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 `HR5546A_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 122 MET GLY HIS HIS HIS HIS HIS HIS SER HIS MET THR GLY 1 > ReadCoordsPdb(): Counting models in file `HR5546A_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 HR5546A_R3_em_bcr3.pdb MODEL 1 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 1891 ATOM records read from file > ReadCoordsPdb(): --> 1891 Regular IUPAC Atoms > ReadCoordsPdb(): --> 0 Pseudo-atoms (DISMAN type) > ReadCoordsPdb(): --> 0 Lone pairs > ReadCoordsPdb(): Bye ... > =============================== INFO ================================ > INFO_mol: # atoms: 1891 (597 C, 931 H, 185 O, 173 N, 5 S, 0 Q, 0 Metals) > INFO_mol: # residues: 122 (Avg. mol. weight: 111.9) > INFO_mol: # -- M.W. : 13652.1 g/mol. (13.65 kD) Estimated RoG : 13.65 > INFO_mol: CenterMass() -- Working PDB model 1 in file, model no. 1 > INFO_mol: CenterMass() -- Molecule `HR5546A_R3_em_bcr3.pdb' model #1, TOTAL RESIDUES: 122 > INFO_mol: Radius of Gyration : 15.9622 angstroms > INFO_mol: Center of Masses: x_cm(-0.636), y_cm(0.785), z_cm(-1.650) > INFO_res: MGHHHHHHSH MTGNVCIEEI DVDGKFIRLK NTSEQDQPMG GWEMIRKIGD > INFO_res: TSVSYKYTSR YVLKAGQTVT IWAANAGVTA SPPTDLIWKN QNSWGTGEDV > INFO_res: KVILKNSQGE EVAQRSTVFK TT > INFO_res: > INFO_res: MET GLY HIS HIS HIS HIS HIS HIS SER HIS MET THR > INFO_res: GLY ASN VAL CYS ILE GLU GLU ILE ASP VAL ASP GLY > INFO_res: LYS PHE ILE ARG LEU LYS ASN THR SER GLU GLN ASP > INFO_res: GLN PRO MET GLY GLY TRP GLU MET ILE ARG LYS ILE > INFO_res: GLY ASP THR SER VAL SER TYR LYS TYR THR SER ARG > INFO_res: TYR VAL LEU LYS ALA GLY GLN THR VAL THR ILE TRP > INFO_res: ALA ALA ASN ALA GLY VAL THR ALA SER PRO PRO THR > INFO_res: ASP LEU ILE TRP LYS ASN GLN ASN SER TRP GLY THR > INFO_res: GLY GLU ASP VAL LYS VAL ILE LEU LYS ASN SER GLN > INFO_res: GLY GLU GLU VAL ALA GLN ARG SER THR VAL PHE LYS > INFO_res: THR THR > INFO_res: > INFO_res: 6 ALA 4 ARG 6 ASN 6 ASP 1 CYS 6 GLN > INFO_res: 7 GLU 11 GLY 7 HIS 8 ILE 4 LEU 9 LYS > INFO_res: 4 MET 2 PHE 3 PRO 9 SER 12 THR 3 TYR > INFO_res: 4 TRP 10 VAL > INFO_res: DISULFIDE: ** NO INFO FOR DISULFIDES IN FILE > ===================================================================== > ReadCoordsPdb(): *** monomer, 1 [1] chains *** PdbStat> > locate_file(): file `HR5546A_R3_em_bcr3.upl' opened