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 `CTR148A_R3_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> EXPDTA NMR, 21 STRUCTURES > ReadCoordsPdb(): >> REMARK PdbStat -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > ReadCoordsPdb(): >> REMARK PdbStat -- PDB COORDINATES FOR TEMP.PDB, 20 MODEL/S TEMP.PDB > ReadCoordsPdb(): >> REMARK PdbStat -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > ReadCoordsPdb(): >> SEQRES 1 A 176 MET THR ASP PHE LEU ALA GLY ILE ARG ILE VAL GLY GLU 1 > ReadCoordsPdb(): Counting models in file `CTR148A_R3_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 CTR148A_R3_em_bcr3.pdb MODEL 1 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 2846 ATOM records read from file > ReadCoordsPdb(): --> 2846 Regular IUPAC Atoms > ReadCoordsPdb(): --> 0 Pseudo-atoms (DISMAN type) > ReadCoordsPdb(): --> 0 Lone pairs > ReadCoordsPdb(): Bye ... > =============================== INFO ================================ > INFO_mol: # atoms: 2846 (884 C, 1440 H, 256 O, 256 N, 10 S, 0 Q, 0 Metals) > INFO_mol: # residues: 176 (Avg. mol. weight: 114.0) > INFO_mol: # -- M.W. : 20070.8 g/mol. (20.07 kD) Estimated RoG : 15.69 > INFO_mol: CenterMass() -- Working PDB model 1 in file, model no. 1 > INFO_mol: CenterMass() -- Molecule `CTR148A_R3_em_bcr3.pdb' model #1, TOTAL RESIDUES: 176 > INFO_mol: Radius of Gyration : 16.6314 angstroms > INFO_mol: Center of Masses: x_cm(-0.503), y_cm(-0.191), z_cm(0.082) > INFO_res: MTDFLAGIRI VGEDKNGMTN QITGVISKFD TNIRTIVLNA KDGIFTCNLM > INFO_res: IFVKNTDKLT TLMDKLRKVQ GVFTVERLSN LEHHHHHHMT DFLAGIRIVG > INFO_res: EDKNGMTNQI TGVISKFDTN IRTIVLNAKD GIFTCNLMIF VKNTDKLTTL > INFO_res: MDKLRKVQGV FTVERLSNLE HHHHHH > INFO_res: > INFO_res: MET THR ASP PHE LEU ALA GLY ILE ARG ILE VAL GLY > INFO_res: GLU ASP LYS ASN GLY MET THR ASN GLN ILE THR GLY > INFO_res: VAL ILE SER LYS PHE ASP THR ASN ILE ARG THR ILE > INFO_res: VAL LEU ASN ALA LYS ASP GLY ILE PHE THR CYS ASN > INFO_res: LEU MET ILE PHE VAL LYS ASN THR ASP LYS LEU THR > INFO_res: THR LEU MET ASP LYS LEU ARG LYS VAL GLN GLY VAL > INFO_res: PHE THR VAL GLU ARG LEU SER ASN LEU GLU HIS HIS > INFO_res: HIS HIS HIS HIS MET THR ASP PHE LEU ALA GLY ILE > INFO_res: ARG ILE VAL GLY GLU ASP LYS ASN GLY MET THR ASN > INFO_res: GLN ILE THR GLY VAL ILE SER LYS PHE ASP THR ASN > INFO_res: ILE ARG THR