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 `HR3646E_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 121 MET GLY HIS HIS HIS HIS HIS HIS SER HIS MET ALA GLN 1 > ReadCoordsPdb(): Counting models in file `HR3646E_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 HR3646E_R3Cons_em_bcr3.pdb MODEL 1 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 1894 ATOM records read from file > ReadCoordsPdb(): --> 1894 Regular IUPAC Atoms > ReadCoordsPdb(): --> 0 Pseudo-atoms (DISMAN type) > ReadCoordsPdb(): --> 0 Lone pairs > ReadCoordsPdb(): Bye ... > =============================== INFO ================================ > INFO_mol: # atoms: 1894 (613 C, 935 H, 169 O, 171 N, 6 S, 0 Q, 0 Metals) > INFO_mol: # residues: 121 (Avg. mol. weight: 112.4) > INFO_mol: # -- M.W. : 13596.3 g/mol. (13.60 kD) Estimated RoG : 13.61 > INFO_mol: CenterMass() -- Working PDB model 1 in file, model no. 1 > INFO_mol: CenterMass() -- Molecule `HR3646E_R3Cons_em_bcr3.pdb' model #1, TOTAL RESIDUES: 121 > INFO_mol: Radius of Gyration : 14.7948 angstroms > INFO_mol: Center of Masses: x_cm(-0.779), y_cm(-46.280), z_cm(-19.746) > INFO_res: MGHHHHHHSH MAQFPTPFGG SLDTWAITVE ERAKHDQQFH SLKPISGFIT > INFO_res: GDQARNFFFQ SGLPQPVLAQ IWALADMNND GRMDQVEFSI AMKLIKLKLQ > INFO_res: GYQLPSALPP VMKQQPVAIS S > INFO_res: > INFO_res: MET GLY HIS HIS HIS HIS HIS HIS SER HIS MET ALA > INFO_res: GLN PHE PRO THR PRO PHE GLY GLY SER LEU ASP THR > INFO_res: TRP ALA ILE THR VAL GLU GLU ARG ALA LYS HIS ASP > INFO_res: GLN GLN PHE HIS SER LEU LYS PRO ILE SER GLY PHE > INFO_res: ILE THR GLY ASP GLN ALA ARG ASN PHE PHE PHE GLN > INFO_res: SER GLY LEU PRO GLN PRO VAL LEU ALA GLN ILE TRP > INFO_res: ALA LEU ALA ASP MET ASN ASN ASP GLY ARG MET ASP > INFO_res: GLN VAL GLU PHE SER ILE ALA MET LYS LEU ILE LYS > INFO_res: LEU LYS LEU GLN GLY TYR GLN LEU PRO SER ALA LEU > INFO_res: PRO PRO VAL MET LYS GLN GLN PRO VAL ALA ILE SER > INFO_res: SER > INFO_res: > INFO_res: 10 ALA 3 ARG 3 ASN 6 ASP 12 GLN 3 GLU > INFO_res: 8 GLY 9 HIS 7 ILE 10 LEU 6 LYS 6 MET > INFO_res: 8 PHE 9 PRO 9 SER 4 THR 1 TYR 2 TRP > INFO_res: 5 VAL > INFO_res: DISULFIDE: ** NO INFO FOR DISULFIDES IN FILE > ===================================================================== > ReadCoordsPdb(): *** monomer, 