for reading 0 SANI-RDC constraints read 1499 NOE-distance constraints (0 Ambiguous NOE/s) read 1499 TOTAL constraints read PdbStat> -------------- SUMMARY OF RESTRAINTS --------------- TOTAL NUMBER OF NOE RESTRAINTS : 1499 INTRA-RESIDUE RESTRAINTS (I=J) : 201 SEQUENTIAL RESTRAINTS (I-J)=1 : 471 BACKBONE-BACKBONE : 107 BACKBONE-SIDE CHAIN : 51 SIDE CHAIN-SIDE CHAIN : 313 MEDIUM RANGE RESTRAINTS 1<(I-J)<5 : 175 BACKBONE-BACKBONE : 36 BACKBONE-SIDE CHAIN : 9 SIDE CHAIN-SIDE CHAIN : 130 LONG RANGE RESTRAINTS (I-J)>=5 : 652 TOTAL HYDROGEN BOND RESTRAINTS : 0 LONG RANGE H-BOND RESTR. (I-J)>=5 : 0 DISULFIDE RESTRAINTS : 0 INTRA-CHAIN RESTRAINTS : 1499 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 GLY A 2 0 0.0 0.0 0.0 0.0 0.0 HIS A 3 0 0.0 0.0 0.0 0.0 0.0 HIS A 4 0 0.0 0.0 0.0 0.0 0.0 HIS A 5 0 0.0 0.0 0.0 0.0 0.0 HIS A 6 0 0.0 0.0 0.0 0.0 0.0 HIS A 7 0 0.0 0.0 0.0 0.0 0.0 HIS A 8 0 1.5 1.5 0.0 0.0 0.0 SER A 9 0 3.0 3.0 0.0 0.0 0.0 HIS A 10 0 2.0 2.0 0.0 0.0 0.0 MET A 11 1 2.5 2.0 0.5 0.0 0.0 THR A 12 1 2.5 2.5 0.0 0.0 0.0 GLY A 13 0 1.5 1.0 0.5 0.0 0.0 ASN A 14 2 5.5 2.5 0.0 3.0 0.0 VAL A 15 0 13.5 5.5 0.0 8.0 0.0 CYS A 16 0 10.0 4.5 0.0 5.5 0.0 ILE A 17 3 19.0 2.0 1.0 16.0 0.0 GLU A 18 0 9.0 2.0 0.0 7.0 0.0 GLU A 19 0 8.0 5.5 1.0 1.5 0.0 ILE A 20 3 14.0 6.5 0.0 7.5 0.0 ASP A 21 0 12.0 3.5 5.5 3.0 0.0 VAL A 22 2 5.5 4.0 1.5 0.0 0.0 ASP A 23 0 5.0 3.5 1.5 0.0 0.0 GLY A 24 0 8.5 2.0 3.5 3.0 0.0 LYS A 25 5 11.0 5.5 4.5 1.0 0.0 PHE A 26 5 17.0 6.5 1.0 9.5 0.0 ILE A 27 3 17.5 5.5 0.5 11.5 0.0 ARG A 28 0 14.5 6.5 0.5 7.5 0.0 LEU A 29 2 21.0 5.5 0.5 15.0 0.0 LYS A 30 8 18.0 5.5 0.5 12.0 0.0 ASN A 31 0 24.0 3.5 1.0 19.5 0.0 THR A 32 1 4.0 0.5 0.5 3.0 0.0 SER A 33 0 7.5 3.0 1.0 3.5 0.0 GLU A 34 2 6.0 4.5 0.0 1.5 0.0 GLN A 35 1 7.5 4.5 1.0 2.0 0.0 ASP A 36 0 14.5 4.5 0.0 10.0 0.0 GLN A 37 2 12.0 5.0 0.0 7.0 0.0 PRO A 38 0 11.5 4.5 3.0 4.0 0.0 MET A 39 4 9.5 2.5 1.0 6.0 0.0 GLY A 40 0 6.5 2.5 3.5 0.5 0.0 GLY A 41 0 2.0 2.0 0.0 0.0 0.0 TRP A 42 3 9.0 2.5 1.5 5.0 0.0 GLU A 43 0 11.0 3.5 3.0 4.5 0.0 MET A 44 5 26.0 4.0 0.0 22.0 0.0 ILE A 45 5 27.0 5.5 6.0 15.5 0.0 ARG A 46 3 18.5 5.5 0.0 13.0 0.0 LYS A 47 2 14.0 5.0 3.5 5.5 0.0 ILE A 48 4 14.0 5.0 2.0 7.0 0.0 GLY A 49 0 3.5 3.0 0.5 0.0 0.0 ASP A 50 0 4.0 3.5 0.5 0.0 0.0 THR A 51 1 8.5 5.5 3.0 0.0 0.0 SER A 52 0 7.0 4.0 0.0 3.0 0.0 VAL A 53 3 18.5 