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 `HR1958_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 143 MET ARG LYS ILE ASP LEU CYS LEU SER SER GLU GLY SER 1 > ReadCoordsPdb(): Counting models in file `HR1958_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 HR1958_R3Cons_em_bcr3.pdb MODEL 1 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 2251 ATOM records read from file > ReadCoordsPdb(): --> 2251 Regular IUPAC Atoms > ReadCoordsPdb(): --> 0 Pseudo-atoms (DISMAN type) > ReadCoordsPdb(): --> 0 Lone pairs > ReadCoordsPdb(): Bye ... > =============================== INFO ================================ > INFO_mol: # atoms: 2251 (725 C, 1110 H, 224 O, 188 N, 4 S, 0 Q, 0 Metals) > INFO_mol: # residues: 143 (Avg. mol. weight: 113.1) > INFO_mol: # -- M.W. : 16171.8 g/mol. (16.17 kD) Estimated RoG : 14.50 > INFO_mol: CenterMass() -- Working PDB model 1 in file, model no. 1 > INFO_mol: CenterMass() -- Molecule `HR1958_R3Cons_em_bcr3.pdb' model #1, TOTAL RESIDUES: 143 > INFO_mol: Radius of Gyration : 14.6011 angstroms > INFO_mol: Center of Masses: x_cm(-1.841), y_cm(3.495), z_cm(-6.762) > INFO_res: MRKIDLCLSS EGSEVILATS SDEKHPPENI IDGNPETFWT TTGMFPQEFI > INFO_res: ICFHKHVRIE RLVIQSYFVQ TLKIEKSTSK EPVDFEQWIE KDLVHTEGQL > INFO_res: QNEEIVAHGS ATYLRFIIVS AFDHFASVHS VSAEGTVVSN LSS > INFO_res: > INFO_res: MET ARG LYS ILE ASP LEU CYS LEU SER SER GLU GLY > INFO_res: SER GLU VAL ILE LEU ALA THR SER SER ASP GLU LYS > INFO_res: HIS PRO PRO GLU ASN ILE ILE ASP GLY ASN PRO GLU > INFO_res: THR PHE TRP THR THR THR GLY MET PHE PRO GLN GLU > INFO_res: PHE ILE ILE CYS PHE HIS LYS HIS VAL ARG ILE GLU > INFO_res: ARG LEU VAL ILE GLN SER TYR PHE VAL GLN THR LEU > INFO_res: LYS ILE GLU LYS SER THR SER LYS GLU PRO VAL ASP > INFO_res: PHE GLU GLN TRP ILE GLU LYS ASP LEU VAL HIS THR > INFO_res: GLU GLY GLN LEU GLN ASN GLU GLU ILE VAL ALA HIS > INFO_res: GLY SER ALA THR TYR LEU ARG PHE ILE ILE VAL SER > INFO_res: ALA PHE ASP HIS PHE ALA SER VAL HIS SER VAL SER > INFO_res: ALA GLU GLY THR VAL VAL SER ASN LEU SER SER > INFO_res: > INFO_res: 6 ALA 4 ARG 4 ASN 6 ASP 2 CYS 6 GLN > INFO_res: 15 GLU 6 GLY 7 HIS 13 ILE 9 LEU 7 LYS > INFO_res: 2 MET 9 PHE 5 PRO 16 SER 10 THR 2 TYR > INFO_res: 2 TRP 12 VAL > INFO_res: DISULFIDE: ** NO INFO FOR DISULFIDES IN FILE > ===================================================================== > ReadCoordsPdb(): *** monomer, 1 [1] chains *** PdbStat> > locate_file(): file `HR1958_R3Cons_em_bcr3.upl' opened for reading 0 SANI-RDC constraints read 893 NOE-distance constraints (0 Ambiguous NOE/s) read 893 TOTAL constraints