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 `UUR17A_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 121 MET LEU SER GLN ALA ASN GLU ASP PHE LYS LYS ILE VAL 1 > ReadCoordsPdb(): Counting models in file `UUR17A_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 UUR17A_R3_em_bcr3.pdb MODEL 1 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 2006 ATOM records read from file > ReadCoordsPdb(): --> 2006 Regular IUPAC Atoms > ReadCoordsPdb(): --> 0 Pseudo-atoms (DISMAN type) > ReadCoordsPdb(): --> 0 Lone pairs > ReadCoordsPdb(): Bye ... > =============================== INFO ================================ > INFO_mol: # atoms: 2006 (653 C, 990 H, 188 O, 173 N, 2 S, 0 Q, 0 Metals) > INFO_mol: # residues: 121 (Avg. mol. weight: 118.5) > INFO_mol: # -- M.W. : 14335.9 g/mol. (14.34 kD) Estimated RoG : 13.61 > INFO_mol: CenterMass() -- Working PDB model 1 in file, model no. 1 > INFO_mol: CenterMass() -- Molecule `UUR17A_R3_em_bcr3.pdb' model #1, TOTAL RESIDUES: 121 > INFO_mol: Radius of Gyration : 15.7947 angstroms > INFO_mol: Center of Masses: x_cm(-0.546), y_cm(-0.255), z_cm(-0.200) > INFO_res: MLSQANEDFK KIVNNIRLKD TFDFKLAAFP NQNYDQLLPS QIYKNYYQGI > INFO_res: EIQQHKYQNE LDIKIINFLY PDGDFGSANK NGTLKLSLML TDKKNNQVYY > INFO_res: KLLEVSGFKS NPYLEHHHHH H > INFO_res: > INFO_res: MET LEU SER GLN ALA ASN GLU ASP PHE LYS LYS ILE > INFO_res: VAL ASN ASN ILE ARG LEU LYS ASP THR PHE ASP PHE > INFO_res: LYS LEU ALA ALA PHE PRO ASN GLN ASN TYR ASP GLN > INFO_res: LEU LEU PRO SER GLN ILE TYR LYS ASN TYR TYR GLN > INFO_res: GLY ILE GLU ILE GLN GLN HIS LYS TYR GLN ASN GLU > INFO_res: LEU ASP ILE LYS ILE ILE ASN PHE LEU TYR PRO ASP > INFO_res: GLY ASP PHE GLY SER ALA ASN LYS ASN GLY THR LEU > INFO_res: LYS LEU SER LEU MET LEU THR ASP LYS LYS ASN ASN > INFO_res: GLN VAL TYR TYR LYS LEU LEU GLU VAL SER GLY PHE > INFO_res: LYS SER ASN PRO TYR LEU GLU HIS HIS HIS HIS HIS > INFO_res: HIS > INFO_res: > INFO_res: 4 ALA 1 ARG 13 ASN 8 ASP 9 GLN 5 GLU > INFO_res: 5 GLY 7 HIS 8 ILE 14 LEU 13 LYS 2 MET > INFO_res: 7 PHE 4 PRO 6 SER 3 THR 9 TYR 3 VAL > INFO_res: DISULFIDE: ** NO INFO FOR DISULFIDES IN FILE > ===================================================================== > ReadCoordsPdb(): *** monomer, 1 [1] chains *** PdbStat> > locate_file(): file `UUR17A_R3_em_bcr3.upl' opened for reading 0 