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 `STR65_R3Cons_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> EXPDTA NMR, 19 STRUCTURES > ReadCoordsPdb(): >> REMARK PdbStat -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > ReadCoordsPdb(): >> REMARK PdbStat -- PDB COORDINATES FOR TEMP_BCM_111.PDB, 18 MODEL/S TEMP_BCM_111.PDB > ReadCoordsPdb(): >> REMARK PdbStat -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > ReadCoordsPdb(): >> SEQRES 1 A 109 VAL ASN PHE LYS ASP LYS SER MET PRO THR ALA ILE GLU 1 > ReadCoordsPdb(): Counting models in file `STR65_R3Cons_em_bcr3.pdb'; Model: 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 > ReadCoordsPdb(): After scanning there is(are) 18 model(s) > ReadCoordsPdb(): what model do you want [(1 to 18) or all] ?_ > ReadCoordsPdb(): I'm reading file STR65_R3Cons_em_bcr3.pdb MODEL 1 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 1700 ATOM records read from file > ReadCoordsPdb(): --> 1700 Regular IUPAC Atoms > ReadCoordsPdb(): --> 0 Pseudo-atoms (DISMAN type) > ReadCoordsPdb(): --> 0 Lone pairs > ReadCoordsPdb(): Bye ... > =============================== INFO ================================ > INFO_mol: # atoms: 1700 (543 C, 848 H, 164 O, 141 N, 4 S, 0 Q, 0 Metals) > INFO_mol: # residues: 109 (Avg. mol. weight: 111.0) > INFO_mol: # -- M.W. : 12103.6 g/mol. (12.10 kD) Estimated RoG : 13.08 > INFO_mol: CenterMass() -- Working PDB model 1 in file, model no. 1 > INFO_mol: CenterMass() -- Molecule `STR65_R3Cons_em_bcr3.pdb' model #1, TOTAL RESIDUES: 109 > INFO_mol: Radius of Gyration : 13.3649 angstroms > INFO_mol: Center of Masses: x_cm(15.908), y_cm(15.106), z_cm(-24.782) > INFO_res: VNFKDKSMPT AIEKALDFIG GMNTSASVPH SMDESTAKGI LKYLHDLGVP > INFO_res: VSPEVVVARG EQEGWNPEFT KKVAGWAEKV ASGNRILIKN PEYFSTYMQE > INFO_res: QLKELVLEH > INFO_res: > INFO_res: VAL ASN PHE LYS ASP LYS SER MET PRO THR ALA ILE > INFO_res: GLU LYS ALA LEU ASP PHE ILE GLY GLY MET ASN THR > INFO_res: SER ALA SER VAL PRO HIS SER MET ASP GLU SER THR > INFO_res: ALA LYS GLY ILE LEU LYS TYR LEU HIS ASP LEU GLY > INFO_res: VAL PRO VAL SER PRO GLU VAL VAL VAL ALA ARG GLY > INFO_res: GLU GLN GLU GLY TRP ASN PRO GLU PHE THR LYS LYS > INFO_res: VAL ALA GLY TRP ALA GLU LYS VAL ALA SER GLY ASN > INFO_res: ARG ILE LEU ILE LYS ASN PRO GLU TYR PHE SER THR > INFO_res: TYR MET GLN GLU GLN LEU LYS GLU LEU VAL LEU GLU > INFO_res: HIS > INFO_res: > INFO_res: 8 