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 `MBR242E_NMR_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> HEADER DNA BINDING PROTEIN 26-JUN-09 2KKO > ReadCoordsPdb(): >> TITLE SOLUTION NMR STRUCTURE OF THE HOMODIMERIC WINGED HELIX-TURN- > ReadCoordsPdb(): >> TITLE 2 HELIX DNA-BINDING DOMAIN (FRAGMENT 1-100) MB0332 FROM > ReadCoordsPdb(): >> TITLE 3 MYCOBACTERIUM BOVIS, A POSSIBLE ARSR-FAMILY TRANSCRIPTIONAL > ReadCoordsPdb(): >> TITLE 4 REGULATOR. NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET 1 > ReadCoordsPdb(): Counting models in file `MBR242E_NMR_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 MBR242E_NMR_em_bcr3.pdb MODEL 1 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 3328 ATOM records read from file > ReadCoordsPdb(): --> 3328 Regular IUPAC Atoms > ReadCoordsPdb(): --> 0 Pseudo-atoms (DISMAN type) > ReadCoordsPdb(): --> 0 Lone pairs > ReadCoordsPdb(): Bye ... > =============================== INFO ================================ > INFO_mol: # atoms: 3328 (1010 C, 1678 H, 306 O, 330 N, 4 S, 0 Q, 0 Metals) > INFO_mol: # residues: 216 (Avg. mol. weight: 108.6) > INFO_mol: # -- M.W. : 23467.9 g/mol. (23.47 kD) Estimated RoG : 16.96 > INFO_mol: CenterMass() -- Working PDB model 1 in file, model no. 1 > INFO_mol: CenterMass() -- Molecule `MBR242E_NMR_em_bcr3.pdb' model #1, TOTAL RESIDUES: 216 > INFO_mol: Radius of Gyration : 20.0666 angstroms > INFO_mol: Center of Masses: x_cm(0.547), y_cm(-1.299), z_cm(-0.268) > INFO_res: MAGQSDRKAA LLDQVARVGK ALANGRRLQI LDLLAQGERA VEAIATATGM > INFO_res: NLTTASANLQ ALKSGGLVEA RREGTRQYYR IAGEDVARLF ALVQVVADEH > INFO_res: LEHHHHHHMA GQSDRKAALL DQVARVGKAL ANGRRLQILD LLAQGERAVE > INFO_res: AIATATGMNL TTASANLQAL KSGGLVEARR EGTRQYYRIA GEDVARLFAL > INFO_res: VQVVADEHLE HHHHHH > INFO_res: > INFO_res: MET ALA GLY GLN SER ASP ARG LYS ALA ALA LEU LEU > INFO_res: ASP GLN VAL ALA ARG VAL GLY LYS ALA LEU ALA ASN > INFO_res: GLY ARG ARG LEU GLN ILE LEU ASP LEU LEU ALA GLN > INFO_res: GLY GLU ARG ALA VAL GLU ALA ILE ALA THR ALA THR > INFO_res: GLY MET ASN LEU THR THR ALA SER ALA ASN LEU GLN > INFO_res: ALA LEU LYS SER GLY GLY LEU VAL GLU ALA ARG ARG > INFO_res: GLU GLY THR ARG GLN TYR TYR ARG ILE ALA GLY GLU > INFO_res: