 in file, model no. 1 > INFO_mol: CenterMass() -- Molecule `DRR147D_NMR_em_bcr3.pdb' model #1, TOTAL RESIDUES: 155 > INFO_mol: Radius of Gyration : 17.4550 angstroms > INFO_mol: Center of Masses: x_cm(4.434), y_cm(-3.236), z_cm(-1.413) > INFO_res: MGETVVRDAV TIGKPAEQLY AVWRDLPGLP LLMTHLRSVE VLDDKRSRWT > INFO_res: VEAPAPLGAV SWEAELTADE PGKRIAWRSL PGARIENSGE VLFRPAPGAR > INFO_res: GTEVVVRLTY RPPGGSAGAV IARMFNQEPS QQLRDDLMRF KREQELGLEH > INFO_res: HHHHH > INFO_res: > INFO_res: MET GLY GLU THR VAL VAL ARG ASP ALA VAL THR ILE > INFO_res: GLY LYS PRO ALA GLU GLN LEU TYR ALA VAL TRP ARG > INFO_res: ASP LEU PRO GLY LEU PRO LEU LEU MET THR HIS LEU > INFO_res: ARG SER VAL GLU VAL LEU ASP ASP LYS ARG SER ARG > INFO_res: TRP THR VAL GLU ALA PRO ALA PRO LEU GLY ALA VAL > INFO_res: SER TRP GLU ALA GLU LEU THR ALA ASP GLU PRO GLY > INFO_res: LYS ARG ILE ALA TRP ARG SER LEU PRO GLY ALA ARG > INFO_res: ILE GLU ASN SER GLY GLU VAL LEU PHE ARG PRO ALA > INFO_res: PRO GLY ALA ARG GLY THR GLU VAL VAL VAL ARG LEU > INFO_res: THR TYR ARG PRO PRO GLY GLY SER ALA GLY ALA VAL > INFO_res: ILE ALA ARG MET PHE ASN GLN GLU PRO SER GLN GLN > INFO_res: LEU ARG ASP ASP LEU MET ARG PHE LYS ARG GLU GLN > INFO_res: GLU LEU GLY LEU GLU HIS HIS HIS HIS HIS HIS > INFO_res: > INFO_res: 15 ALA 16 ARG 2 ASN 7 ASP 5 GLN 14 GLU > INFO_res: 13 GLY 7 HIS 4 ILE 16 LEU 4 LYS 4 MET > INFO_res: 3 PHE 12 PRO 7 SER 7 THR 2 TYR 4 TRP > INFO_res: 13 VAL > INFO_res: DISULFIDE: ** NO INFO FOR DISULFIDES IN FILE > ===================================================================== > ReadCoordsPdb(): *** monomer, 1 [1] chains *** PdbStat> > locate_file(): file `DRR147D_NMR_em_bcr3.upl' opened for reading 0 SANI-RDC constraints read 1362 NOE-distance constraints (0 Ambiguous NOE/s) read 1362 TOTAL constraints read PdbStat> -------------- SUMMARY OF RESTRAINTS --------------- TOTAL NUMBER OF NOE RESTRAINTS : 1362 INTRA-RESIDUE RESTRAINTS (I=J) : 260 SEQUENTIAL RESTRAINTS (I-J)=1 : 478 BACKBONE-BACKBONE : 105 BACKBONE-SIDE CHAIN : 28 SIDE CHAIN-SIDE CHAIN : 345 MEDIUM RANGE RESTRAINTS 1<(I-J)<5 : 144 BACKBONE-BACKBONE : 24 BACKBONE-SIDE CHAIN : 28 SIDE CHAIN-SIDE CHAIN : 92 LONG RANGE RESTRAINTS (I-J)>=5 : 480 TOTAL HYDROGEN BOND RESTRAINTS : 0 LONG RANGE H-BOND RESTR. (I-J)>=5 : 0 DISULFIDE RESTRAINTS : 0 INTRA-CHAIN RESTRAINTS : 1362 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 GLY A 2 0 0.0 0.0 0.0 0.0 0.0 GLU A 3 0 2.0 2.0 0.0 0.0 