ALA 2 ARG 5 ASN 4 ASP 3 GLN 11 GLU > INFO_res: 8 GLY 3 HIS 5 ILE 8 LEU 10 LYS 4 MET > INFO_res: 4 PHE 6 PRO 8 SER 5 THR 3 TYR 2 TRP > INFO_res: 10 VAL > INFO_res: DISULFIDE: ** NO INFO FOR DISULFIDES IN FILE > ===================================================================== > ReadCoordsPdb(): *** monomer, 1 [1] chains *** PdbStat> > locate_file(): file `STR65_R3Cons_em_bcr3.upl' opened for reading 0 SANI-RDC constraints read 1226 NOE-distance constraints (0 Ambiguous NOE/s) read 1226 TOTAL constraints read PdbStat> -------------- SUMMARY OF RESTRAINTS --------------- TOTAL NUMBER OF NOE RESTRAINTS : 1226 INTRA-RESIDUE RESTRAINTS (I=J) : 263 SEQUENTIAL RESTRAINTS (I-J)=1 : 374 BACKBONE-BACKBONE : 95 BACKBONE-SIDE CHAIN : 37 SIDE CHAIN-SIDE CHAIN : 242 MEDIUM RANGE RESTRAINTS 1<(I-J)<5 : 324 BACKBONE-BACKBONE : 116 BACKBONE-SIDE CHAIN : 93 SIDE CHAIN-SIDE CHAIN : 115 LONG RANGE RESTRAINTS (I-J)>=5 : 265 TOTAL HYDROGEN BOND RESTRAINTS : 0 LONG RANGE H-BOND RESTR. (I-J)>=5 : 0 DISULFIDE RESTRAINTS : 0 INTRA-CHAIN RESTRAINTS : 1226 INTER-CHAIN RESTRAINTS : 0 AMBIGUOUS RESTRAINTS : 0 ----------------------------------------------------- ----------------------------------------------------- ----------------------------------------------------- RES # INTRA INTER seq med lng InterChain VAL A 1 0 1.0 1.0 0.0 0.0 0.0 ASN A 2 2 2.5 2.5 0.0 0.0 0.0 PHE A 3 2 3.0 3.0 0.0 0.0 0.0 LYS A 4 2 2.5 2.5 0.0 0.0 0.0 ASP A 5 0 2.5 2.5 0.0 0.0 0.0 LYS A 6 3 3.5 3.5 0.0 0.0 0.0 SER A 7 1 3.0 3.0 0.0 0.0 0.0 MET A 8 2 2.5 2.5 0.0 0.0 0.0 PRO A 9 0 2.5 2.5 0.0 0.0 0.0 THR A 10 1 4.5 3.5 1.0 0.0 0.0 ALA A 11 0 8.5 5.0 3.0 0.5 0.0 ILE A 12 4 7.5 5.0 2.5 0.0 0.0 GLU A 13 3 8.5 3.5 5.0 0.0 0.0 LYS A 14 8 7.0 3.0 4.0 0.0 0.0 ALA A 15 0 10.5 3.0 6.0 1.5 0.0 LEU A 16 5 11.0 3.0 5.0 3.0 0.0 ASP A 17 0 7.0 3.5 3.5 0.0 0.0 PHE A 18 3 15.5 3.0 2.5 10.0 0.0 ILE A 19 6 19.0 4.0 4.0 11.0 0.0 GLY A 20 0 7.5 3.0 1.0 3.5 0.0 GLY A 21 0 2.5 1.0 1.5 0.0 0.0 MET A 22 2 2.0 2.0 0.0 0.0 0.0 ASN A 23 2 2.5 2.5 0.0 0.0 0.0 THR A 24 1 1.5 1.5 0.0 0.0 0.0 SER A 25 0 2.0 2.0 0.0 0.0 0.0 ALA A 26 0 3.5 2.0 1.5 0.0 0.0 SER A 27 1 10.0 3.0 2.0 5.0 0.0 VAL A 28 1 5.5 4.5 1.0 0.0 0.0 PRO A 29 0 2.0 2.0 0.0 0.0 0.0 HIS A 30 3 3.0 0.5 2.5 0.0 0.0 SER A 31 0 2.0 1.0 1.0 0.0 0.0 MET A 32 0 5.0 1.5 2.0 1.5 0.0 ASP A 33 0 3.5 2.5 1.0 0.0 0.0 GLU A 34 2 9.5 3.5 2.5 3.5 0.0 SER A 35 1 6.0 3.0 2.0 1.0 0.0 THR A 36 2 8.5 2.0 4.5 2.0 0.0 