ILE VAL LEU ASN ALA LYS ASP GLY ILE > INFO_res: PHE THR CYS ASN LEU MET ILE PHE VAL LYS ASN THR > INFO_res: ASP LYS LEU THR THR LEU MET ASP LYS LEU ARG LYS > INFO_res: VAL GLN GLY VAL PHE THR VAL GLU ARG LEU SER ASN > INFO_res: LEU GLU HIS HIS HIS HIS HIS HIS > INFO_res: > INFO_res: 4 ALA 8 ARG 14 ASN 12 ASP 2 CYS 4 GLN > INFO_res: 6 GLU 12 GLY 12 HIS 16 ILE 16 LEU 14 LYS > INFO_res: 8 MET 10 PHE 4 SER 20 THR 14 VAL > INFO_res: DISULFIDE: ** NO INFO FOR DISULFIDES IN FILE > ===================================================================== > ReadCoordsPdb(): *** x-mer, 2 [2] chains PdbStat> > locate_file(): file `CTR148A_R3_em_bcr3.upl' opened for reading > CNSTR_rdr: Converting DYANA UPL input file > CNSTR_rdr: 2531 constraints read PdbStat> -------------- SUMMARY OF RESTRAINTS --------------- TOTAL NUMBER OF NOE RESTRAINTS : 2531 INTRA-RESIDUE RESTRAINTS (I=J) : 433 SEQUENTIAL RESTRAINTS (I-J)=1 : 592 BACKBONE-BACKBONE : 98 BACKBONE-SIDE CHAIN : 117 SIDE CHAIN-SIDE CHAIN : 377 MEDIUM RANGE RESTRAINTS 1<(I-J)<5 : 536 BACKBONE-BACKBONE : 86 BACKBONE-SIDE CHAIN : 149 SIDE CHAIN-SIDE CHAIN : 301 LONG RANGE RESTRAINTS (I-J)>=5 : 970 TOTAL HYDROGEN BOND RESTRAINTS : 0 LONG RANGE H-BOND RESTR. (I-J)>=5 : 0 DISULFIDE RESTRAINTS : 0 INTRA-CHAIN RESTRAINTS : 2531 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 THR A 2 1 1.0 0.5 0.5 0.0 0.0 ASP A 3 0 8.0 1.5 0.0 6.5 0.0 PHE A 4 3 30.5 5.5 4.0 21.0 0.0 LEU A 5 11 40.0 9.0 0.0 31.0 0.0 ALA A 6 1 24.5 7.0 3.0 14.5 0.0 GLY A 7 0 22.0 5.5 0.5 16.0 0.0 ILE A 8 10 38.5 5.5 3.0 30.0 0.0 ARG A 9 5 29.0 8.5 2.5 18.0 0.0 ILE A 10 8 46.0 10.5 2.5 33.0 0.0 VAL A 11 5 31.0 7.5 3.0 20.5 0.0 GLY A 12 0 18.0 4.5 0.0 13.5 0.0 GLU A 13 4 32.5 3.5 6.5 22.5 0.0 ASP A 14 1 15.0 4.0 1.0 10.0 0.0 LYS A 15 8 29.5 9.5 17.0 3.0 0.0 ASN A 16 4 11.5 11.0 0.5 0.0 0.0 GLY A 17 0 11.0 7.5 3.5 0.0 0.0 MET A 18 11 41.5 7.0 22.5 12.0 0.0 THR A 19 5 22.0 5.5 7.0 9.5 0.0 ASN A 20 7 13.5 8.0 5.0 0.5 0.0 GLN A 21 11 37.5 15.0 17.0 5.5 0.0 ILE A 22 10 48.5 15.0 16.5 17.0 0.0 THR A 23 5 25.0 8.0 11.5 5.5 0.0 GLY A 24 0 13.0 4.0 9.0 0.0 0.0 VAL A 25 5 35.0 5.5 25.5 4.0 0.0 ILE A 26 7 30.5 7.5 16.5 6.5 0.0 SER A 27 4 18.5 8.0 8.0 2.5 0.0 LYS A 28 15 21.5 7.0 13.5 1.0 0.0 PHE A 29 6 42.0 3.5 13.5 25.0 0.0 ASP A 30 0 5.0 3.5 0.0 1.5 0.0 THR A 31 2 21.0 4.5 5.5 11.0 0.0 ASN A 32 5 8.5 6.5 