0.0 THR A 4 0 4.0 4.0 0.0 0.0 0.0 VAL A 5 1 7.0 3.5 0.0 3.5 0.0 VAL A 6 0 7.5 5.0 0.0 2.5 0.0 ARG A 7 4 9.0 8.0 0.0 1.0 0.0 ASP A 8 0 12.0 6.5 0.0 5.5 0.0 ALA A 9 0 14.0 4.0 0.0 10.0 0.0 VAL A 10 0 22.5 4.5 0.5 17.5 0.0 THR A 11 2 13.0 4.5 0.0 8.5 0.0 ILE A 12 5 26.0 5.5 3.5 17.0 0.0 GLY A 13 0 9.0 4.0 0.0 5.0 0.0 LYS A 14 14 22.5 7.0 3.0 12.5 0.0 PRO A 15 0 15.0 11.0 4.0 0.0 0.0 ALA A 16 0 17.0 6.0 4.5 6.5 0.0 GLU A 17 4 9.0 5.0 3.5 0.5 0.0 GLN A 18 5 12.0 6.5 5.5 0.0 0.0 LEU A 19 6 30.5 5.5 6.5 18.5 0.0 TYR A 20 4 12.0 5.0 1.5 5.5 0.0 ALA A 21 1 7.5 4.5 2.5 0.5 0.0 VAL A 22 3 10.5 2.0 2.5 6.0 0.0 TRP A 23 0 0.5 0.5 0.0 0.0 0.0 ARG A 24 7 2.0 2.0 0.0 0.0 0.0 ASP A 25 3 2.5 2.5 0.0 0.0 0.0 LEU A 26 3 12.5 5.5 0.5 6.5 0.0 PRO A 27 0 6.5 6.5 0.0 0.0 0.0 GLY A 28 0 3.0 2.0 1.0 0.0 0.0 LEU A 29 7 6.0 0.0 2.5 3.5 0.0 PRO A 30 0 0.0 0.0 0.0 0.0 0.0 LEU A 31 4 1.5 0.5 1.0 0.0 0.0 LEU A 32 2 6.5 2.5 2.5 1.5 0.0 MET A 33 0 2.0 2.0 0.0 0.0 0.0 THR A 34 0 0.0 0.0 0.0 0.0 0.0 HIS A 35 0 0.0 0.0 0.0 0.0 0.0 LEU A 36 0 0.0 0.0 0.0 0.0 0.0 ARG A 37 2 2.5 2.5 0.0 0.0 0.0 SER A 38 0 3.5 3.5 0.0 0.0 0.0 VAL A 39 0 5.5 2.0 0.0 3.5 0.0 GLU A 40 3 4.0 4.0 0.0 0.0 0.0 VAL A 41 1 7.0 5.5 0.5 1.0 0.0 LEU A 42 2 7.0 6.0 0.0 1.0 0.0 ASP A 43 0 6.5 5.5 1.0 0.0 0.0 ASP A 44 2 5.5 4.0 0.0 1.5 0.0 LYS A 45 18 9.0 6.5 0.0 2.5 0.0 ARG A 46 7 9.0 8.5 0.5 0.0 0.0 SER A 47 0 8.0 5.5 0.0 2.5 0.0 ARG A 48 2 2.0 1.5 0.0 0.5 0.0 TRP A 49 0 0.0 0.0 0.0 0.0 0.0 THR A 50 0 0.0 0.0 0.0 0.0 0.0 VAL A 51 0 2.5 1.0 0.0 1.5 0.0 GLU A 52 2 3.0 3.0 0.0 0.0 0.0 ALA A 53 0 3.0 3.0 0.0 0.0 0.0 PRO A 54 0 4.0 4.0 0.0 0.0 0.0 ALA A 55 0 7.0 4.5 2.5 0.0 0.0 PRO A 56 0 10.0 6.0 0.5 3.5 0.0 LEU A 57 5 9.0 6.5 1.0 1.5 0.0 GLY A 58 0 4.0 2.0 2.0 0.0 0.0 ALA A 59 0 0.0 0.0 0.0 0.0 0.0 VAL A 60 0 3.0 0.5 0.0 2.5 0.0 SER A 61 0 0.5 0.5 0.0 0.0 0.0 TRP A 62 0 1.5 1.5 0.0 0.0 0.0 GLU A 63 3 15.0 5.0 0.0 10.0 0.0 ALA A 64 0 8.5 4.0 0.0 4.5 0.0 GLU A 65 2 16.5 4.0 0.0 12.5 0.0 LEU A 66 1 21.0 7.0 3.0 11.0 0.0 THR A 67 0 14.5 5.0 0.0 9.5 0.0 ALA A 68 1 12.0 3.0 4.5 4.5 0.0 ASP A 69 3 5.0 4.0 0.0 1.0 0.0 GLU A 70 3 12.5 2.5 8.5 1.5 0.0 PRO A 71 0 0.0 0.0 0.0 0.0 0.0 GLY A 72 0 3.0 0.0 0.5 2.5 0.0 LYS A 73 13 7.5 3.0 3.0 1.5 0.0 ARG A 74 4 19.0 6.0 4.5 8.5 0.0 ILE A 75 2 18.0 6.0 0.0 12.0 0.0 ALA A 76 0 14.5 4.0 1.0 9.5 0.0 TRP A 77 1 11.0 3.0 0.0 8.0 0.0 ARG A 78 2 12.5 4.5 0.0 8.0 0.0 SER A 79 0 6.5 2.5 0.5 3.5 0.0 LEU A 80 4 36.0 7.0 2.5 26.5 0.0 PRO A 