ALA A 37 0 13.0 2.5 4.5 6.0 0.0 LYS A 38 3 14.5 3.5 6.0 5.0 0.0 GLY A 39 0 6.0 3.0 1.5 1.5 0.0 ILE A 40 7 16.0 3.5 3.5 9.0 0.0 LEU A 41 5 18.0 4.5 6.0 7.5 0.0 LYS A 42 4 12.0 4.0 3.0 5.0 0.0 TYR A 43 3 20.0 6.5 3.5 10.0 0.0 LEU A 44 5 12.0 6.0 5.0 1.0 0.0 HIS A 45 3 10.5 2.5 1.5 6.5 0.0 ASP A 46 0 6.5 3.5 3.0 0.0 0.0 LEU A 47 7 13.0 3.5 6.0 3.5 0.0 GLY A 48 0 2.5 2.0 0.5 0.0 0.0 VAL A 49 3 5.0 3.0 2.0 0.0 0.0 PRO A 50 0 9.0 3.0 0.0 6.0 0.0 VAL A 51 2 2.5 2.0 0.0 0.5 0.0 SER A 52 0 10.0 4.5 5.5 0.0 0.0 PRO A 53 0 18.5 6.0 3.0 9.5 0.0 GLU A 54 4 13.5 6.5 7.0 0.0 0.0 VAL A 55 3 10.5 6.0 4.5 0.0 0.0 VAL A 56 3 17.5 3.5 5.0 9.0 0.0 VAL A 57 3 13.5 5.5 6.0 2.0 0.0 ALA A 58 0 9.5 4.5 5.0 0.0 0.0 ARG A 59 7 11.5 2.0 7.0 2.5 0.0 GLY A 60 0 9.0 2.0 3.5 3.5 0.0 GLU A 61 2 8.0 2.5 5.0 0.5 0.0 GLN A 62 2 9.5 5.5 4.0 0.0 0.0 GLU A 63 1 13.0 4.5 8.0 0.5 0.0 GLY A 64 0 3.5 2.0 1.5 0.0 0.0 TRP A 65 6 26.5 2.5 5.5 18.5 0.0 ASN A 66 0 5.0 3.5 0.5 1.0 0.0 PRO A 67 0 7.0 5.0 2.0 0.0 0.0 GLU A 68 2 10.5 4.5 2.5 3.5 0.0 PHE A 69 2 11.0 4.5 4.5 2.0 0.0 THR A 70 1 13.5 4.5 4.0 5.0 0.0 LYS A 71 8 8.5 5.0 3.5 0.0 0.0 LYS A 72 10 13.5 5.5 8.0 0.0 0.0 VAL A 73 3 15.0 4.0 7.0 4.0 0.0 ALA A 74 0 14.0 3.0 5.0 6.0 0.0 GLY A 75 0 6.5 1.5 5.0 0.0 0.0 TRP A 76 9 26.0 3.5 11.5 11.0 0.0 ALA A 77 0 15.5 4.5 4.0 7.0 0.0 GLU A 78 2 12.5 4.0 6.0 2.5 0.0 LYS A 79 4 15.5 6.0 3.0 6.5 0.0 VAL A 80 3 19.5 6.5 4.0 9.0 0.0 ALA A 81 0 10.0 4.0 2.5 3.5 0.0 SER A 82 0 5.5 2.0 3.5 0.0 0.0 GLY A 83 0 4.0 2.0 2.0 0.0 0.0 ASN A 84 6 9.0 4.0 2.0 3.0 0.0 ARG A 85 4 7.0 7.0 0.0 0.0 0.0 ILE A 86 7 17.0 6.5 0.0 10.5 0.0 LEU A 87 7 5.5 5.5 0.0 0.0 0.0 ILE A 88 6 15.5 4.0 7.0 4.5 0.0 LYS A 89 3 3.0 3.0 0.0 0.0 0.0 ASN A 90 4 7.0 4.0 3.0 0.0 0.0 PRO A 91 0 7.5 3.0 4.5 0.0 0.0 GLU A 92 2 3.5 2.5 1.0 0.0 0.0 TYR A 93 2 2.5 2.5 0.0 0.0 0.0 PHE A 94 3 15.0 1.0 3.5 10.5 0.0 SER A 95 0 3.5 2.0 1.5 0.0 0.0 THR A 96 2 7.0 4.0 3.0 0.0 0.0 TYR A 97 5 9.5 5.5 4.0 0.0 0.0 MET A 98 4 13.0 5.0 4.0 4.0 0.0 GLN A 99 2 11.5 3.0 3.5 5.0 0.0 GLU A 100 3 8.0 2.5 5.5 0.0 0.0 GLN A 101 3 9.0 3.5 3.5 2.0 0.0 LEU A 102 5 16.5 4.0 4.5 8.0 0.0 LYS A 103 4 13.5 3.5 5.0 5.0 0.0 GLU A 104 2 6.0 3.0 3.0 0.0 0.0 LEU A 105 5 6.0 2.5 3.5 0.0 0.0 VAL A 106 2 7.5 3.5 2.5 1.5 0.0 LEU A 107 6 9.0 5.0 4.0 0.0 0.0 GLU A 108 2 4.5 3.0 1.5 0.0 0.0 HIS A 109 0 0.0 0.0 0.0 0.0 0.0 TOTAL 263 963.0 374.0 324.0 265.0 0.0 > ANALYZE_cns: Do you want a CONS.OUT file [default no] ?_