SANI-RDC constraints read 2064 NOE-distance constraints (0 Ambiguous NOE/s) read 2064 TOTAL constraints read PdbStat> -------------- SUMMARY OF RESTRAINTS --------------- TOTAL NUMBER OF NOE RESTRAINTS : 2064 INTRA-RESIDUE RESTRAINTS (I=J) : 388 SEQUENTIAL RESTRAINTS (I-J)=1 : 611 BACKBONE-BACKBONE : 130 BACKBONE-SIDE CHAIN : 92 SIDE CHAIN-SIDE CHAIN : 389 MEDIUM RANGE RESTRAINTS 1<(I-J)<5 : 440 BACKBONE-BACKBONE : 92 BACKBONE-SIDE CHAIN : 97 SIDE CHAIN-SIDE CHAIN : 251 LONG RANGE RESTRAINTS (I-J)>=5 : 625 TOTAL HYDROGEN BOND RESTRAINTS : 0 LONG RANGE H-BOND RESTR. (I-J)>=5 : 0 DISULFIDE RESTRAINTS : 0 INTRA-CHAIN RESTRAINTS : 2064 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 LEU A 2 3 1.5 1.5 0.0 0.0 0.0 SER A 3 0 3.0 3.0 0.0 0.0 0.0 GLN A 4 3 6.0 5.5 0.5 0.0 0.0 ALA A 5 1 12.0 7.0 5.0 0.0 0.0 ASN A 6 6 9.0 5.5 3.5 0.0 0.0 GLU A 7 2 8.5 4.0 4.5 0.0 0.0 ASP A 8 1 14.0 4.5 9.5 0.0 0.0 PHE A 9 3 14.0 6.0 8.0 0.0 0.0 LYS A 10 6 15.5 5.0 10.5 0.0 0.0 LYS A 11 5 16.0 4.5 11.5 0.0 0.0 ILE A 12 11 19.0 7.0 7.5 4.5 0.0 VAL A 13 5 37.5 9.5 10.0 18.0 0.0 ASN A 14 5 15.5 6.0 7.0 2.5 0.0 ASN A 15 3 10.0 4.0 6.0 0.0 0.0 ILE A 16 9 29.0 6.5 8.5 14.0 0.0 ARG A 17 7 23.5 10.0 9.5 4.0 0.0 LEU A 18 10 38.0 13.0 3.0 22.0 0.0 LYS A 19 8 14.0 8.0 4.0 2.0 0.0 ASP A 20 2 8.5 3.0 5.5 0.0 0.0 THR A 21 0 10.5 4.0 3.5 3.0 0.0 PHE A 22 4 19.0 4.0 1.5 13.5 0.0 ASP A 23 0 11.0 3.0 0.0 8.0 0.0 PHE A 24 6 25.0 5.0 3.0 17.0 0.0 LYS A 25 4 21.0 8.5 0.0 12.5 0.0 LEU A 26 5 28.5 7.5 14.0 7.0 0.0 ALA A 27 0 12.0 5.0 2.0 5.0 0.0 ALA A 28 0 13.0 6.0 2.5 4.5 0.0 PHE A 29 1 31.0 6.0 18.0 7.0 0.0 PRO A 30 0 12.0 7.5 1.5 3.0 0.0 ASN A 31 4 9.0 7.5 1.5 0.0 0.0 GLN A 32 2 15.5 4.5 7.5 3.5 0.0 ASN A 33 5 10.0 3.5 6.5 0.0 0.0 TYR A 34 4 22.5 4.5 3.0 15.0 0.0 ASP A 35 1 7.0 4.5 2.0 0.5 0.0 GLN A 36 1 8.0 4.5 3.5 0.0 0.0 LEU A 37 6 20.0 5.0 6.5 8.5 0.0 LEU A 38 2 6.5 2.0 4.5 0.0 0.0 PRO A 39 0 7.0 2.0 2.0 3.0 0.0 SER A 40 0 6.5 4.0 2.5 0.0 0.0 GLN A 41 3 15.5 4.0 10.0 1.5 0.0 ILE A 42 6 24.0 6.0 6.5 11.5 0.0 TYR A 43 3 14.0 9.5 4.0 0.5 0.0 LYS A 44 8 10.0 6.5 3.5 0.0 0.0 ASN A 45 0 14.5 3.5 5.0 6.0 0.0 TYR A 46 0 8.5 2.5 5.5 0.5 0.0 TYR A 47 0 1.5 1.5 0.0 0.0 0.0 GLN A 48 3 9.5 3.0 2.0 4.5 0.0 GLY A 49 0 3.5 2.0 0.0 1.5 0.0 ILE A 50 8 24.0 3.5 6.0 14.5 0.0 GLU A 51 2 11.5 6.0 0.0 5.5 0.0 ILE A 52 8 30.5 7.0 4.0 19.5 0.0 GLN