81 0 8.5 8.5 0.0 0.0 0.0 GLY A 82 0 4.5 2.0 2.5 0.0 0.0 ALA A 83 0 2.5 1.5 0.5 0.5 0.0 ARG A 84 1 1.0 1.0 0.0 0.0 0.0 ILE A 85 0 0.0 0.0 0.0 0.0 0.0 GLU A 86 0 0.0 0.0 0.0 0.0 0.0 ASN A 87 0 2.0 2.0 0.0 0.0 0.0 SER A 88 0 3.5 2.0 0.0 1.5 0.0 GLY A 89 0 0.5 0.0 0.0 0.5 0.0 GLU A 90 0 8.0 2.5 1.5 4.0 0.0 VAL A 91 1 20.0 4.5 0.5 15.0 0.0 LEU A 92 4 14.5 5.0 1.5 8.0 0.0 PHE A 93 0 21.5 5.0 0.5 16.0 0.0 ARG A 94 7 14.5 3.5 0.0 11.0 0.0 PRO A 95 0 3.5 3.5 0.0 0.0 0.0 ALA A 96 1 18.0 4.0 3.5 10.5 0.0 PRO A 97 0 4.5 4.0 0.5 0.0 0.0 GLY A 98 0 2.5 2.5 0.0 0.0 0.0 ALA A 99 2 3.0 2.0 1.0 0.0 0.0 ARG A 100 9 8.5 5.0 3.0 0.5 0.0 GLY A 101 0 13.0 5.5 0.0 7.5 0.0 THR A 102 1 17.5 4.5 1.0 12.0 0.0 GLU A 103 6 27.0 7.5 5.0 14.5 0.0 VAL A 104 1 27.0 7.0 1.5 18.5 0.0 VAL A 105 1 24.5 4.5 5.0 15.0 0.0 VAL A 106 1 11.0 5.0 0.5 5.5 0.0 ARG A 107 2 5.5 4.5 0.0 1.0 0.0 LEU A 108 0 7.5 3.5 2.0 2.0 0.0 THR A 109 0 5.5 3.0 0.0 2.5 0.0 TYR A 110 0 9.5 5.0 2.0 2.5 0.0 ARG A 111 6 3.5 3.5 0.0 0.0 0.0 PRO A 112 0 0.0 0.0 0.0 0.0 0.0 PRO A 113 0 0.0 0.0 0.0 0.0 0.0 GLY A 114 0 0.0 0.0 0.0 0.0 0.0 GLY A 115 0 0.5 0.5 0.0 0.0 0.0 SER A 116 0 3.0 2.0 1.0 0.0 0.0 ALA A 117 1 2.0 2.0 0.0 0.0 0.0 GLY A 118 0 1.5 1.5 0.0 0.0 0.0 ALA A 119 0 3.5 2.5 1.0 0.0 0.0 VAL A 120 1 4.0 2.5 1.5 0.0 0.0 ILE A 121 0 2.5 2.5 0.0 0.0 0.0 ALA A 122 0 2.0 2.0 0.0 0.0 0.0 ARG A 123 4 4.5 3.0 1.5 0.0 0.0 MET A 124 0 2.5 2.5 0.0 0.0 0.0 PHE A 125 0 0.0 0.0 0.0 0.0 0.0 ASN A 126 0 0.0 0.0 0.0 0.0 0.0 GLN A 127 0 0.0 0.0 0.0 0.0 0.0 GLU A 128 0 0.0 0.0 0.0 0.0 0.0 PRO A 129 0 0.0 0.0 0.0 0.0 0.0 SER A 130 0 0.0 0.0 0.0 0.0 0.0 GLN A 131 0 0.0 0.0 0.0 0.0 0.0 GLN A 132 0 0.0 0.0 0.0 0.0 0.0 LEU A 133 0 0.0 0.0 0.0 0.0 0.0 ARG A 134 2 0.5 0.5 0.0 0.0 0.0 ASP A 135 0 2.0 2.0 0.0 0.0 0.0 ASP A 136 0 2.0 2.0 0.0 0.0 0.0 LEU A 137 3 16.5 3.5 2.0 11.0 0.0 MET A 138 4 6.5 4.5 1.5 0.5 0.0 ARG A 139 2 4.5 4.5 0.0 0.0 0.0 PHE A 140 0 19.0 5.0 4.0 10.0 0.0 LYS A 141 5 14.0 5.5 1.5 7.0 0.0 ARG A 142 10 8.0 6.5 0.5 1.0 0.0 GLU A 143 9 15.0 5.5 9.5 0.0 0.0 GLN A 144 8 15.5 5.5 0.0 10.0 0.0 GLU A 145 3 9.0 5.0 0.0 4.0 0.0 LEU A 146 1 10.5 4.0 6.5 0.0 0.0 GLY A 147 0 2.5 2.0 0.5 0.0 0.0 LEU A 148 3 1.5 1.5 0.0 0.0 0.0 GLU A 149 3 1.5 1.5 0.0 0.0 0.0 HIS A 150 0 0.0 0.0 0.0 0.0 0.0 HIS A 151 0 0.0 0.0 0.0 0.0 0.0 HIS 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 TOTAL 260 1102.0 478.0 144.0 480.0 0.0 > ANALYZE_cns: Do you want a CONS.OUT file [default no] ?_