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 `SRR115C_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 99 GLU ASP PRO GLU ASP PRO PHE THR ARG TYR ALA LEU ALA 1 > ReadCoordsPdb(): Counting models in file `SRR115C_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 SRR115C_R3Cons_em_bcr3.pdb MODEL 1 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 1558 ATOM records read from file > ReadCoordsPdb(): --> 1558 Regular IUPAC Atoms > ReadCoordsPdb(): --> 0 Pseudo-atoms (DISMAN type) > ReadCoordsPdb(): --> 0 Lone pairs > ReadCoordsPdb(): Bye ... > =============================== INFO ================================ > INFO_mol: # atoms: 1558 (503 C, 746 H, 167 O, 142 N, 0 S, 0 Q, 0 Metals) > INFO_mol: # residues: 99 (Avg. mol. weight: 115.7) > INFO_mol: # -- M.W. : 11454.1 g/mol. (11.45 kD) Estimated RoG : 12.61 > INFO_mol: CenterMass() -- Working PDB model 1 in file, model no. 1 > INFO_mol: CenterMass() -- Molecule `SRR115C_R3Cons_em_bcr3.pdb' model #1, TOTAL RESIDUES: 99 > INFO_mol: Radius of Gyration : 14.2416 angstroms > INFO_mol: Center of Masses: x_cm(6.015), y_cm(-9.793), z_cm(5.984) > INFO_res: EDPEDPFTRY ALAQEHLKHD NASRALALFE ELVETDPDYV GTYYHLGKLY > INFO_res: ERLDRTDDAI DTYAQGIEVA REEGTQKDLS ELQDAKLKAE GLEHHHHHH > INFO_res: > INFO_res: GLU ASP PRO GLU ASP PRO PHE THR ARG TYR ALA LEU > INFO_res: ALA GLN GLU HIS LEU LYS HIS ASP ASN ALA SER ARG > INFO_res: ALA LEU ALA LEU PHE GLU GLU LEU VAL GLU THR ASP > INFO_res: PRO ASP TYR VAL GLY THR TYR TYR HIS LEU GLY LYS > INFO_res: LEU TYR GLU ARG LEU ASP ARG THR ASP ASP ALA ILE > INFO_res: ASP THR TYR ALA GLN GLY ILE GLU VAL ALA ARG GLU > INFO_res: GLU GLY THR GLN LYS ASP LEU SER GLU LEU GLN ASP > INFO_res: ALA LYS LEU LYS ALA GLU GLY LEU GLU HIS HIS HIS > INFO_res: HIS HIS HIS > INFO_res: > INFO_res: 10 ALA 5 ARG 1 ASN 11 ASP 4 GLN 13 GLU > INFO_res: 5 GLY 9 HIS 2 ILE 12 LEU 5 LYS 2 PHE > INFO_res: 3 PRO 2 SER 6 THR 6 TYR 3 VAL > INFO_res: DISULFIDE: ** NO INFO FOR DISULFIDES IN FILE > ===================================================================== > ReadCoordsPdb(): *** monomer, 1 [1] chains *** PdbStat> > locate_file(): file `SRR115C_R3Cons_em_bcr3.upl' opened