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 `CTR107_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 166 MET ASP PHE GLU CYS GLN PHE VAL CYS GLU LEU LYS GLU 1 > ReadCoordsPdb(): Counting models in file `CTR107_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 CTR107_R3_em_bcr3.pdb MODEL 1 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 2487 ATOM records read from file > ReadCoordsPdb(): --> 2487 Regular IUPAC Atoms > ReadCoordsPdb(): --> 0 Pseudo-atoms (DISMAN type) > ReadCoordsPdb(): --> 0 Lone pairs > ReadCoordsPdb(): Bye ... > =============================== INFO ================================ > INFO_mol: # atoms: 2487 (813 C, 1210 H, 248 O, 209 N, 7 S, 0 Q, 0 Metals) > INFO_mol: # residues: 166 (Avg. mol. weight: 109.1) > INFO_mol: # -- M.W. : 18103.8 g/mol. (18.10 kD) Estimated RoG : 15.35 > INFO_mol: CenterMass() -- Working PDB model 1 in file, model no. 1 > INFO_mol: CenterMass() -- Molecule `CTR107_R3_em_bcr3.pdb' model #1, TOTAL RESIDUES: 166 > INFO_mol: Radius of Gyration : 15.8867 angstroms > INFO_mol: Center of Masses: x_cm(-1.882), y_cm(-3.219), z_cm(-0.274) > INFO_res: MDFECQFVCE LKELAPVPAL LIRTQTAMSE LGSLFEAGYH DILQLLAGQG > INFO_res: KSPSGPPFAR YFGMSAGTFE VEFGFPVEGG VEGSGRVVTG LTPSGKAASS > INFO_res: LYIGPYGEIE AVYDALMKWV DDNGFDLSGE AYEIYLDNPA ETAPDQLRTR > INFO_res: VSLMLHESLE HHHHHH > INFO_res: > INFO_res: MET ASP PHE GLU CYS GLN PHE VAL CYS GLU LEU LYS > INFO_res: GLU LEU ALA PRO VAL PRO ALA LEU LEU ILE ARG THR > INFO_res: GLN THR ALA MET SER GLU LEU GLY SER LEU PHE GLU > INFO_res: ALA GLY TYR HIS ASP ILE LEU GLN LEU LEU ALA GLY > INFO_res: GLN GLY LYS SER PRO SER GLY PRO PRO PHE ALA ARG > INFO_res: TYR PHE GLY MET SER ALA GLY THR PHE GLU VAL GLU > INFO_res: PHE GLY PHE PRO VAL GLU GLY GLY VAL GLU GLY SER > INFO_res: GLY ARG VAL VAL THR GLY LEU THR PRO SER GLY LYS > INFO_res: ALA ALA SER SER LEU TYR ILE GLY PRO TYR GLY GLU > INFO_res: ILE GLU ALA VAL TYR ASP ALA LEU MET LYS TRP VAL > INFO_res: ASP ASP ASN GLY PHE ASP LEU SER GLY GLU ALA TYR > INFO_res: GLU ILE TYR LEU ASP ASN PRO ALA GLU THR ALA PRO > INFO_res: ASP GLN LEU ARG THR ARG VAL SER LEU MET LEU HIS > INFO_res: GLU SER LEU GLU HIS HIS HIS HIS HIS HIS > INFO_res: > INFO_res: 14 ALA 5 ARG 2 ASN 8 ASP 2 CYS 5 GLN > INFO_res: 16 GLU 18 GLY 8 HIS 5 ILE 18 LEU 4 LYS > INFO_res: 5 MET 9 PHE 10 PRO 12 SER 7 THR 7 TYR > INFO_res: 1 TRP 10 VAL > INFO_res: DISULFIDE: ** NO INFO FOR DISULFIDES IN FILE > ===================================================================== > ReadCoordsPdb(): *** monomer, 1 [1] chains *** PdbStat> > locate_file(): file `CTR107_R3_em_bcr3.upl' opened for reading 0 SANI-RDC constraints read 1106 NOE-distance