0.0 2.0 0.0 ILE A 33 8 19.0 6.5 2.5 10.0 0.0 ARG A 34 3 13.5 4.0 0.5 9.0 0.0 THR A 35 3 23.0 5.5 4.0 13.5 0.0 ILE A 36 5 18.0 8.5 1.0 8.5 0.0 VAL A 37 4 30.0 9.5 4.0 16.5 0.0 LEU A 38 8 34.0 8.5 2.5 23.0 0.0 ASN A 39 7 17.0 6.0 4.5 6.5 0.0 ALA A 40 1 18.5 5.0 4.0 9.5 0.0 LYS A 41 8 22.0 8.0 11.5 2.5 0.0 ASP A 42 0 11.5 6.0 5.5 0.0 0.0 GLY A 43 0 9.5 4.5 2.0 3.0 0.0 ILE A 44 10 41.0 8.5 14.0 18.5 0.0 PHE A 45 3 56.0 10.0 6.5 39.5 0.0 THR A 46 2 26.5 6.5 3.0 17.0 0.0 CYS A 47 0 29.5 3.5 4.0 22.0 0.0 ASN A 48 3 33.5 5.5 1.5 26.5 0.0 LEU A 49 8 35.5 10.5 0.0 25.0 0.0 MET A 50 8 47.0 12.5 1.0 33.5 0.0 ILE A 51 9 44.5 11.5 2.5 30.5 0.0 PHE A 52 3 31.5 11.0 0.5 20.0 0.0 VAL A 53 4 49.0 10.0 6.0 33.0 0.0 LYS A 54 14 17.0 10.5 1.0 5.5 0.0 ASN A 55 0 15.0 7.0 7.0 1.0 0.0 THR A 56 2 17.0 3.5 9.5 4.0 0.0 ASP A 57 1 11.0 6.0 5.0 0.0 0.0 LYS A 58 8 38.0 7.0 20.0 11.0 0.0 LEU A 59 11 46.5 8.0 17.0 21.5 0.0 THR A 60 3 20.5 7.0 12.0 1.5 0.0 THR A 61 3 20.5 7.5 13.0 0.0 0.0 LEU A 62 10 61.0 10.5 28.5 22.0 0.0 MET A 63 6 34.0 6.5 14.5 13.0 0.0 ASP A 64 2 20.5 7.0 12.5 1.0 0.0 LYS A 65 15 35.5 7.0 17.5 11.0 0.0 LEU A 66 7 25.0 4.5 10.5 10.0 0.0 ARG A 67 11 25.0 6.5 8.5 10.0 0.0 LYS A 68 16 19.5 11.5 7.5 0.5 0.0 VAL A 69 5 36.5 15.0 9.5 12.0 0.0 GLN A 70 5 12.5 10.0 2.0 0.5 0.0 GLY A 71 0 12.5 4.5 1.0 7.0 0.0 VAL A 72 5 32.5 6.5 9.5 16.5 0.0 PHE A 73 2 30.0 10.5 1.5 18.0 0.0 THR A 74 2 19.0 8.5 4.0 6.5 0.0 VAL A 75 4 26.0 5.0 2.5 18.5 0.0 GLU A 76 4 16.0 4.5 3.0 8.5 0.0 ARG A 77 13 25.5 8.0 1.5 16.0 0.0 LEU A 78 10 38.0 9.5 2.5 26.0 0.0 SER A 79 0 8.5 4.5 4.0 0.0 0.0 ASN A 80 1 5.0 4.0 1.0 0.0 0.0 LEU A 81 11 24.5 6.5 6.5 11.5 0.0 GLU A 82 7 9.0 8.5 0.0 0.5 0.0 HIS A 83 4 15.5 5.5 4.0 6.0 0.0 HIS A 84 0 0.0 0.0 0.0 0.0 0.0 HIS A 85 0 0.0 0.0 0.0 0.0 0.0 HIS A 86 0 0.0 0.0 0.0 0.0 0.0 HIS A 87 0 0.0 0.0 0.0 0.0 0.0 HIS A 88 0 0.0 0.0 0.0 0.0 0.0 MET B 1 0 0.0 0.0 0.0 0.0 0.0 THR B 2 0 0.0 0.0 0.0 0.0 0.0 ASP B 3 0 0.0 0.0 0.0 0.0 0.0 PHE B 4 0 0.0 0.0 0.0 0.0 0.0 LEU B 5 0 0.0 0.0 0.0 0.0 0.0 ALA B 6 0 0.0 0.0 0.0 0.0 0.0 GLY B 7 0 0.0 0.0 0.0 0.0 0.0 ILE B 8 0 0.0 0.0 0.0 0.0 0.0 ARG B 9 0 0.0 0.0 0.0 0.0 0.0 ILE B 10 0 0.0 0.0 0.0 0.0 0.0 VAL B 11 0 0.0 0.0 0.0 0.0 0.0 GLY B 12 0 0.0 0.0 0.0 0.0 0.0 GLU B 13 0 0.0 0.0 0.0 0.0 0.0 ASP B 14 0 0.0 0.0 0.0 0.0 0.0 LYS B 15 0 0.0 0.0 0.0 0.0 0.0 ASN B 16 0 0.0 0.0 0.0 