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 `PFR193A_NMR_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 30-JUN-09 2KL6 > ReadCoordsPdb(): >> TITLE SOLUTION NMR STRUCTURE OF THE CARDB DOMAIN OF PF1109 FROM > ReadCoordsPdb(): >> TITLE 2 PYROCOCCUS FURIOSUS. NORTHEAST STRUCTURAL GENOMICS > ReadCoordsPdb(): >> TITLE 3 CONSORTIUM TARGET PFR193A > ReadCoordsPdb(): >> COMPND MOL_ID: 1; 1 > ReadCoordsPdb(): Counting models in file `PFR193A_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 PFR193A_NMR_em_bcr3.pdb MODEL 1 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 1689 ATOM records read from file > ReadCoordsPdb(): --> 1689 Regular IUPAC Atoms > ReadCoordsPdb(): --> 0 Pseudo-atoms (DISMAN type) > ReadCoordsPdb(): --> 0 Lone pairs > ReadCoordsPdb(): Bye ... > =============================== INFO ================================ > INFO_mol: # atoms: 1689 (540 C, 842 H, 169 O, 136 N, 2 S, 0 Q, 0 Metals) > INFO_mol: # residues: 108 (Avg. mol. weight: 111.2) > INFO_mol: # -- M.W. : 12007.3 g/mol. (12.01 kD) Estimated RoG : 13.04 > INFO_mol: CenterMass() -- Working PDB model 1 in file, model no. 1 > INFO_mol: CenterMass() -- Molecule `PFR193A_NMR_em_bcr3.pdb' model #1, TOTAL RESIDUES: 108 > INFO_mol: Radius of Gyration : 15.2506 angstroms > INFO_mol: Center of Masses: x_cm(0.215), y_cm(-0.059), z_cm(-0.166) > INFO_res: MEFPDLTVEI KGPDVVGVNK LAEYEVHVKN LGGIGVPSTK VRVYINGTLY > INFO_res: KNWTVSLGPK EEKVLTFSWT PTQEGMYRIN ATVDEENTVV ELNENNNVAT > INFO_res: FDVSVVLE > INFO_res: > INFO_res: MET GLU PHE PRO ASP LEU THR VAL GLU ILE LYS GLY > INFO_res: PRO ASP VAL VAL GLY VAL ASN LYS LEU ALA GLU TYR > INFO_res: GLU VAL HIS VAL LYS ASN LEU GLY GLY ILE GLY VAL > INFO_res: PRO SER THR LYS VAL ARG VAL TYR ILE ASN GLY THR > INFO_res: LEU TYR LYS ASN TRP THR VAL SER LEU GLY PRO LYS > INFO_res: GLU GLU LYS VAL LEU THR PHE SER TRP THR PRO THR > INFO_res: GLN GLU GLY MET TYR ARG ILE ASN ALA THR VAL ASP > INFO_res: GLU GLU ASN THR VAL VAL GLU LEU ASN GLU ASN ASN > INFO_res: ASN VAL ALA THR PHE ASP VAL SER VAL VAL LEU GLU > INFO_res: > INFO_res: > INFO_res: 3 ALA 2 ARG 10 ASN 4 ASP 1 GLN 12 GLU > INFO_res: 8 GLY 1 HIS 4 ILE 8 LEU 7 LYS 2 MET > INFO_res: 3 PHE 5 PRO 4 SER 10 THR 4 TYR 2 TRP > INFO_res: 18 VAL > INFO_res: DISULFIDE: ** NO INFO FOR DISULFIDES IN FILE > ===================================================================== > ReadCoordsPdb(): *** monomer, 1 [1] chains *** PdbStat> > locate_file(): file `PFR193A_NMR_em_bcr3.upl' opened for reading 0 SANI-RDC constraints read 2719 NOE-distance constraints (0 Ambiguous NOE/s) read 2719 TOTAL constraints read PdbStat> -------------- SUMMARY OF RESTRAINTS --------------- TOTAL NUMBER OF NOE RESTRAINTS : 2719 INTRA-RESIDUE RESTRAINTS (I=J) : 523 SEQUENTIAL RESTRAINTS (I-J)=1 : 686 BACKBONE-BACKBONE : 167 BACKBONE-SIDE CHAIN : 137 SIDE CHAIN-SIDE CHAIN : 382 MEDIUM RANGE RESTRAINTS 1<(I-J)<5 : 271 BACKBONE-BACKBONE : 25 BACKBONE-SIDE CHAIN : 32 SIDE CHAIN-SIDE CHAIN : 214 LONG RANGE RESTRAINTS (I-J)>=5 : 1239 TOTAL HYDROGEN BOND RESTRAINTS : 0 LONG RANGE H-BOND RESTR. (I-J)>=5 : 0 DISULFIDE RESTRAINTS : 0 INTRA-CHAIN RESTRAINTS : 2719 INTER-CHAIN RESTRAINTS : 0 AMBIGUOUS RESTRAINTS : 0 ----------------------------------------------------- ----------------------------------------------------- ----------------------------------------------------- RES # INTRA INTER seq med lng InterChain MET A 1 1 2.5 0.0 2.5 0.0 0.0 GLU A 2 1 9.0 2.0 0.0 7.0 0.0 PHE A 3 3 23.0 7.5 2.5 13.0 0.0 PRO A 4 0 29.5 9.5 1.5 18.5 0.0 ASP A 5 0 23.5 6.0 0.5 17.0 0.0 LEU A 6 11 29.5 6.0 1.5 22.0 0.0 THR A 7 3 26.0 10.0 1.5 14.5 0.0 VAL A 8 2 29.0 10.5 0.5 18.0 0.0 GLU A 9 2 21.0 8.0 1.5 11.5 0.0 ILE A 10 12 33.0 6.5 1.0 25.5 0.0 LYS A 11 18 12.5 6.5 0.5 5.5 0.0 GLY A 12 0 13.5 7.5 0.5 5.5 0.0 PRO A 13 0 21.0 6.0 5.0 10.0 0.0 ASP A 14 2 14.0 6.5 1.0 6.5 0.0 VAL A 15 5 18.0 8.0 2.0 8.0 0.0 VAL A 16 4 27.0 8.0 6.0 13.0 0.0 GLY A 17 0 16.0 7.5 5.5 3.0 0.0 VAL A 18 5 31.5 10.0 2.0 19.5 0.0 ASN A 19 4 16.5 9.0 0.0 7.5 0.0 LYS A 20 18 19.0 7.5 8.5 3.0 0.0 LEU A 21 12 20.5 10.0 2.0 8.5 0.0 ALA A 22 1 20.0 7.0 2.0 11.0 0.0 GLU A 23 6 18.0 6.5 2.0 9.5 0.0 TYR A 24 6 39.0 7.0 2.0 30.0 0.0 GLU A 25 5 20.0 5.0 1.0 14.0 0.0 VAL A 26 5 25.5 4.0 0.0 21.5 0.0 HIS A 27 3 19.5 4.0 1.0 14.5 0.0 VAL A 28 2 22.0 7.5 0.0 14.5 0.0 LYS A 29 11 28.0 8.5 4.5 15.0 0.0 ASN A 30 6 34.5 6.5 2.0 26.0 0.0 LEU A 31 9 22.0 5.5 5.0 11.5 0.0 GLY A 32 0 11.5 3.0 3.5 5.0 0.0 GLY A 33 0 9.0 3.0 0.5 5.5 0.0 ILE A 34 10 33.0 7.0 3.5 22.5 0.0 GLY A 35 0 17.5 6.0 0.0 11.5 0.0 VAL A 36 5 23.5 6.0 4.5 13.0 0.0 PRO A 37 0 12.5 9.5 0.5 2.5 0.0 SER A 38 1 10.0 7.5 2.5 0.0 0.0 THR A 39 2 16.0 6.5 2.5 7.0 0.0 LYS A 40 16 17.0 