ASP VAL ALA ARG LEU PHE ALA LEU VAL GLN VAL VAL > INFO_res: ALA ASP GLU HIS LEU GLU HIS HIS HIS HIS HIS HIS > INFO_res: MET ALA GLY GLN SER ASP ARG LYS ALA ALA LEU LEU > INFO_res: ASP GLN VAL ALA ARG VAL GLY LYS ALA LEU ALA ASN > INFO_res: GLY ARG ARG LEU GLN ILE LEU ASP LEU LEU ALA GLN > INFO_res: GLY GLU ARG ALA VAL GLU ALA ILE ALA THR ALA THR > INFO_res: GLY MET ASN LEU THR THR ALA SER ALA ASN LEU GLN > INFO_res: ALA LEU LYS SER GLY GLY LEU VAL GLU ALA ARG ARG > INFO_res: GLU GLY THR ARG GLN TYR TYR ARG ILE ALA GLY GLU > INFO_res: ASP VAL ALA ARG LEU PHE ALA LEU VAL GLN VAL VAL > INFO_res: ALA ASP GLU HIS LEU GLU HIS HIS HIS HIS HIS HIS > INFO_res: > INFO_res: > INFO_res: 38 ALA 20 ARG 6 ASN 10 ASP 14 GLN 14 GLU > INFO_res: 18 GLY 14 HIS 6 ILE 28 LEU 6 LYS 4 MET > INFO_res: 2 PHE 6 SER 10 THR 4 TYR 16 VAL > INFO_res: DISULFIDE: ** NO INFO FOR DISULFIDES IN FILE > ===================================================================== > ReadCoordsPdb(): *** x-mer, 2 [2] chains PdbStat> > locate_file(): file `MBR242E_NMR_em_bcr3.upl' opened for reading 0 SANI-RDC constraints read 2386 NOE-distance constraints (0 Ambiguous NOE/s) read 2386 TOTAL constraints read PdbStat> -------------- SUMMARY OF RESTRAINTS --------------- TOTAL NUMBER OF NOE RESTRAINTS : 2386 INTRA-RESIDUE RESTRAINTS (I=J) : 572 SEQUENTIAL RESTRAINTS (I-J)=1 : 588 BACKBONE-BACKBONE : 150 BACKBONE-SIDE CHAIN : 56 SIDE CHAIN-SIDE CHAIN : 382 MEDIUM RANGE RESTRAINTS 1<(I-J)<5 : 594 BACKBONE-BACKBONE : 152 BACKBONE-SIDE CHAIN : 194 SIDE CHAIN-SIDE CHAIN : 248 LONG RANGE RESTRAINTS (I-J)>=5 : 632 TOTAL HYDROGEN BOND RESTRAINTS : 0 LONG RANGE H-BOND RESTR. (I-J)>=5 : 0 DISULFIDE RESTRAINTS : 0 INTRA-CHAIN RESTRAINTS : 2260 INTER-CHAIN RESTRAINTS : 126 AMBIGUOUS RESTRAINTS : 0 ----------------------------------------------------- ----------------------------------------------------- ----------------------------------------------------- RES # INTRA INTER seq med lng InterChain MET A 1 0 0.0 0.0 0.0 0.0 0.0 ALA A 2 0 0.0 0.0 0.0 0.0 0.0 GLY A 3 0 0.0 0.0 0.0 0.0 0.0 GLN A 4 2 0.0 0.0 0.0 0.0 0.0 SER A 5 0 1.0 1.0 0.0 0.0 0.0 ASP A 6 1 3.5 2.5 1.0 0.0 0.0 ARG A 7 5 3.5 2.5 1.0 0.0 0.0 LYS A 8 7 2.5 1.5 1.0 0.0 0.0 ALA