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 `CCR55_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 116 MET THR LEU ILE TYR LYS ILE LEU SER ARG ALA GLU TRP 1 > ReadCoordsPdb(): Counting models in file `CCR55_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 CCR55_R3_em_bcr3.pdb MODEL 1 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 1772 ATOM records read from file > ReadCoordsPdb(): --> 1772 Regular IUPAC Atoms > ReadCoordsPdb(): --> 0 Pseudo-atoms (DISMAN type) > ReadCoordsPdb(): --> 0 Lone pairs > ReadCoordsPdb(): Bye ... > =============================== INFO ================================ > INFO_mol: # atoms: 1772 (567 C, 875 H, 173 O, 156 N, 1 S, 0 Q, 0 Metals) > INFO_mol: # residues: 116 (Avg. mol. weight: 109.3) > INFO_mol: # -- M.W. : 12676.9 g/mol. (12.68 kD) Estimated RoG : 13.39 > INFO_mol: CenterMass() -- Working PDB model 1 in file, model no. 1 > INFO_mol: CenterMass() -- Molecule `CCR55_R3_em_bcr3.pdb' model #1, TOTAL RESIDUES: 116 > INFO_mol: Radius of Gyration : 13.4993 angstroms > INFO_mol: Center of Masses: x_cm(2.002), y_cm(1.033), z_cm(0.466) > INFO_res: MTLIYKILSR AEWDAAKAQG RFEGSAVDLA DGFIHLSAGE QAQETAAKWF > INFO_res: RGQANLVLLA VEAEPLGEDL KWEASRGGAR FPHLYRPLLV SEVTREADLD > INFO_res: LDADGVPQLG DHLALE > INFO_res: > INFO_res: MET THR LEU ILE TYR LYS ILE LEU SER ARG ALA GLU > INFO_res: TRP ASP ALA ALA LYS ALA GLN GLY ARG PHE GLU GLY > INFO_res: SER ALA VAL ASP LEU ALA ASP GLY PHE ILE HIS LEU > INFO_res: SER ALA GLY GLU GLN ALA GLN GLU THR ALA ALA LYS > INFO_res: TRP PHE ARG GLY GLN ALA ASN LEU VAL LEU LEU ALA > INFO_res: VAL GLU ALA GLU PRO LEU GLY GLU ASP LEU LYS TRP > INFO_res: GLU ALA SER ARG GLY GLY ALA ARG PHE PRO HIS LEU > INFO_res: TYR ARG PRO LEU LEU VAL SER GLU VAL THR ARG GLU > INFO_res: ALA ASP LEU ASP LEU ASP ALA ASP GLY VAL PRO GLN > INFO_res: LEU GLY ASP HIS LEU ALA LEU GLU > INFO_res: > INFO_res: 18 ALA 7 ARG 1 ASN 9 ASP 5 GLN 11 GLU > INFO_res: 10 GLY 3 HIS 3 ILE 17 LEU 4 LYS 1 MET > INFO_res: 4 PHE 4 PRO 5 SER 3 THR 2 TYR 3 TRP > INFO_res: 6 VAL > INFO_res: DISULFIDE: ** NO INFO FOR DISULFIDES IN FILE > ===================================================================== > ReadCoordsPdb(): *** monomer, 1 [1] chains *** PdbStat> > locate_file(): file `CCR55_R3_em_bcr3.upl' opened for reading 0 SANI-RDC constraints read 1200 NOE-distance constraints (0 Ambiguous NOE/s) read 1200 TOTAL constraints read PdbStat> -------------- SUMMARY OF RESTRAINTS --------------- TOTAL NUMBER OF NOE RESTRAINTS : 1200 INTRA-RESIDUE RESTRAINTS (I=J) : 221 SEQUENTIAL RESTRAINTS (I-J)=1 : 360 BACKBONE-BACKBONE : 119 BACKBONE-SIDE CHAIN : 23 SIDE CHAIN-SIDE CHAIN : 218 MEDIUM RANGE RESTRAINTS 1<(I-J)<5 : 244 BACKBONE-BACKBONE : 64 BACKBONE-SIDE CHAIN : 53 SIDE CHAIN-SIDE CHAIN : 127 LONG RANGE RESTRAINTS (I-J)>=5 : 375 TOTAL HYDROGEN BOND RESTRAINTS : 0 LONG RANGE H-BOND RESTR. (I-J)>=5 : 0 DISULFIDE RESTRAINTS : 0 INTRA-CHAIN RESTRAINTS : 1200 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 0 2.0 1.0 0.0 1.0 0.0 LEU A 3 4 8.0 2.5 1.5 4.0 0.0 ILE A 4 3 15.5 5.0 0.0 10.5 0.0 TYR A 5 2 19.5 6.0 1.5 12.0 0.0 LYS A 6 4 14.5 4.5 0.0 10.0 0.0 ILE A 7 7 14.5 4.5 0.0 10.0 0.0 LEU A 8 4 16.0 4.0 1.5 10.5 0.0 SER A 9 0 8.0 3.5 2.5 2.0 0.0 ARG A 10 4 11.5 3.5 5.0 3.0 0.0 ALA A 11 0 4.5 2.5 2.0 0.0 0.0 GLU A 12 2 8.5 2.5 6.0 0.0 0.0 TRP A 13 6 32.0 3.0 10.5 18.5 0.0 ASP A 14 0 10.0 4.5 5.5 0.0 0.0 ALA A 15 0 7.5 4.0 3.5 0.0 0.0 ALA A 16 0 12.0 2.0 6.5 3.5 0.0 LYS A 17 9 12.5 3.0 7.5 2.0 0.0 ALA A 18 0 6.0 4.5 1.5 0.0 0.0 GLN A 19 3 10.0 3.5 6.5 0.0 0.0 GLY A 20 0 4.0 1.5 1.0 1.5 0.0 ARG A 21 5 12.0 2.5 2.5 7.0 0.0 PHE A 22 3 15.5 3.5 0.0 12.0 0.0 GLU A 23 2 4.0 1.5 0.0 2.5 0.0 GLY A 24 0 3.5 0.0 2.0 1.5 0.0 SER A 25 0 4.0 0.5 3.0 0.5 0.0 ALA A 26 0 4.5 2.0 2.5 0.0 0.0 VAL A 27 3 7.0 3.5 3.0 0.5 0.0 ASP A 28 0 10.0 3.5 4.5 2.0 0.0 LEU A 29 5 6.0 2.5 3.5 0.0 0.0 ALA A 30 0 5.5 2.0 3.5 0.0 0.0 ASP A 31 0 3.5 2.0 1.5 0.0 0.0 GLY A 32 0 3.0 1.5 1.5 0.0 0.0 PHE A 33 2 7.0 3.0 1.0 3.0 0.0 ILE A 34 4 16.5 4.0 1.5 11.0 0.0 HIS A 35 1 5.0 3.0 0.0 2.0 0.0 LEU A 36 5 13.5 3.5 1.5 8.5 0.0 SER A 37 0 10.5 4.0 2.0 4.5 0.0 ALA A 38 0 8.0 2.5 2.0 3.5 0.0 GLY A 39 0 6.0 1.0 1.5 3.5 0.0 GLU A 40 2 3.5 1.5 2.0 0.0 0.0 GLN A 41 2 10.0 2.5 5.0 2.5 0.0 ALA A 42 0 13.0 2.5 4.5 6.0 0.0 GLN A 43 2 11.0 2.5 2.5 6.0 0.0 GLU A 44 2 6.0 3.0 3.0 0.0 0.0 THR A 45 2 11.0 3.0 6.0 2.0 0.0 ALA A 46 0 10.5 2.5 5.0 3.0 0.0 ALA A 47 0 7.5 2.0 3.0 2.5 0.0 LYS A 48 8 7.5 6.0 1.5 0.0 0.0 TRP A 49 