A 53 1 14.0 6.0 0.0 8.0 0.0 GLN A 54 3 7.5 3.5 3.0 1.0 0.0 HIS A 55 2 10.0 4.5 2.0 3.5 0.0 LYS A 56 6 15.5 9.0 4.0 2.5 0.0 TYR A 57 3 14.5 8.5 5.0 1.0 0.0 GLN A 58 12 25.5 4.5 13.0 8.0 0.0 ASN A 59 5 4.5 4.0 0.5 0.0 0.0 GLU A 60 3 14.5 9.5 3.0 2.0 0.0 LEU A 61 6 29.5 11.0 10.5 8.0 0.0 ASP A 62 0 14.5 8.0 1.5 5.0 0.0 ILE A 63 4 37.5 8.5 2.5 26.5 0.0 LYS A 64 4 13.5 5.0 0.5 8.0 0.0 ILE A 65 4 21.5 1.5 3.0 17.0 0.0 ILE A 66 3 11.5 2.5 0.0 9.0 0.0 ASN A 67 0 8.0 4.0 1.5 2.5 0.0 PHE A 68 2 25.0 5.5 2.5 17.0 0.0 LEU A 69 2 12.0 8.0 0.5 3.5 0.0 TYR A 70 5 12.5 4.5 3.5 4.5 0.0 PRO A 71 0 0.0 0.0 0.0 0.0 0.0 ASP A 72 0 1.5 1.5 0.0 0.0 0.0 GLY A 73 0 3.5 2.0 1.5 0.0 0.0 ASP A 74 0 12.0 3.0 9.0 0.0 0.0 PHE A 75 4 7.5 6.5 1.0 0.0 0.0 GLY A 76 0 8.5 4.5 4.0 0.0 0.0 SER A 77 3 15.0 4.0 11.0 0.0 0.0 ALA A 78 0 16.0 5.0 7.0 4.0 0.0 ASN A 79 0 7.0 3.5 3.5 0.0 0.0 LYS A 80 10 17.5 6.5 7.0 4.0 0.0 ASN A 81 1 13.0 6.5 5.0 1.5 0.0 GLY A 82 0 6.5 3.0 2.5 1.0 0.0 THR A 83 2 16.0 3.0 4.0 9.0 0.0 LEU A 84 4 27.0 5.5 1.5 20.0 0.0 LYS A 85 6 18.5 7.0 0.0 11.5 0.0 LEU A 86 2 28.5 6.0 4.0 18.5 0.0 SER A 87 0 13.5 5.5 0.0 8.0 0.0 LEU A 88 5 28.0 5.0 3.0 20.0 0.0 MET A 89 0 16.5 4.5 0.0 12.0 0.0 LEU A 90 5 31.0 5.0 0.5 25.5 0.0 THR A 91 2 14.0 3.5 2.5 8.0 0.0 ASP A 92 0 17.5 5.0 6.5 6.0 0.0 LYS A 93 7 10.0 4.5 4.0 1.5 0.0 LYS A 94 3 8.0 4.5 3.5 0.0 0.0 ASN A 95 6 12.5 7.0 5.5 0.0 0.0 ASN A 96 6 10.5 4.5 4.5 1.5 0.0 GLN A 97 11 10.0 4.0 2.5 3.5 0.0 VAL A 98 6 16.0 7.5 2.5 6.0 0.0 TYR A 99 1 17.5 7.5 1.5 8.5 0.0 TYR A 100 4 15.5 5.5 3.0 7.0 0.0 LYS A 101 6 31.0 9.0 2.5 19.5 0.0 LEU A 102 4 17.5 11.0 0.5 6.0 0.0 LEU A 103 6 20.0 7.0 2.0 11.0 0.0 GLU A 104 2 8.5 3.5 0.0 5.0 0.0 VAL A 105 4 20.0 4.5 2.5 13.0 0.0 SER A 106 0 10.0 5.0 1.0 4.0 0.0 GLY A 107 0 4.0 3.0 0.5 0.5 0.0 PHE A 108 3 17.5 3.0 2.5 12.0 0.0 LYS A 109 6 7.5 7.0 0.5 0.0 0.0 SER A 110 0 7.5 7.0 0.0 0.5 0.0 ASN A 111 6 19.0 5.0 10.5 3.5 0.0 PRO A 112 0 11.0 7.0 1.5 2.5 0.0 TYR A 113 9 11.5 10.0 1.5 0.0 0.0 LEU A 114 9 17.5 7.5 10.0 0.0 0.0 GLU A 115 4 4.0 2.5 1.5 0.0 0.0 HIS A 116 0 2.0 2.0 0.0 0.0 0.0 HIS A 117 0 1.0 1.0 0.0 0.0 0.0 HIS A 118 0 0.0 0.0 0.0 0.0 0.0 HIS A 119 0 0.0 0.0 0.0 0.0 0.0 HIS A 120 0 0.0 0.0 0.0 0.0 0.0 HIS A 121 0 0.0 0.0 0.0 0.0 0.0 TOTAL 388 1676.0 611.0 440.0 625.0 0.0 > ANALYZE_cns: Do you want a CONS.OUT file [default no] ?_