0.0 0.0 GLY B 17 0 0.0 0.0 0.0 0.0 0.0 MET B 18 0 0.0 0.0 0.0 0.0 0.0 THR B 19 0 0.0 0.0 0.0 0.0 0.0 ASN B 20 0 0.0 0.0 0.0 0.0 0.0 GLN B 21 0 0.0 0.0 0.0 0.0 0.0 ILE B 22 0 0.0 0.0 0.0 0.0 0.0 THR B 23 0 0.0 0.0 0.0 0.0 0.0 GLY B 24 0 0.0 0.0 0.0 0.0 0.0 VAL B 25 0 0.0 0.0 0.0 0.0 0.0 ILE B 26 0 0.0 0.0 0.0 0.0 0.0 SER B 27 0 0.0 0.0 0.0 0.0 0.0 LYS B 28 0 0.0 0.0 0.0 0.0 0.0 PHE B 29 0 0.0 0.0 0.0 0.0 0.0 ASP B 30 0 0.0 0.0 0.0 0.0 0.0 THR B 31 0 0.0 0.0 0.0 0.0 0.0 ASN B 32 0 0.0 0.0 0.0 0.0 0.0 ILE B 33 0 0.0 0.0 0.0 0.0 0.0 ARG B 34 0 0.0 0.0 0.0 0.0 0.0 THR B 35 0 0.0 0.0 0.0 0.0 0.0 ILE B 36 0 0.0 0.0 0.0 0.0 0.0 VAL B 37 0 0.0 0.0 0.0 0.0 0.0 LEU B 38 0 0.0 0.0 0.0 0.0 0.0 ASN B 39 0 0.0 0.0 0.0 0.0 0.0 ALA B 40 0 0.0 0.0 0.0 0.0 0.0 LYS B 41 0 0.0 0.0 0.0 0.0 0.0 ASP B 42 0 0.0 0.0 0.0 0.0 0.0 GLY B 43 0 0.0 0.0 0.0 0.0 0.0 ILE B 44 0 0.0 0.0 0.0 0.0 0.0 PHE B 45 0 0.0 0.0 0.0 0.0 0.0 THR B 46 0 0.0 0.0 0.0 0.0 0.0 CYS B 47 0 0.0 0.0 0.0 0.0 0.0 ASN B 48 0 0.0 0.0 0.0 0.0 0.0 LEU B 49 0 0.0 0.0 0.0 0.0 0.0 MET B 50 0 0.0 0.0 0.0 0.0 0.0 ILE B 51 0 0.0 0.0 0.0 0.0 0.0 PHE B 52 0 0.0 0.0 0.0 0.0 0.0 VAL B 53 0 0.0 0.0 0.0 0.0 0.0 LYS B 54 0 0.0 0.0 0.0 0.0 0.0 ASN B 55 0 0.0 0.0 0.0 0.0 0.0 THR B 56 0 0.0 0.0 0.0 0.0 0.0 ASP B 57 0 0.0 0.0 0.0 0.0 0.0 LYS B 58 0 0.0 0.0 0.0 0.0 0.0 LEU B 59 0 0.0 0.0 0.0 0.0 0.0 THR B 60 0 0.0 0.0 0.0 0.0 0.0 THR B 61 0 0.0 0.0 0.0 0.0 0.0 LEU B 62 0 0.0 0.0 0.0 0.0 0.0 MET B 63 0 0.0 0.0 0.0 0.0 0.0 ASP B 64 0 0.0 0.0 0.0 0.0 0.0 LYS B 65 0 0.0 0.0 0.0 0.0 0.0 LEU B 66 0 0.0 0.0 0.0 0.0 0.0 ARG B 67 0 0.0 0.0 0.0 0.0 0.0 LYS B 68 0 0.0 0.0 0.0 0.0 0.0 VAL B 69 0 0.0 0.0 0.0 0.0 0.0 GLN B 70 0 0.0 0.0 0.0 0.0 0.0 GLY B 71 0 0.0 0.0 0.0 0.0 0.0 VAL B 72 0 0.0 0.0 0.0 0.0 0.0 PHE B 73 0 0.0 0.0 0.0 0.0 0.0 THR B 74 0 0.0 0.0 0.0 0.0 0.0 VAL B 75 0 0.0 0.0 0.0 0.0 0.0 GLU B 76 0 0.0 0.0 0.0 0.0 0.0 ARG B 77 0 0.0 0.0 0.0 0.0 0.0 LEU B 78 0 0.0 0.0 0.0 0.0 0.0 SER B 79 0 0.0 0.0 0.0 0.0 0.0 ASN B 80 0 0.0 0.0 0.0 0.0 0.0 LEU B 81 0 0.0 0.0 0.0 0.0 0.0 GLU B 82 0 0.0 0.0 0.0 0.0 0.0 HIS B 83 0 0.0 0.0 0.0 0.0 0.0 HIS B 84 0 0.0 0.0 0.0 0.0 0.0 HIS B 85 0 0.0 0.0 0.0 0.0 0.0 HIS B 86 0 0.0 0.0 0.0 0.0 0.0 HIS B 87 0 0.0 0.0 0.0 0.0 0.0 HIS B 88 0 0.0 0.0 0.0 0.0 0.0 TOTAL 433 2098.0 592.0 536.0 970.0 0.0 > ANALYZE_cns: Do you want a CONS.OUT file [default no] ?_