6 10.5 7.5 3.0 0.0 0.0 PHE A 50 2 16.0 5.5 5.0 5.5 0.0 ARG A 51 3 6.0 6.0 0.0 0.0 0.0 GLY A 52 0 5.0 4.0 0.0 1.0 0.0 GLN A 53 1 10.0 3.0 6.0 1.0 0.0 ALA A 54 0 6.5 5.0 1.5 0.0 0.0 ASN A 55 4 5.5 5.0 0.0 0.5 0.0 LEU A 56 5 15.0 4.0 4.5 6.5 0.0 VAL A 57 2 18.0 3.5 1.5 13.0 0.0 LEU A 58 3 12.0 3.5 0.5 8.0 0.0 LEU A 59 4 16.5 3.0 1.5 12.0 0.0 ALA A 60 0 8.5 2.5 0.5 5.5 0.0 VAL A 61 3 11.0 3.0 1.0 7.0 0.0 GLU A 62 3 7.0 2.5 0.0 4.5 0.0 ALA A 63 0 10.0 2.5 2.0 5.5 0.0 GLU A 64 1 4.5 4.5 0.0 0.0 0.0 PRO A 65 0 4.5 4.0 0.5 0.0 0.0 LEU A 66 5 5.0 2.5 2.0 0.5 0.0 GLY A 67 0 4.0 3.0 1.0 0.0 0.0 GLU A 68 3 4.5 4.0 0.5 0.0 0.0 ASP A 69 0 7.5 4.0 1.0 2.5 0.0 LEU A 70 4 13.5 3.5 3.0 7.0 0.0 LYS A 71 2 7.5 4.0 0.0 3.5 0.0 TRP A 72 7 15.0 3.5 2.0 9.5 0.0 GLU A 73 0 4.0 2.5 0.0 1.5 0.0 ALA A 74 0 3.0 1.5 0.0 1.5 0.0 SER A 75 0 1.5 1.0 0.0 0.5 0.0 ARG A 76 1 0.5 0.5 0.0 0.0 0.0 GLY A 77 0 0.0 0.0 0.0 0.0 0.0 GLY A 78 0 1.0 1.0 0.0 0.0 0.0 ALA A 79 0 4.5 2.0 1.5 1.0 0.0 ARG A 80 0 6.0 3.5 0.0 2.5 0.0 PHE A 81 2 10.0 4.0 1.5 4.5 0.0 PRO A 82 0 9.5 2.5 0.0 7.0 0.0 HIS A 83 1 8.0 2.5 1.0 4.5 0.0 LEU A 84 1 17.5 5.0 4.5 8.0 0.0 TYR A 85 3 10.5 4.5 1.0 5.0 0.0 ARG A 86 6 7.5 3.0 3.5 1.0 0.0 PRO A 87 0 6.5 4.0 0.5 2.0 0.0 LEU A 88 2 14.5 5.0 2.0 7.5 0.0 LEU A 89 7 15.0 5.5 4.5 5.0 0.0 VAL A 90 3 15.0 4.5 1.5 9.0 0.0 SER A 91 0 4.5 2.5 1.5 0.5 0.0 GLU A 92 1 6.5 1.0 4.5 1.0 0.0 VAL A 93 3 13.0 3.5 3.0 6.5 0.0 THR A 94 2 8.5 4.5 0.0 4.0 0.0 ARG A 95 4 7.0 4.0 0.5 2.5 0.0 GLU A 96 2 10.0 4.5 1.0 4.5 0.0 ALA A 97 0 6.0 2.5 0.0 3.5 0.0 ASP A 98 0 3.0 2.5 0.0 0.5 0.0 LEU A 99 4 7.0 4.5 0.0 2.5 0.0 ASP A 100 0 4.5 4.5 0.0 0.0 0.0 LEU A 101 4 12.0 4.5 2.0 5.5 0.0 ASP A 102 0 7.5 4.5 2.0 1.0 0.0 ALA A 103 0 4.0 3.0 1.0 0.0 0.0 ASP A 104 0 7.0 3.0 4.0 0.0 0.0 GLY A 105 0 6.5 3.0 3.5 0.0 0.0 VAL A 106 3 12.0 2.0 6.5 3.5 0.0 PRO A 107 0 4.0 1.0 0.0 3.0 0.0 GLN A 108 3 7.0 1.5 3.0 2.5 0.0 LEU A 109 7 16.0 2.5 9.0 4.5 0.0 GLY A 110 0 3.5 1.5 2.0 0.0 0.0 ASP A 111 0 2.5 2.0 0.5 0.0 0.0 HIS A 112 1 9.5 3.5 5.5 0.5 0.0 LEU A 113 4 11.5 4.5 4.0 3.0 0.0 ALA A 114 0 3.0 3.0 0.0 0.0 0.0 LEU A 115 2 2.0 2.0 0.0 0.0 0.0 GLU A 116 1 1.5 1.5 0.0 0.0 0.0 TOTAL 221 979.0 360.0 244.0 375.0 0.0 > ANALYZE_cns: Do you want a CONS.OUT file [default no] ?_