for reading 0 SANI-RDC constraints read 3081 NOE-distance constraints (0 Ambiguous NOE/s) read 3081 TOTAL constraints read PdbStat> -------------- SUMMARY OF RESTRAINTS --------------- TOTAL NUMBER OF NOE RESTRAINTS : 3081 INTRA-RESIDUE RESTRAINTS (I=J) : 557 SEQUENTIAL RESTRAINTS (I-J)=1 : 703 BACKBONE-BACKBONE : 106 BACKBONE-SIDE CHAIN : 112 SIDE CHAIN-SIDE CHAIN : 485 MEDIUM RANGE RESTRAINTS 1<(I-J)<5 : 1017 BACKBONE-BACKBONE : 276 BACKBONE-SIDE CHAIN : 266 SIDE CHAIN-SIDE CHAIN : 475 LONG RANGE RESTRAINTS (I-J)>=5 : 804 TOTAL HYDROGEN BOND RESTRAINTS : 0 LONG RANGE H-BOND RESTR. (I-J)>=5 : 0 DISULFIDE RESTRAINTS : 0 INTRA-CHAIN RESTRAINTS : 3081 INTER-CHAIN RESTRAINTS : 0 AMBIGUOUS RESTRAINTS : 0 ----------------------------------------------------- ----------------------------------------------------- ----------------------------------------------------- RES # INTRA INTER seq med lng InterChain GLU A 1 0 2.5 2.5 0.0 0.0 0.0 ASP A 2 3 10.5 9.0 1.5 0.0 0.0 PRO A 3 0 15.5 9.5 2.0 4.0 0.0 GLU A 4 7 7.5 5.5 0.5 1.5 0.0 ASP A 5 1 15.5 7.0 8.5 0.0 0.0 PRO A 6 0 17.5 9.0 4.5 4.0 0.0 PHE A 7 4 21.5 7.5 12.0 2.0 0.0 THR A 8 3 19.5 7.0 8.0 4.5 0.0 ARG A 9 16 34.0 9.5 11.0 13.5 0.0 TYR A 10 4 38.5 8.5 15.5 14.5 0.0 ALA A 11 1 17.0 5.0 12.0 0.0 0.0 LEU A 12 10 24.0 6.5 15.0 2.5 0.0 ALA A 13 1 34.5 7.5 14.0 13.0 0.0 GLN A 14 8 29.0 6.5 14.0 8.5 0.0 GLU A 15 5 19.5 7.0 12.5 0.0 0.0 HIS A 16 5 40.0 8.0 12.0 20.0 0.0 LEU A 17 10 35.0 9.0 12.0 14.0 0.0 LYS A 18 15 17.0 10.5 6.5 0.0 0.0 HIS A 19 5 15.0 8.5 6.5 0.0 0.0 ASP A 20 3 10.5 5.5 5.0 0.0 0.0 ASN A 21 6 34.0 7.5 19.0 7.5 0.0 ALA A 22 1 23.0 6.5 6.5 10.0 0.0 SER A 23 1 16.5 4.5 10.5 1.5 0.0 ARG A 24 14 24.0 5.5 16.0 2.5 0.0 ALA A 25 1 39.0 5.5 17.0 16.5 0.0 LEU A 26 11 43.5 6.0 16.5 21.0 0.0 ALA A 27 1 18.0 8.0 9.0 1.0 0.0 LEU A 28 12 39.0 8.5 12.5 18.0 0.0 PHE A 29 4 56.5 6.5 16.0 34.0 0.0 GLU A 30 5 25.0 5.0 13.0 7.0 0.0 GLU A 31 4 20.5 7.0 11.5 2.0 0.0 LEU A 32 10 47.5 10.5 16.5 20.5 0.0 VAL A 33 5 34.5 11.0 12.0 11.5 0.0 GLU A 34 4 17.0 11.5 5.5 0.0 0.0 THR A 35 2 17.0 8.0 9.0 0.0 0.0 ASP A 36 1 18.0 4.0 14.0 0.0 0.0 PRO A 37 0 13.0 5.0 4.0 4.0 0.0 ASP