A 9 1 3.0 0.5 2.5 0.0 0.0 ALA A 10 1 5.5 2.0 3.5 0.0 0.0 LEU A 11 3 8.0 4.0 2.0 2.0 2.0 LEU A 12 8 16.5 4.0 3.5 9.0 9.0 ASP A 13 1 7.0 3.5 3.5 0.0 0.0 GLN A 14 3 10.5 2.5 3.0 5.0 5.0 VAL A 15 4 8.5 3.0 1.5 4.0 4.0 ALA A 16 1 7.5 3.5 2.0 2.0 2.0 ARG A 17 3 8.0 2.0 4.5 1.5 0.5 VAL A 18 5 6.5 3.5 2.5 0.5 0.0 GLY A 19 0 9.0 3.0 6.0 0.0 2.0 LYS A 20 10 9.5 3.0 6.5 0.0 3.0 ALA A 21 1 9.5 4.0 4.0 1.5 0.5 LEU A 22 8 12.0 3.5 4.0 4.5 1.5 ALA A 23 1 10.5 3.5 7.0 0.0 4.0 ASN A 24 1 2.0 1.0 1.0 0.0 0.0 GLY A 25 0 3.0 0.0 2.5 0.5 0.5 ARG A 26 1 1.5 0.0 1.5 0.0 0.0 ARG A 27 2 4.5 0.5 1.5 2.5 0.0 LEU A 28 4 17.0 1.0 7.5 8.5 5.0 GLN A 29 4 11.0 2.0 2.5 6.5 3.5 ILE A 30 5 20.0 4.0 5.5 10.5 0.0 LEU A 31 7 25.0 5.0 5.5 14.5 0.0 ASP A 32 1 10.0 4.0 2.5 3.5 2.5 LEU A 33 8 14.0 3.0 7.0 4.0 0.0 LEU A 34 7 8.5 1.5 3.5 3.5 0.0 ALA A 35 1 7.5 2.0 3.0 2.5 0.0 GLN A 36 3 6.0 3.0 3.0 0.0 0.0 GLY A 37 0 5.5 3.0 2.5 0.0 0.0 GLU A 38 2 6.0 3.5 0.0 2.5 0.0 ARG A 39 2 8.0 3.5 1.0 3.5 0.0 ALA A 40 1 13.5 5.0 4.0 4.5 0.0 VAL A 41 5 19.5 5.0 5.0 9.5 0.0 GLU A 42 3 14.0 4.5 4.0 5.5 0.0 ALA A 43 1 10.5 4.5 5.5 0.5 0.0 ILE A 44 5 19.5 5.0 7.5 7.0 0.0 ALA A 45 1 12.0 4.5 4.5 3.0 0.0 THR A 46 3 6.5 3.5 3.0 0.0 0.0 ALA A 47 1 7.0 3.5 2.5 1.0 0.0 THR A 48 2 11.5 2.5 6.0 3.0 0.0 GLY A 49 0 2.0 1.0 1.0 0.0 0.0 MET A 50 6 13.0 1.5 4.5 7.0 0.0 ASN A 51 1 6.0 3.0 3.0 0.0 0.0 LEU A 52 7 14.5 3.0 4.0 7.5 0.0 THR A 53 2 4.5 3.0 1.5 0.0 0.0 THR A 54 2 7.0 3.0 4.0 0.0 0.0 ALA A 55 1 18.0 3.0 7.0 8.0 0.0 SER A 56 1 10.0 3.5 4.5 2.0 0.0 ALA A 57 1 6.0 3.0 3.0 0.0 0.0 ASN A 58 1 8.5 2.0 4.0 2.5 0.0 LEU A 59 6 23.0 3.5 5.0 14.5 0.0 GLN A 60 4 9.0 6.0 3.0 0.0 0.0 ALA A 61 1 6.5 4.5 1.5 0.5 0.0 LEU A 62 7 12.5 2.5 2.0 8.0 0.0 LYS A 63 4 14.0 3.0 2.0 9.0 0.0 SER A 64 1 4.5 3.0 1.0 0.5 0.0 GLY A 65 0 5.5 2.0 1.0 2.5 0.0 GLY A 66 0 2.5 2.0 0.5 0.0 0.0 LEU A 67 6 12.5 5.0 1.5 6.0 0.0 VAL A 68 3 22.5 7.0 0.0 15.5 0.0 GLU A 69 3 13.0 7.0 0.0 6.0 0.0 ALA A 70 1 12.0 5.0 0.0 7.0 0.0 ARG A 71 3 5.5 3.5 0.0 2.0 0.0 ARG A 72 8 6.0 4.0 0.0 2.0 0.0 GLU A 73 2 6.0 2.0 1.5 2.5 0.0 GLY A 74 0 1.0 0.5 0.5 0.0 0.0 THR A 75 2 2.0 2.0 0.0 0.0 0.0 ARG A 76 8 8.5 4.5 3.5 0.5 0.0 GLN A 77 6 10.5 4.5 1.5 4.5 0.0 TYR A 78 1 12.0 2.0 2.0 8.0 0.0 TYR A 79 2 16.0 