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 `SR213_NMR_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 23-JUN-06 2HFI > ReadCoordsPdb(): >> TITLE SOLUTION NMR STRUCTURE OF PROTEIN YPPE FROM BACILLUS > ReadCoordsPdb(): >> TITLE 2 SUBTILIS. NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET > ReadCoordsPdb(): >> TITLE 3 SR213 > ReadCoordsPdb(): >> COMPND MOL_ID: 1; 1 > ReadCoordsPdb(): Counting models in file `SR213_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 SR213_NMR_em_bcr3.pdb MODEL 1 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 2031 ATOM records read from file > ReadCoordsPdb(): --> 2031 Regular IUPAC Atoms > ReadCoordsPdb(): --> 0 Pseudo-atoms (DISMAN type) > ReadCoordsPdb(): --> 0 Lone pairs > ReadCoordsPdb(): Bye ... > =============================== INFO ================================ > INFO_mol: # atoms: 2031 (642 C, 1013 H, 196 O, 177 N, 3 S, 0 Q, 0 Metals) > INFO_mol: # residues: 123 (Avg. mol. weight: 117.4) > INFO_mol: # -- M.W. : 14443.1 g/mol. (14.44 kD) Estimated RoG : 13.70 > INFO_mol: CenterMass() -- Working PDB model 1 in file, model no. 1 > INFO_mol: CenterMass() -- Molecule `SR213_NMR_em_bcr3.pdb' model #1, TOTAL RESIDUES: 123 > INFO_mol: Radius of Gyration : 15.9795 angstroms > INFO_mol: Center of Masses: x_cm(-0.234), y_cm(-0.065), z_cm(0.064) > INFO_res: MLSQTLLEMT EQMIEVAEKG ADRYQEGKNS NHSYDFFETI KPAVEENDEL > INFO_res: AARWAEGALE LIKVRRPKYV HKEQIEAVKD NFLELVLQSY VHHIHKKRFK > INFO_res: DITESVLYTL HAVKDEIARE DSR > INFO_res: > INFO_res: MET LEU SER GLN THR LEU LEU GLU MET THR GLU GLN > INFO_res: MET ILE GLU VAL ALA GLU LYS GLY ALA ASP ARG TYR > INFO_res: GLN GLU GLY LYS ASN SER ASN HIS SER TYR ASP PHE > INFO_res: PHE GLU THR ILE LYS PRO ALA VAL GLU GLU ASN ASP > INFO_res: GLU LEU ALA ALA ARG TRP ALA GLU GLY ALA LEU GLU > INFO_res: LEU ILE LYS VAL ARG ARG PRO LYS TYR VAL HIS LYS > INFO_res: GLU GLN ILE GLU ALA VAL LYS ASP ASN PHE LEU GLU > INFO_res: LEU VAL LEU GLN SER TYR VAL HIS HIS ILE HIS LYS > INFO_res: LYS ARG PHE LYS ASP ILE THR GLU SER VAL LEU TYR > INFO_res: THR LEU HIS ALA VAL LYS ASP GLU ILE ALA ARG GLU > INFO_res: ASP SER ARG > INFO_res: > INFO_res: 10 ALA 7 ARG 4 ASN 7 ASP 5 GLN 17 GLU > INFO_res: 3 GLY 6 HIS 7 ILE 11 LEU 11 LYS 3 MET > INFO_res: 4 PHE 2 PRO 6 SER 5 THR 5 TYR 1 TRP > INFO_res: 9 VAL > INFO_res: DISULFIDE: ** NO INFO FOR DISULFIDES IN FILE > ===================================================================== > ReadCoordsPdb(): *** monomer, 1 [1] chains *** PdbStat> > locate_file(): file `SR213_NMR_em_bcr3.upl' opened for reading 0 SANI-RDC constraints read 2023 NOE-distance constraints (0 Ambiguous NOE/s) read 2023 TOTAL constraints read PdbStat> -------------- SUMMARY OF RESTRAINTS --------------- TOTAL NUMBER OF NOE RESTRAINTS : 2023 INTRA-RESIDUE RESTRAINTS (I=J) : 419 SEQUENTIAL RESTRAINTS (I-J)=1 : 498 BACKBONE-BACKBONE : 91 BACKBONE-SIDE CHAIN : 24 SIDE CHAIN-SIDE CHAIN : 383 MEDIUM RANGE RESTRAINTS 1<(I-J)<5 : 626 BACKBONE-BACKBONE : 249 BACKBONE-SIDE CHAIN : 197 SIDE CHAIN-SIDE CHAIN : 180 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 : 2023 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 LEU A 2 0 0.0 0.0 0.0 0.0 0.0 SER A 3 0 0.0 0.0 0.0 0.0 0.0 GLN 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 LEU A 6 1 16.5 1.0 3.0 12.5 0.0 LEU A 7 2 20.5 4.5 8.5 7.5 0.0 GLU A 8 6 9.5 6.5 3.0 0.0 0.0 MET A 9 5 15.5 4.5 4.5 6.5 0.0 THR A 10 2 28.0 3.5 10.5 14.0 0.0 GLU A 11 5 16.5 5.5 11.0 0.0 0.0 GLN A 12 13 23.0 7.0 11.5 4.5 0.0 MET A 13 7 25.0 6.5 7.0 11.5 0.0 ILE A 14 3 29.0 6.0 11.0 12.0 0.0 GLU A 15 8 19.0 8.0 10.5 0.5 0.0 VAL A 16 3 25.0 7.5 10.0 7.5 0.0 ALA A 17 0 16.0 4.0 5.5 6.5 0.0 GLU A 18 8 17.0 4.5 7.5 5.0 0.0 LYS A 19 11 14.0 6.0 8.0 0.0 0.0 GLY A 20 0 10.5 3.5 5.5 1.5 0.0 ALA A 21 0 16.0 2.5 7.5 6.0 0.0 ASP A 22 1 9.0 2.5 6.5 0.0 0.0 ARG A 23 2 8.0 2.5 5.5 0.0 0.0 TYR A 24 3 16.0 5.0 5.5 5.5 0.0 GLN A 25 2 8.5 4.5 4.0 0.0 0.0 GLU A 26 3 3.5 1.5 2.0 0.0 0.0 GLY A 27 0 0.0 0.0 0.0 0.0 0.0 LYS A 28 0 0.0 0.0 0.0 0.0 0.0 ASN A 29 0 0.0 0.0 0.0 0.0 0.0 SER A 30 0 0.0 0.0 0.0 0.0 0.0 ASN A 31 0 0.0 0.0 0.0 0.0 0.0 HIS A 32 0 0.0 0.0 0.0 0.0 0.0 SER A 33 0 0.0 0.0 0.0 0.0 0.0 TYR A 34 0 3.0 0.0 0.0 3.0 0.0 ASP A 35 0 0.0 0.0 0.0 0.0 0.0 PHE A 36 0 8.5 1.0 4.5 3.0 0.0 PHE A 37 0 5.5 2.0 3.5 0.0 0.0 GLU A 38 10 3.5 3.5 0.0 0.0 0.0 THR A 39 1 7.0 4.5 0.0 2.5 0.0 ILE A 40 5 18.5 5.0 8.0 5.5 0.0 LYS A 41 0 10.5 5.5 4.0 1.0 0.0 PRO A 42 0 4.5 3.5 1.0 0.0 0.0 ALA A 43 1 12.0 2.0 8.5 1.5 0.0 VAL A 44 2 11.0 3.0 6.0 2.0 0.0 GLU A 45 8 10.0 4.5 5.5 0.0 0.0 GLU A 46 4 14.0 5.0 9.0 0.0 0.0 ASN A 47 5 20.5 4.0 9.5 7.0 0.0 ASP A 48 2 13.0 4.0 6.0 3.0 0.0 GLU A 49 6 12.5 5.0 7.5 0.0 0.0 LEU A 50 8 26.5 5.5 9.5 11.5 0.0 ALA A 51 0 16.5 4.5 7.5 4.5 0.0 ALA A 52 0 9.5 2.5 7.0 0.0 0.0 ARG A 53 7 