read PdbStat> -------------- SUMMARY OF RESTRAINTS --------------- TOTAL NUMBER OF NOE RESTRAINTS : 893 INTRA-RESIDUE RESTRAINTS (I=J) : 2 SEQUENTIAL RESTRAINTS (I-J)=1 : 129 BACKBONE-BACKBONE : 99 BACKBONE-SIDE CHAIN : 6 SIDE CHAIN-SIDE CHAIN : 24 MEDIUM RANGE RESTRAINTS 1<(I-J)<5 : 121 BACKBONE-BACKBONE : 21 BACKBONE-SIDE CHAIN : 13 SIDE CHAIN-SIDE CHAIN : 87 LONG RANGE RESTRAINTS (I-J)>=5 : 641 TOTAL HYDROGEN BOND RESTRAINTS : 0 LONG RANGE H-BOND RESTR. (I-J)>=5 : 0 DISULFIDE RESTRAINTS : 0 INTRA-CHAIN RESTRAINTS : 893 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 ARG A 2 0 2.5 0.0 0.0 2.5 0.0 LYS A 3 0 2.5 0.0 0.0 2.5 0.0 ILE A 4 0 7.5 1.0 2.5 4.0 0.0 ASP A 5 0 5.0 1.5 2.0 1.5 0.0 LEU A 6 0 17.0 0.5 2.5 14.0 0.0 CYS A 7 0 7.0 0.0 0.5 6.5 0.0 LEU A 8 0 12.0 0.5 7.5 4.0 0.0 SER A 9 0 5.0 0.5 0.5 4.0 0.0 SER A 10 0 2.5 0.0 2.5 0.0 0.0 GLU A 11 0 8.0 0.5 6.5 1.0 0.0 GLY A 12 0 1.5 1.0 0.5 0.0 0.0 SER A 13 0 8.0 1.0 2.0 5.0 0.0 GLU A 14 0 4.5 1.0 0.0 3.5 0.0 VAL A 15 0 13.0 1.0 0.5 11.5 0.0 ILE A 16 0 11.0 0.5 0.0 10.5 0.0 LEU A 17 0 4.5 0.5 0.0 4.0 0.0 ALA A 18 0 7.5 0.5 1.0 6.0 0.0 THR A 19 0 1.5 0.0 0.0 1.5 0.0 SER A 20 0 3.5 0.0 0.5 3.0 0.0 SER A 21 0 1.5 0.0 0.0 1.5 0.0 ASP A 22 0 2.5 0.5 0.5 1.5 0.0 GLU A 23 0 1.5 1.0 0.5 0.0 0.0 LYS A 24 0 1.0 1.0 0.0 0.0 0.0 HIS A 25 0 2.0 0.5 0.5 1.0 0.0 PRO A 26 0 1.5 0.0 1.0 0.5 0.0 PRO A 27 0 10.5 0.0 2.5 8.0 0.0 GLU A 28 0 2.0 0.5 1.5 0.0 0.0 ASN A 29 0 1.5 1.0 0.5 0.0 0.0 ILE A 30 0 13.0 1.0 2.5 9.5 0.0 ILE A 31 0 12.5 1.0 1.0 10.5 0.0 ASP A 32 0 2.5 1.0 0.5 1.0 0.0 GLY A 33 0 2.0 1.0 0.0 1.0 0.0 ASN A 34 0 0.5 0.5 0.0 0.0 0.0 PRO A 35 0 0.0 0.0 0.0 0.0 0.0 GLU A 36 0 0.0 0.0 0.0 0.0 0.0 THR A 37 0 0.5 0.5 0.0 0.0 0.0 PHE A 38 0 3.0 1.0 1.5 0.5 0.0 TRP A 39 1 14.5 1.0 1.5 12.0 0.0 THR A 40 0 6.5 1.0 1.5 4.0 0.0 THR A 41 0 5.0 0.5 2.0 2.5 0.0 THR A 42 0 2.0 0.5 0.0 1.5 0.0 GLY A 43 0 1.5 1.0 0.5 0.0 0.0 MET A 44 0 1.0 1.0 0.0 0.0 0.0 PHE A 45 0 6.5 1.5 1.0 4.0 0.0 PRO A 46 0 5.0 1.0 0.0 4.0 0.0 GLN A 47 0 3.0 0.5 1.0 1.5 0.0 GLU A 48 0 4.0 1.0 0.0 3.0 0.0 PHE A 49 0 13.5 1.0 0.5 12.0 0.0 ILE A 50 0 16.0 1.0 0.5 14.5 0.0 ILE A 51 0 18.5 1.0 0.5 17.0 0.0 CYS A 52 0 6.0 1.0 0.5 4.5 0.0 PHE A 53 0 15.0 1.0 2.5 11.5 0.0 HIS A 54 0 4.0 1.5 0.0 2.5 0.0 LYS A 55 0 2.0 1.5 0.5 0.0 0.0 HIS A 56 0 5.0 1.0 0.0 4.0 0.0 VAL A 57 0 14.0 1.0 4.5 8.5 0.0 ARG A 58 0 4.0 1.0 0.0 3.0 0.0 ILE A 59 0 20.5 1.5 4.5 14.5 0.0 GLU A 60 0 4.0 1.5 0.0 2.5 0.0 ARG A 61 0 7.0 1.0 1.0 5.0 0.0 LEU A 62 0 22.0 1.0 4.0 17.0 0.0 VAL A 63 0 10.5 1.0 0.5 9.0 0.0 ILE A 64 0 15.0 1.5 1.5 12.0 0.0 GLN A 65 0 10.0 1.0 0.0 