1 [1] chains *** PdbStat> > locate_file(): file `HR3646E_R3Cons_em_bcr3.upl' opened for reading 0 SANI-RDC constraints read 1571 NOE-distance constraints (0 Ambiguous NOE/s) read 1571 TOTAL constraints read PdbStat> -------------- SUMMARY OF RESTRAINTS --------------- TOTAL NUMBER OF NOE RESTRAINTS : 1571 INTRA-RESIDUE RESTRAINTS (I=J) : 333 SEQUENTIAL RESTRAINTS (I-J)=1 : 481 BACKBONE-BACKBONE : 106 BACKBONE-SIDE CHAIN : 29 SIDE CHAIN-SIDE CHAIN : 346 MEDIUM RANGE RESTRAINTS 1<(I-J)<5 : 425 BACKBONE-BACKBONE : 104 BACKBONE-SIDE CHAIN : 110 SIDE CHAIN-SIDE CHAIN : 211 LONG RANGE RESTRAINTS (I-J)>=5 : 332 TOTAL HYDROGEN BOND RESTRAINTS : 0 LONG RANGE H-BOND RESTR. (I-J)>=5 : 0 DISULFIDE RESTRAINTS : 0 INTRA-CHAIN RESTRAINTS : 1571 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 0.0 0.0 0.0 0.0 0.0 SER A 9 0 0.0 0.0 0.0 0.0 0.0 HIS A 10 0 0.0 0.0 0.0 0.0 0.0 MET A 11 0 0.0 0.0 0.0 0.0 0.0 ALA A 12 0 0.0 0.0 0.0 0.0 0.0 GLN A 13 0 0.0 0.0 0.0 0.0 0.0 PHE A 14 0 0.0 0.0 0.0 0.0 0.0 PRO A 15 0 2.0 2.0 0.0 0.0 0.0 THR A 16 1 5.0 5.0 0.0 0.0 0.0 PRO A 17 0 6.0 6.0 0.0 0.0 0.0 PHE A 18 3 3.0 3.0 0.0 0.0 0.0 GLY A 19 0 0.5 0.5 0.0 0.0 0.0 GLY A 20 0 1.0 1.0 0.0 0.0 0.0 SER A 21 0 2.5 2.5 0.0 0.0 0.0 LEU A 22 6 5.5 5.5 0.0 0.0 0.0 ASP A 23 2 8.5 5.5 3.0 0.0 0.0 THR A 24 1 10.5 6.5 2.0 2.0 0.0 TRP A 25 4 15.0 6.0 0.5 8.5 0.0 ALA A 26 1 12.0 2.5 6.0 3.5 0.0 ILE A 27 4 20.0 4.0 10.5 5.5 0.0 THR A 28 1 14.0 4.0 10.0 0.0 0.0 VAL A 29 1 7.5 3.5 4.0 0.0 0.0 GLU A 30 6 9.5 5.5 4.0 0.0 0.0 GLU A 31 3 27.5 6.0 20.5 1.0 0.0 ARG A 32 0 8.0 4.5 2.5 1.0 0.0 ALA A 33 0 10.5 2.0 8.5 0.0 0.0 LYS A 34 18 9.0 4.5 4.5 0.0 0.0 HIS A 35 0 5.5 5.5 0.0 0.0 0.0 ASP A 36 3 8.0 3.5 4.5 0.0 0.0 GLN A 37 5 7.5 5.0 2.5 0.0 0.0 GLN A 38 9 6.5 4.0 2.5 0.0 0.0 PHE A 39 1 15.5 3.5 4.0 8.0 0.0 HIS A 40 2 10.0 4.5 5.5 0.0 0.0 SER A 41 3 7.0 4.0 3.0 0.0 0.0 LEU A 42 7 21.5 5.0 3.0 13.5 0.0 LYS A 43 12 7.5 5.5 1.5 0.5 0.0 PRO A 44 0 18.5 5.5 6.5 6.5 0.0 ILE A 45 3 8.5 5.5 3.0 0.0 0.0 SER A 46 0 4.5 3.5 1.0 0.0 0.0 GLY A 47 0 3.0 1.5 1.5 0.0 0.0 PHE A 48 5 9.0 3.5 4.5 1.0 0.0 ILE A 49 3 25.5 5.5 4.0 16.0 0.0 THR A 50 1 11.0 4.5 5.5 1.0 0.0 GLY A 51 0 6.0 2.5 2.0 1.5 0.0 ASP A 52 3 5.0 2.0 3.0 0.0 0.0 GLN A 53 9 14.5 4.5 8.5 1.5 0.0 ALA A 54 0 11.5 3.5 4.5 3.5 