11.0 5.0 6.0 0.0 0.0 TRP A 54 3 44.5 8.5 9.5 26.5 0.0 ALA A 55 1 17.0 7.0 7.0 3.0 0.0 GLU A 56 11 16.0 5.5 10.5 0.0 0.0 GLY A 57 0 14.5 3.5 7.5 3.5 0.0 ALA A 58 0 20.5 1.5 10.0 9.0 0.0 LEU A 59 8 24.5 4.5 12.0 8.0 0.0 GLU A 60 4 18.5 6.5 12.0 0.0 0.0 LEU A 61 5 17.5 7.0 7.5 3.0 0.0 ILE A 62 5 21.5 6.5 5.0 10.0 0.0 LYS A 63 11 16.0 9.5 6.5 0.0 0.0 VAL A 64 6 13.5 10.5 3.0 0.0 0.0 ARG A 65 1 6.0 3.5 2.5 0.0 0.0 ARG A 66 0 0.0 0.0 0.0 0.0 0.0 PRO A 67 0 0.5 0.0 0.0 0.5 0.0 LYS A 68 10 7.5 6.0 1.0 0.5 0.0 TYR A 69 0 13.5 8.0 0.0 5.5 0.0 VAL A 70 3 21.5 4.5 2.0 15.0 0.0 HIS A 71 4 7.0 2.5 3.0 1.5 0.0 LYS A 72 3 12.0 2.5 4.0 5.5 0.0 GLU A 73 9 9.0 5.5 3.5 0.0 0.0 GLN A 74 9 13.5 6.5 6.0 1.0 0.0 ILE A 75 7 38.0 8.0 6.5 23.5 0.0 GLU A 76 6 18.5 7.0 8.0 3.5 0.0 ALA A 77 1 11.0 4.0 7.0 0.0 0.0 VAL A 78 3 31.0 4.5 13.5 13.0 0.0 LYS A 79 12 16.0 7.5 6.5 2.0 0.0 ASP A 80 2 11.0 6.5 4.5 0.0 0.0 ASN A 81 5 19.0 4.5 9.5 5.0 0.0 PHE A 82 2 31.0 8.0 10.0 13.0 0.0 LEU A 83 9 20.0 8.5 7.0 4.5 0.0 GLU A 84 0 12.0 4.5 5.5 2.0 0.0 LEU A 85 5 30.5 6.0 6.0 18.5 0.0 VAL A 86 2 20.5 6.5 6.5 7.5 0.0 LEU A 87 7 11.5 5.0 4.5 2.0 0.0 GLN A 88 2 11.0 4.5 3.0 3.5 0.0 SER A 89 0 6.0 2.0 2.5 1.5 0.0 TYR A 90 3 10.5 3.5 2.5 4.5 0.0 VAL A 91 1 14.0 6.5 5.0 2.5 0.0 HIS A 92 2 8.0 4.0 1.0 3.0 0.0 HIS A 93 1 7.0 3.5 2.5 1.0 0.0 ILE A 94 4 12.0 3.5 0.0 8.5 0.0 HIS A 95 0 0.5 0.5 0.0 0.0 0.0 LYS A 96 0 2.0 0.0 0.0 2.0 0.0 LYS A 97 3 2.0 1.0 1.0 0.0 0.0 ARG A 98 0 4.5 2.0 2.5 0.0 0.0 PHE A 99 2 19.5 2.5 4.5 12.5 0.0 LYS A 100 13 9.0 6.0 3.0 0.0 0.0 ASP A 101 2 11.5 6.0 5.5 0.0 0.0 ILE A 102 5 23.5 5.5 8.5 9.5 0.0 THR A 103 3 16.0 5.5 5.5 5.0 0.0 GLU A 104 9 12.0 5.5 6.5 0.0 0.0 SER A 105 1 11.0 5.5 5.5 0.0 0.0 VAL A 106 3 26.5 4.0 9.0 13.5 0.0 LEU A 107 9 26.0 5.5 10.5 10.0 0.0 TYR A 108 2 14.0 6.0 7.0 1.0 0.0 THR A 109 1 17.5 5.0 5.0 7.5 0.0 LEU A 110 9 30.5 6.0 12.5 12.0 0.0 HIS A 111 5 20.0 6.0 11.0 3.0 0.0 ALA A 112 1 18.5 5.0 7.5 6.0 0.0 VAL A 113 2 31.0 6.5 10.0 14.5 0.0 LYS A 114 10 27.5 6.5 9.0 12.0 0.0 ASP A 115 4 11.5 4.5 6.5 0.5 0.0 GLU A 116 6 13.0 4.5 5.5 3.0 0.0 ILE A 117 5 25.0 7.5 8.0 9.5 0.0 ALA A 118 1 8.0 5.5 2.0 0.5 0.0 ARG A 119 6 5.5 1.0 3.5 1.0 0.0 GLU A 120 5 1.5 0.0 1.5 0.0 0.0 ASP A 121 0 0.0 0.0 0.0 0.0 0.0 SER A 122 0 0.0 0.0 0.0 0.0 0.0 ARG A 123 1 0.0 0.0 0.0 0.0 0.0 TOTAL 419 1604.0 498.0 626.0 480.0 0.0 > ANALYZE_cns: Do you want a CONS.OUT file [default no] ?_