9.0 0.0 SER A 66 0 0.0 0.0 0.0 0.0 0.0 TYR A 67 0 5.0 0.5 0.0 4.5 0.0 PHE A 68 0 5.5 0.5 0.0 5.0 0.0 VAL A 69 0 7.0 0.5 1.0 5.5 0.0 GLN A 70 0 4.5 1.0 0.0 3.5 0.0 THR A 71 0 5.5 1.0 0.0 4.5 0.0 LEU A 72 0 11.5 1.0 1.0 9.5 0.0 LYS A 73 0 7.5 1.0 0.0 6.5 0.0 ILE A 74 0 16.0 1.0 0.0 15.0 0.0 GLU A 75 0 5.5 1.0 0.0 4.5 0.0 LYS A 76 0 8.0 1.0 0.0 7.0 0.0 SER A 77 0 6.0 1.0 1.0 4.0 0.0 THR A 78 0 8.5 1.0 0.0 7.5 0.0 SER A 79 0 5.5 0.5 3.5 1.5 0.0 LYS A 80 0 1.5 0.0 0.0 1.5 0.0 GLU A 81 0 5.5 0.5 4.5 0.5 0.0 PRO A 82 0 8.0 2.0 0.5 5.5 0.0 VAL A 83 0 7.0 3.0 4.0 0.0 0.0 ASP A 84 0 2.5 1.5 0.0 1.0 0.0 PHE A 85 0 5.0 1.0 0.5 3.5 0.0 GLU A 86 0 3.5 1.0 0.0 2.5 0.0 GLN A 87 0 1.5 0.5 0.0 1.0 0.0 TRP A 88 1 15.5 4.0 0.0 11.5 0.0 ILE A 89 0 14.5 4.0 0.5 10.0 0.0 GLU A 90 0 2.5 1.0 0.0 1.5 0.0 LYS A 91 0 4.5 1.0 0.5 3.0 0.0 ASP A 92 0 3.0 1.0 0.0 2.0 0.0 LEU A 93 0 3.0 1.0 0.0 2.0 0.0 VAL A 94 0 3.5 1.0 0.0 2.5 0.0 HIS A 95 0 1.5 1.5 0.0 0.0 0.0 THR A 96 0 5.5 2.0 3.5 0.0 0.0 GLU A 97 0 2.0 1.5 0.5 0.0 0.0 GLY A 98 0 1.0 1.0 0.0 0.0 0.0 GLN A 99 0 5.5 1.0 4.0 0.5 0.0 LEU A 100 0 7.0 1.0 0.5 5.5 0.0 GLN A 101 0 1.5 1.0 0.0 0.5 0.0 ASN A 102 0 6.5 1.0 0.5 5.0 0.0 GLU A 103 0 3.5 1.0 0.0 2.5 0.0 GLU A 104 0 4.0 1.0 0.0 3.0 0.0 ILE A 105 0 12.5 1.0 1.5 10.0 0.0 VAL A 106 0 3.0 1.5 0.5 1.0 0.0 ALA A 107 0 13.5 2.0 1.5 10.0 0.0 HIS A 108 0 6.0 1.5 0.5 4.0 0.0 GLY A 109 0 4.5 0.5 0.0 4.0 0.0 SER A 110 0 4.0 0.5 0.0 3.5 0.0 ALA A 111 0 8.0 1.0 1.5 5.5 0.0 THR A 112 0 9.5 1.0 0.0 8.5 0.0 TYR A 113 0 10.5 1.0 0.5 9.0 0.0 LEU A 114 0 13.0 1.0 2.0 10.0 0.0 ARG A 115 0 6.0 0.5 1.5 4.0 0.0 PHE A 116 0 23.0 0.0 1.0 22.0 0.0 ILE A 117 0 10.0 0.5 1.5 8.0 0.0 ILE A 118 0 12.5 1.0 1.5 10.0 0.0 VAL A 119 0 7.5 2.0 0.0 5.5 0.0 SER A 120 0 4.0 2.0 0.5 1.5 0.0 ALA A 121 0 7.5 0.5 2.5 4.5 0.0 PHE A 122 0 7.5 0.5 0.0 7.0 0.0 ASP A 123 0 3.5 0.5 2.5 0.5 0.0 HIS A 124 0 1.0 1.0 0.0 0.0 0.0 PHE A 125 0 3.0 1.0 2.0 0.0 0.0 ALA A 126 0 6.0 0.5 0.0 5.5 0.0 SER A 127 0 4.0 1.0 0.0 3.0 0.0 VAL A 128 0 8.0 0.5 1.5 6.0 0.0 HIS A 129 0 0.5 0.5 0.0 0.0 0.0 SER A 130 0 5.5 1.5 1.5 2.5 0.0 VAL A 131 0 9.0 1.5 0.0 7.5 0.0 SER A 132 0 7.0 1.0 0.0 6.0 0.0 ALA A 133 0 11.5 1.0 0.0 10.5 0.0 GLU A 134 0 5.5 1.0 0.0 4.5 0.0 GLY A 135 0 7.5 1.5 0.0 6.0 0.0 THR A 136 0 9.0 1.0 0.0 8.0 0.0 VAL A 137 0 4.5 0.5 0.5 3.5 0.0 VAL A 138 0 5.5 1.0 0.0 4.5 0.0 SER A 139 0 3.0 1.0 0.0 2.0 0.0 ASN A 140 0 1.0 0.5 0.5 0.0 0.0 LEU A 141 0 0.5 0.0 0.0 0.5 0.0 SER A 142 0 0.0 0.0 0.0 0.0 0.0 SER A 143 0 0.0 0.0 0.0 0.0 0.0 TOTAL 2 891.0 129.0 121.0 641.0 0.0 > ANALYZE_cns: Do you want a CONS.OUT file [default no] ?_