8.0 0.0 9.0 0.0 VAL A 41 5 24.0 6.5 0.0 17.5 0.0 ARG A 42 1 18.5 5.5 1.0 12.0 0.0 VAL A 43 5 29.5 6.5 1.5 21.5 0.0 TYR A 44 3 32.0 6.5 4.5 21.0 0.0 ILE A 45 11 30.0 8.0 3.0 19.0 0.0 ASN A 46 4 12.0 5.0 0.0 7.0 0.0 GLY A 47 0 2.0 1.0 1.0 0.0 0.0 THR A 48 3 8.5 4.5 4.0 0.0 0.0 LEU A 49 12 27.0 8.5 6.0 12.5 0.0 TYR A 50 3 29.5 11.0 0.5 18.0 0.0 LYS A 51 12 26.5 12.0 10.0 4.5 0.0 ASN A 52 3 19.0 8.5 3.5 7.0 0.0 TRP A 53 8 41.0 6.0 11.0 24.0 0.0 THR A 54 3 11.0 7.0 0.0 4.0 0.0 VAL A 55 4 25.5 8.5 3.5 13.5 0.0 SER A 56 1 11.0 7.5 0.0 3.5 0.0 LEU A 57 9 38.5 6.5 5.5 26.5 0.0 GLY A 58 0 17.0 7.0 5.5 4.5 0.0 PRO A 59 0 21.5 6.0 0.5 15.0 0.0 LYS A 60 17 10.5 5.0 0.0 5.5 0.0 GLU A 61 7 23.5 6.0 12.5 5.0 0.0 GLU A 62 7 18.0 7.5 1.5 9.0 0.0 LYS A 63 13 31.0 8.5 7.0 15.5 0.0 VAL A 64 5 20.5 8.5 2.0 10.0 0.0 LEU A 65 9 33.5 7.5 5.5 20.5 0.0 THR A 66 3 17.5 6.0 0.5 11.0 0.0 PHE A 67 3 32.0 5.5 1.5 25.0 0.0 SER A 68 1 17.0 4.5 0.0 12.5 0.0 TRP A 69 2 31.5 4.0 5.0 22.5 0.0 THR A 70 3 17.5 6.0 2.0 9.5 0.0 PRO A 71 0 22.5 4.0 4.5 14.0 0.0 THR A 72 4 10.5 1.5 2.0 7.0 0.0 GLN A 73 8 10.0 5.0 2.0 3.0 0.0 GLU A 74 7 28.5 8.0 2.0 18.5 0.0 GLY A 75 0 13.0 6.5 1.5 5.0 0.0 MET A 76 10 12.5 5.5 0.0 7.0 0.0 TYR A 77 3 35.0 6.0 4.5 24.5 0.0 ARG A 78 16 17.0 5.5 1.0 10.5 0.0 ILE A 79 9 33.5 6.0 0.5 27.0 0.0 ASN A 80 3 26.0 6.5 2.5 17.0 0.0 ALA A 81 1 21.5 5.0 0.5 16.0 0.0 THR A 82 3 25.0 4.5 8.5 12.0 0.0 VAL A 83 4 26.5 7.0 1.0 18.5 0.0 ASP A 84 0 18.0 7.0 1.5 9.5 0.0 GLU A 85 4 14.5 4.5 8.5 1.5 0.0 GLU A 86 7 6.0 3.0 3.0 0.0 0.0 ASN A 87 2 5.0 2.5 2.5 0.0 0.0 THR A 88 2 7.0 4.0 3.0 0.0 0.0 VAL A 89 7 14.0 5.5 3.0 5.5 0.0 VAL A 90 5 10.5 8.0 0.0 2.5 0.0 GLU A 91 6 21.0 9.0 4.5 7.5 0.0 LEU A 92 7 22.0 7.0 0.0 15.0 0.0 ASN A 93 7 10.5 3.0 6.0 1.5 0.0 GLU A 94 1 2.0 0.5 1.5 0.0 0.0 ASN A 95 6 3.5 2.5 1.0 0.0 0.0 ASN A 96 1 11.5 2.5 4.5 4.5 0.0 ASN A 97 6 17.5 5.0 1.5 11.0 0.0 VAL A 98 5 23.0 8.5 2.0 12.5 0.0 ALA A 99 1 18.5 7.5 0.0 11.0 0.0 THR A 100 3 17.5 6.0 1.0 10.5 0.0 PHE A 101 1 29.0 6.5 2.0 20.5 0.0 ASP A 102 3 11.0 8.0 0.5 2.5 0.0 VAL A 103 5 35.0 9.0 3.5 22.5 0.0 SER A 104 3 23.0 9.0 1.0 13.0 0.0 VAL A 105 5 37.0 7.0 1.5 28.5 0.0 VAL A 106 4 20.0 7.5 4.0 8.5 0.0 LEU A 107 9 20.0 7.5 0.0 12.5 0.0 GLU A 108 7 7.0 3.0 3.0 1.0 0.0 TOTAL 523 2196.0 686.0 271.0 1239.0 0.0 > ANALYZE_cns: Do you want a CONS.OUT file [default no] ?_