1.0 1.0 14.0 0.0 ARG A 80 3 7.5 1.5 0.0 6.0 0.0 ILE A 81 7 18.5 3.5 1.0 14.0 0.0 ALA A 82 0 12.0 3.5 1.5 7.0 0.0 GLY A 83 0 4.5 1.5 3.0 0.0 0.0 GLU A 84 2 5.5 1.0 4.5 0.0 0.0 ASP A 85 0 4.5 2.0 2.5 0.0 0.0 VAL A 86 3 16.0 3.5 6.0 6.5 0.0 ALA A 87 1 11.5 4.0 3.5 4.0 0.0 ARG A 88 7 9.0 2.0 6.5 0.5 1.0 LEU A 89 4 9.5 1.5 7.5 0.5 2.5 PHE A 90 2 19.5 5.0 4.0 10.5 1.5 ALA A 91 1 8.5 4.0 4.5 0.0 0.0 LEU A 92 0 11.0 2.5 8.5 0.0 3.5 VAL A 93 5 9.0 4.0 4.0 1.0 0.0 GLN A 94 3 8.5 3.0 4.5 1.0 1.0 VAL A 95 5 10.5 3.5 7.0 0.0 0.0 VAL A 96 4 7.0 4.5 2.5 0.0 0.0 ALA A 97 1 11.0 3.5 3.0 4.5 4.5 ASP A 98 2 7.5 2.5 3.0 2.0 2.0 GLU A 99 3 5.5 3.0 2.5 0.0 0.0 HIS A 100 1 3.5 2.0 1.5 0.0 0.0 LEU A 101 6 4.5 1.5 1.0 2.0 2.0 GLU A 102 1 1.5 1.5 0.0 0.0 0.0 HIS A 103 0 0.0 0.0 0.0 0.0 0.0 HIS A 104 0 0.0 0.0 0.0 0.0 0.0 HIS A 105 0 0.0 0.0 0.0 0.0 0.0 HIS A 106 0 0.0 0.0 0.0 0.0 0.0 HIS A 107 0 0.5 0.5 0.0 0.0 0.0 HIS A 108 0 0.5 0.5 0.0 0.0 0.0 MET B 1 0 0.0 0.0 0.0 0.0 0.0 ALA B 2 0 0.0 0.0 0.0 0.0 0.0 GLY B 3 0 0.0 0.0 0.0 0.0 0.0 GLN B 4 2 0.0 0.0 0.0 0.0 0.0 SER B 5 0 1.0 1.0 0.0 0.0 0.0 ASP B 6 1 3.5 2.5 1.0 0.0 0.0 ARG B 7 5 3.5 2.5 1.0 0.0 0.0 LYS B 8 7 2.5 1.5 1.0 0.0 0.0 ALA B 9 1 3.0 0.5 2.5 0.0 0.0 ALA B 10 1 5.5 2.0 3.5 0.0 0.0 LEU B 11 3 8.0 4.0 2.0 2.0 2.0 LEU B 12 8 16.5 4.0 3.5 9.0 9.0 ASP B 13 1 7.0 3.5 3.5 0.0 0.0 GLN B 14 3 10.5 2.5 3.0 5.0 5.0 VAL B 15 4 8.5 3.0 1.5 4.0 4.0 ALA B 16 1 7.5 3.5 2.0 2.0 2.0 ARG B 17 3 8.0 2.0 4.5 1.5 0.5 VAL B 18 5 6.5 3.5 2.5 0.5 0.0 GLY B 19 0 9.0 3.0 6.0 0.0 2.0 LYS B 20 10 9.5 3.0 6.5 0.0 3.0 ALA B 21 1 9.5 4.0 4.0 1.5 0.5 LEU B 22 8 12.0 3.5 4.0 4.5 1.5 ALA B 23 1 10.5 3.5 7.0 0.0 4.0 ASN B 24 1 2.0 1.0 1.0 0.0 0.0 GLY B 25 0 3.0 0.0 2.5 0.5 0.5 ARG B 26 1 1.5 0.0 1.5 0.0 0.0 ARG B 27 2 4.5 0.5 1.5 2.5 0.0 LEU B 28 4 17.0 1.0 7.5 8.5 5.0 GLN B 29 4 11.0 2.0 2.5 6.5 3.5 ILE B 30 5 20.0 4.0 5.5 10.5 0.0 LEU B 31 7 25.0 5.0 5.5 14.5 0.0 ASP B 32 1 10.0 4.0 2.5 3.5 2.5 LEU B 33 8 14.0 3.0 7.0 4.0 0.0 LEU B 34 7 8.5 1.5 3.5 3.5 0.0 ALA B 35 1 7.5 2.0 3.0 2.5 0.0 GLN B 36 3 6.0 3.0 3.0 0.0 0.0 GLY B 37 0 5.5 3.0 2.5 0.0 0.0 GLU B 38 2 6.0 3.5 0.0 2.5 0.0 ARG B 39 2 8.0 3.5 1.0 3.5 0.0 ALA B 40 1 13.5 5.0 4.0 4.5 0.0 VAL B 41 5 19.5 5.0 5.0 9.5 0.0 