5.0 0.5 13.0 0.0 SER A 54 0 14.5 4.5 0.0 10.0 0.0 TYR A 55 5 24.5 3.0 4.0 17.5 0.0 LYS A 56 3 4.5 4.0 0.0 0.5 0.0 TYR A 57 4 19.5 5.0 3.5 11.0 0.0 THR A 58 1 9.0 5.5 3.5 0.0 0.0 SER A 59 0 4.5 4.0 0.5 0.0 0.0 ARG A 60 1 7.5 5.0 2.5 0.0 0.0 TYR A 61 5 18.5 9.5 6.0 3.0 0.0 VAL A 62 2 21.0 9.0 2.5 9.5 0.0 LEU A 63 3 18.5 4.0 7.0 7.5 0.0 LYS A 64 10 15.5 4.0 6.5 5.0 0.0 ALA A 65 0 19.0 5.0 3.5 10.5 0.0 GLY A 66 0 5.0 3.0 0.0 2.0 0.0 GLN A 67 7 14.0 2.5 9.5 2.0 0.0 THR A 68 1 15.5 3.5 0.0 12.0 0.0 VAL A 69 0 17.0 5.5 2.0 9.5 0.0 THR A 70 0 14.5 4.5 2.0 8.0 0.0 ILE A 71 5 23.5 3.0 2.0 18.5 0.0 TRP A 72 3 26.0 5.0 4.0 17.0 0.0 ALA A 73 0 15.0 3.5 2.5 9.0 0.0 ALA A 74 0 10.0 1.5 1.5 7.0 0.0 ASN A 75 2 6.0 1.5 2.5 2.0 0.0 ALA A 76 0 9.0 2.0 7.0 0.0 0.0 GLY A 77 0 5.0 3.0 2.0 0.0 0.0 VAL A 78 2 11.0 4.0 2.5 4.5 0.0 THR A 79 1 4.0 4.0 0.0 0.0 0.0 ALA A 80 0 6.0 2.5 0.0 3.5 0.0 SER A 81 0 3.0 2.5 0.0 0.5 0.0 PRO A 82 0 6.5 3.5 2.5 0.5 0.0 PRO A 83 0 4.0 4.0 0.0 0.0 0.0 THR A 84 1 5.0 3.0 2.0 0.0 0.0 ASP A 85 0 10.0 4.0 0.5 5.5 0.0 LEU A 86 2 17.0 5.0 0.0 12.0 0.0 ILE A 87 5 20.0 5.0 3.0 12.0 0.0 TRP A 88 5 33.5 6.0 3.0 24.5 0.0 LYS A 89 10 10.0 5.5 3.0 1.5 0.0 ASN A 90 2 7.5 4.0 2.5 1.0 0.0 GLN A 91 2 13.0 5.0 1.5 6.5 0.0 ASN A 92 2 10.0 6.0 0.0 4.0 0.0 SER A 93 0 7.0 4.5 0.0 2.5 0.0 TRP A 94 1 16.5 4.5 0.0 12.0 0.0 GLY A 95 0 4.5 3.0 0.0 1.5 0.0 THR A 96 1 3.0 2.0 1.0 0.0 0.0 GLY A 97 0 3.0 3.0 0.0 0.0 0.0 GLU A 98 1 5.0 4.0 1.0 0.0 0.0 ASP A 99 0 4.5 4.5 0.0 0.0 0.0 VAL A 100 2 19.0 4.5 0.0 14.5 0.0 LYS A 101 3 13.0 5.5 2.0 5.5 0.0 VAL A 102 0 22.0 7.0 0.0 15.0 0.0 ILE A 103 3 23.0 5.5 4.5 13.0 0.0 LEU A 104 3 24.5 4.0 0.0 20.5 0.0 LYS A 105 3 18.0 4.5 4.5 9.0 0.0 ASN A 106 4 10.5 3.5 2.5 4.5 0.0 SER A 107 0 6.5 5.0 0.5 1.0 0.0 GLN A 108 3 8.5 5.0 3.5 0.0 0.0 GLY A 109 0 6.0 3.0 3.0 0.0 0.0 GLU A 110 1 7.5 3.0 3.5 1.0 0.0 GLU A 111 0 8.5 3.0 0.0 5.5 0.0 VAL A 112 3 13.5 5.5 0.0 8.0 0.0 ALA A 113 0 14.0 5.5 0.0 8.5 0.0 GLN A 114 4 14.5 3.5 0.0 11.0 0.0 ARG A 115 0 15.5 5.5 0.0 10.0 0.0 SER A 116 0 12.5 5.0 0.0 7.5 0.0 THR A 117 1 11.0 3.5 0.0 7.5 0.0 VAL A 118 1 5.5 5.5 0.0 0.0 0.0 PHE A 119 4 5.0 5.0 0.0 0.0 0.0 LYS A 120 8 4.5 4.5 0.0 0.0 0.0 THR A 121 0 4.5 4.5 0.0 0.0 0.0 THR A 122 0 1.5 1.5 0.0 0.0 0.0 TOTAL 201 1298.0 471.0 175.0 652.0 0.0 > ANALYZE_cns: Do you want a CONS.OUT file [default no] ?_