0.0 ARG A 55 9 7.5 4.0 3.5 0.0 0.0 ASN A 56 2 10.0 5.0 5.0 0.0 0.0 PHE A 57 5 11.0 4.0 2.0 5.0 0.0 PHE A 58 4 14.0 4.5 3.0 6.5 0.0 PHE A 59 5 12.5 4.5 4.0 4.0 0.0 GLN A 60 7 6.0 4.5 0.5 1.0 0.0 SER A 61 2 12.0 4.0 3.0 5.0 0.0 GLY A 62 0 4.5 3.0 0.5 1.0 0.0 LEU A 63 7 31.5 9.0 6.0 16.5 0.0 PRO A 64 0 21.0 10.0 11.0 0.0 0.0 GLN A 65 4 11.0 5.5 5.5 0.0 0.0 PRO A 66 0 14.0 10.0 4.0 0.0 0.0 VAL A 67 2 35.5 8.5 19.5 7.5 0.0 LEU A 68 6 23.0 5.0 8.0 10.0 0.0 ALA A 69 0 12.5 4.0 8.5 0.0 0.0 GLN A 70 5 23.5 5.5 18.0 0.0 0.0 ILE A 71 4 40.0 8.0 14.0 18.0 0.0 TRP A 72 3 22.5 7.0 6.5 9.0 0.0 ALA A 73 1 16.0 5.5 9.0 1.5 0.0 LEU A 74 6 22.5 5.5 10.5 6.5 0.0 ALA A 75 0 17.0 4.0 6.0 7.0 0.0 ASP A 76 3 10.0 2.5 5.0 2.5 0.0 MET A 77 5 15.0 5.5 1.5 8.0 0.0 ASN A 78 2 6.5 4.0 2.0 0.5 0.0 ASN A 79 4 6.0 2.0 2.5 1.5 0.0 ASP A 80 3 6.0 3.0 3.0 0.0 0.0 GLY A 81 0 5.0 2.0 0.5 2.5 0.0 ARG A 82 5 5.5 4.5 0.5 0.5 0.0 MET A 83 9 24.5 8.5 4.5 11.5 0.0 ASP A 84 2 12.5 7.0 4.5 1.0 0.0 GLN A 85 12 13.5 5.5 4.0 4.0 0.0 VAL A 86 1 11.5 5.0 6.5 0.0 0.0 GLU A 87 3 15.5 4.5 7.0 4.0 0.0 PHE A 88 4 11.5 5.0 4.5 2.0 0.0 SER A 89 0 6.5 3.0 3.5 0.0 0.0 ILE A 90 3 25.5 2.5 4.5 18.5 0.0 ALA A 91 0 3.5 2.0 0.5 1.0 0.0 MET A 92 0 1.5 1.0 0.5 0.0 0.0 LYS A 93 0 1.5 1.5 0.0 0.0 0.0 LEU A 94 3 22.0 7.0 4.5 10.5 0.0 ILE A 95 4 28.0 10.5 5.0 12.5 0.0 LYS A 96 8 11.0 8.0 3.0 0.0 0.0 LEU A 97 5 26.0 5.5 7.0 13.5 0.0 LYS A 98 10 29.0 4.5 4.0 20.5 0.0 LEU A 99 5 17.0 5.5 4.5 7.0 0.0 GLN A 100 3 11.5 4.5 7.0 0.0 0.0 GLY A 101 0 3.0 3.0 0.0 0.0 0.0 TYR A 102 4 20.0 4.5 3.5 12.0 0.0 GLN A 103 0 3.5 3.5 0.0 0.0 0.0 LEU A 104 0 0.0 0.0 0.0 0.0 0.0 PRO A 105 0 5.0 2.5 2.0 0.5 0.0 SER A 106 3 6.0 4.5 0.0 1.5 0.0 ALA A 107 0 6.5 3.0 2.0 1.5 0.0 LEU A 108 4 8.0 1.0 3.5 3.5 0.0 PRO A 109 0 0.0 0.0 0.0 0.0 0.0 PRO A 110 0 7.5 3.5 4.0 0.0 0.0 VAL A 111 2 23.0 7.5 8.5 7.0 0.0 MET A 112 9 18.0 7.0 4.0 7.0 0.0 LYS A 113 14 20.0 8.0 7.5 4.5 0.0 GLN A 114 5 14.0 8.5 5.5 0.0 0.0 GLN A 115 4 7.5 7.5 0.0 0.0 0.0 PRO A 116 0 7.0 7.0 0.0 0.0 0.0 VAL A 117 1 5.5 5.5 0.0 0.0 0.0 ALA A 118 0 3.0 3.0 0.0 0.0 0.0 ILE A 119 4 1.5 1.5 0.0 0.0 0.0 SER A 120 0 1.5 1.5 0.0 0.0 0.0 SER A 121 0 0.5 0.5 0.0 0.0 0.0 TOTAL 333 1238.0 481.0 425.0 332.0 0.0 > ANALYZE_cns: Do you want a CONS.OUT file [default no] ?_