GLU B 42 3 14.0 4.5 4.0 5.5 0.0 ALA B 43 1 10.5 4.5 5.5 0.5 0.0 ILE B 44 5 19.5 5.0 7.5 7.0 0.0 ALA B 45 1 12.0 4.5 4.5 3.0 0.0 THR B 46 3 6.5 3.5 3.0 0.0 0.0 ALA B 47 1 7.0 3.5 2.5 1.0 0.0 THR B 48 2 11.5 2.5 6.0 3.0 0.0 GLY B 49 0 2.0 1.0 1.0 0.0 0.0 MET B 50 6 13.0 1.5 4.5 7.0 0.0 ASN B 51 1 6.0 3.0 3.0 0.0 0.0 LEU B 52 7 14.5 3.0 4.0 7.5 0.0 THR B 53 2 4.5 3.0 1.5 0.0 0.0 THR B 54 2 7.0 3.0 4.0 0.0 0.0 ALA B 55 1 18.0 3.0 7.0 8.0 0.0 SER B 56 1 10.0 3.5 4.5 2.0 0.0 ALA B 57 1 6.0 3.0 3.0 0.0 0.0 ASN B 58 1 8.5 2.0 4.0 2.5 0.0 LEU B 59 6 23.0 3.5 5.0 14.5 0.0 GLN B 60 4 9.0 6.0 3.0 0.0 0.0 ALA B 61 1 6.5 4.5 1.5 0.5 0.0 LEU B 62 7 12.5 2.5 2.0 8.0 0.0 LYS B 63 4 14.0 3.0 2.0 9.0 0.0 SER B 64 1 4.5 3.0 1.0 0.5 0.0 GLY B 65 0 5.5 2.0 1.0 2.5 0.0 GLY B 66 0 2.5 2.0 0.5 0.0 0.0 LEU B 67 6 12.5 5.0 1.5 6.0 0.0 VAL B 68 3 22.5 7.0 0.0 15.5 0.0 GLU B 69 3 13.0 7.0 0.0 6.0 0.0 ALA B 70 1 12.0 5.0 0.0 7.0 0.0 ARG B 71 3 5.5 3.5 0.0 2.0 0.0 ARG B 72 8 6.0 4.0 0.0 2.0 0.0 GLU B 73 2 6.0 2.0 1.5 2.5 0.0 GLY B 74 0 1.0 0.5 0.5 0.0 0.0 THR B 75 2 2.0 2.0 0.0 0.0 0.0 ARG B 76 8 8.5 4.5 3.5 0.5 0.0 GLN B 77 6 10.5 4.5 1.5 4.5 0.0 TYR B 78 1 12.0 2.0 2.0 8.0 0.0 TYR B 79 2 16.0 1.0 1.0 14.0 0.0 ARG B 80 3 7.5 1.5 0.0 6.0 0.0 ILE B 81 7 18.5 3.5 1.0 14.0 0.0 ALA B 82 0 12.0 3.5 1.5 7.0 0.0 GLY B 83 0 4.5 1.5 3.0 0.0 0.0 GLU B 84 2 5.5 1.0 4.5 0.0 0.0 ASP B 85 0 4.5 2.0 2.5 0.0 0.0 VAL B 86 3 16.0 3.5 6.0 6.5 0.0 ALA B 87 1 11.5 4.0 3.5 4.0 0.0 ARG B 88 7 9.0 2.0 6.5 0.5 1.0 LEU B 89 4 9.5 1.5 7.5 0.5 2.5 PHE B 90 2 19.5 5.0 4.0 10.5 1.5 ALA B 91 1 8.5 4.0 4.5 0.0 0.0 LEU B 92 0 11.0 2.5 8.5 0.0 3.5 VAL B 93 5 9.0 4.0 4.0 1.0 0.0 GLN B 94 3 8.5 3.0 4.5 1.0 1.0 VAL B 95 5 10.5 3.5 7.0 0.0 0.0 VAL B 96 4 7.0 4.5 2.5 0.0 0.0 ALA B 97 1 11.0 3.5 3.0 4.5 4.5 ASP B 98 2 7.5 2.5 3.0 2.0 2.0 GLU B 99 3 5.5 3.0 2.5 0.0 0.0 HIS B 100 1 3.5 2.0 1.5 0.0 0.0 LEU B 101 6 4.5 1.5 1.0 2.0 2.0 GLU B 102 1 1.5 1.5 0.0 0.0 0.0 HIS B 103 0 0.0 0.0 0.0 0.0 0.0 HIS B 104 0 0.0 0.0 0.0 0.0 0.0 HIS B 105 0 0.0 0.0 0.0 0.0 0.0 HIS B 106 0 0.0 0.0 0.0 0.0 0.0 HIS B 107 0 0.5 0.5 0.0 0.0 0.0 HIS B 108 0 0.5 0.5 0.0 0.0 0.0 TOTAL 572 1814.0 588.0 594.0 632.0 126.0 > ANALYZE_cns: Do you want a CONS.OUT file [default no] ?_