A 38 0 9.0 5.0 1.5 2.5 0.0 TYR A 39 5 34.0 10.0 13.5 10.5 0.0 VAL A 40 5 42.0 11.0 7.5 23.5 0.0 GLY A 41 0 11.0 4.5 6.5 0.0 0.0 THR A 42 5 30.5 4.5 13.5 12.5 0.0 TYR A 43 6 46.0 5.0 14.5 26.5 0.0 TYR A 44 3 34.0 7.0 9.5 17.5 0.0 HIS A 45 7 26.5 10.0 9.0 7.5 0.0 LEU A 46 11 54.0 9.0 20.0 25.0 0.0 GLY A 47 0 26.0 5.5 11.0 9.5 0.0 LYS A 48 25 21.5 5.0 12.5 4.0 0.0 LEU A 49 11 53.5 8.0 21.0 24.5 0.0 TYR A 50 6 57.5 8.0 17.0 32.5 0.0 GLU A 51 5 23.0 6.5 5.5 11.0 0.0 ARG A 52 13 21.0 8.5 10.0 2.5 0.0 LEU A 53 10 31.0 10.0 17.0 4.0 0.0 ASP A 54 3 13.0 9.0 4.0 0.0 0.0 ARG A 55 13 31.5 8.5 13.5 9.5 0.0 THR A 56 3 29.5 6.5 8.5 14.5 0.0 ASP A 57 1 13.5 5.0 8.0 0.5 0.0 ASP A 58 2 21.5 5.0 10.0 6.5 0.0 ALA A 59 1 35.5 7.0 12.0 16.5 0.0 ILE A 60 11 48.0 9.5 18.0 20.5 0.0 ASP A 61 2 15.0 7.0 8.0 0.0 0.0 THR A 62 3 31.0 5.0 10.5 15.5 0.0 TYR A 63 5 47.5 7.5 14.0 26.0 0.0 ALA A 64 1 26.0 8.0 13.0 5.0 0.0 GLN A 65 14 32.5 8.0 15.0 9.5 0.0 GLY A 66 0 29.0 6.5 12.5 10.0 0.0 ILE A 67 12 56.0 8.5 19.0 28.5 0.0 GLU A 68 5 27.5 11.0 16.0 0.5 0.0 VAL A 69 5 43.5 9.0 23.5 11.0 0.0 ALA A 70 1 38.0 6.0 17.5 14.5 0.0 ARG A 71 18 25.5 9.0 10.0 6.5 0.0 GLU A 72 8 20.5 12.0 8.5 0.0 0.0 GLU A 73 4 24.0 8.5 12.0 3.5 0.0 GLY A 74 0 15.5 5.5 5.0 5.0 0.0 THR A 75 2 13.0 6.0 6.5 0.5 0.0 GLN A 76 9 18.5 6.5 10.0 2.0 0.0 LYS A 77 17 13.0 6.0 7.0 0.0 0.0 ASP A 78 2 25.5 7.0 12.0 6.5 0.0 LEU A 79 11 46.5 9.5 22.5 14.5 0.0 SER A 80 1 20.5 8.0 11.0 1.5 0.0 GLU A 81 3 18.0 5.0 9.0 4.0 0.0 LEU A 82 12 55.0 7.0 13.0 35.0 0.0 GLN A 83 13 36.5 8.5 18.0 10.0 0.0 ASP A 84 2 20.0 8.0 11.5 0.5 0.0 ALA A 85 1 23.5 6.0 11.0 6.5 0.0 LYS A 86 24 44.5 8.5 10.5 25.5 0.0 LEU A 87 9 26.0 11.0 13.5 1.5 0.0 LYS A 88 19 21.0 11.0 9.5 0.5 0.0 ALA A 89 1 21.0 9.5 6.5 5.0 0.0 GLU A 90 6 22.5 6.0 9.0 7.5 0.0 GLY A 91 0 9.5 6.0 3.5 0.0 0.0 LEU A 92 11 15.0 7.5 2.5 5.0 0.0 GLU A 93 7 11.5 8.5 1.0 2.0 0.0 HIS A 94 0 6.5 6.5 0.0 0.0 0.0 HIS A 95 0 2.0 2.0 0.0 0.0 0.0 HIS A 96 0 0.0 0.0 0.0 0.0 0.0 HIS A 97 0 0.0 0.0 0.0 0.0 0.0 HIS A 98 0 0.0 0.0 0.0 0.0 0.0 HIS A 99 0 0.0 0.0 0.0 0.0 0.0 TOTAL 557 2524.0 703.0 1017.0 804.0 0.0 > ANALYZE_cns: Do you want a CONS.OUT file [default no] ?_