constraints (0 Ambiguous NOE/s) read 1106 TOTAL constraints read PdbStat> -------------- SUMMARY OF RESTRAINTS --------------- TOTAL NUMBER OF NOE RESTRAINTS : 1106 INTRA-RESIDUE RESTRAINTS (I=J) : 211 SEQUENTIAL RESTRAINTS (I-J)=1 : 406 BACKBONE-BACKBONE : 131 BACKBONE-SIDE CHAIN : 7 SIDE CHAIN-SIDE CHAIN : 268 MEDIUM RANGE RESTRAINTS 1<(I-J)<5 : 105 BACKBONE-BACKBONE : 15 BACKBONE-SIDE CHAIN : 35 SIDE CHAIN-SIDE CHAIN : 55 LONG RANGE RESTRAINTS (I-J)>=5 : 384 TOTAL HYDROGEN BOND RESTRAINTS : 0 LONG RANGE H-BOND RESTR. (I-J)>=5 : 0 DISULFIDE RESTRAINTS : 0 INTRA-CHAIN RESTRAINTS : 1106 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 ASP A 2 0 3.5 3.5 0.0 0.0 0.0 PHE A 3 0 4.0 4.0 0.0 0.0 0.0 GLU A 4 3 1.0 1.0 0.0 0.0 0.0 CYS A 5 0 0.5 0.5 0.0 0.0 0.0 GLN A 6 3 2.5 2.5 0.0 0.0 0.0 PHE A 7 3 8.0 3.5 0.0 4.5 0.0 VAL A 8 1 4.5 4.0 0.0 0.5 0.0 CYS A 9 0 7.0 5.0 0.0 2.0 0.0 GLU A 10 2 7.0 4.5 0.0 2.5 0.0 LEU A 11 4 14.0 6.5 0.0 7.5 0.0 LYS A 12 10 11.5 7.5 2.5 1.5 0.0 GLU A 13 4 8.0 6.5 0.0 1.5 0.0 LEU A 14 3 14.0 6.0 2.5 5.5 0.0 ALA A 15 0 3.0 3.0 0.0 0.0 0.0 PRO A 16 0 2.5 1.0 0.0 1.5 0.0 VAL A 17 0 9.0 4.0 0.0 5.0 0.0 PRO A 18 0 10.5 4.5 0.0 6.0 0.0 ALA A 19 0 6.5 2.0 0.0 4.5 0.0 LEU A 20 1 16.5 3.0 0.0 13.5 0.0 LEU A 21 0 4.0 2.5 0.0 1.5 0.0 ILE A 22 1 10.0 1.5 1.5 7.0 0.0 ARG A 23 4 4.5 4.5 0.0 0.0 0.0 THR A 24 0 8.5 4.5 2.0 2.0 0.0 GLN A 25 2 7.5 4.5 0.0 3.0 0.0 THR A 26 0 9.0 4.5 0.5 4.0 0.0 ALA A 27 0 4.0 2.0 2.0 0.0 0.0 MET A 28 2 1.5 1.0 0.5 0.0 0.0 SER A 29 0 1.5 1.0 0.5 0.0 0.0 GLU A 30 2 4.0 2.0 2.0 0.0 0.0 LEU A 31 2 9.5 3.5 4.5 1.5 0.0 GLY A 32 0 2.5 2.5 0.0 0.0 0.0 SER A 33 0 4.0 1.0 3.0 0.0 0.0 LEU A 34 5 8.5 3.5 2.5 2.5 0.0 PHE A 35 0 10.5 5.0 2.5 3.0 0.0 GLU A 36 5 8.0 5.0 3.0 0.0 0.0 ALA A 37 0 4.5 3.5 1.0 0.0 0.0 GLY A 38 0 1.0 1.0 0.0 0.0 0.0 TYR A 39 0 5.0 2.5 1.5 1.0 0.0 HIS A 40 3 4.0 4.0 0.0 0.0 0.0 ASP A 41 0 2.0 2.0 0.0 0.0 0.0 ILE A 42 0 3.0 0.0 1.0 2.0 0.0 LEU A 43 0 0.0 0.0 0.0 0.0 0.0 GLN A 44 0 1.0 0.5 0.5 0.0 0.0 LEU A 45 2 12.5 3.0 1.0 8.5 0.0 LEU A 46 3 14.5 5.5 0.5 8.5 0.0 ALA A 47 0 4.5 3.5 1.0 0.0 0.0 GLY A 48 0 1.0 1.0 0.0 0.0 0.0 GLN A 49 5 11.5 1.0 2.0 8.5 0.0 GLY A 50 0 1.0 1.0 0.0 0.0 0.0 LYS A 51 15 13.0 5.0 1.0 7.0 0.0 SER A 52 3 6.0 4.5 0.0 1.5 0.0 PRO A 53 0 10.0 3.5 2.0 4.5 0.0 SER A 54 0 5.0 4.0 0.0 1.0 0.0 GLY A 55 0 2.5 0.5 2.0 0.0 0.0 PRO A 56 0 0.0 0.0 0.0 0.0 0.0 PRO A 57 0 0.5 0.5 0.0 0.0 0.0 PHE A 58 0 7.5 2.5 0.0 5.0 0.0 ALA A 59 0 4.5 2.5 0.0 2.0 0.0 ARG A 60 0 3.0 1.5 0.0 1.5 0.0 TYR A 61 0 8.0 1.5 0.0 6.5 0.0 PHE A 62 0 0.5 0.5 0.0 0.0 0.0 GLY A 63 0 0.0 0.0 0.0 0.0 0.0 MET A 64 5 0.5 0.0 0.0 0.5 0.0 SER A 65 0 0.0 0.0 0.0 0.0 0.0 ALA A 66 0 0.0 0.0 0.0 0.0 0.0 GLY A 67 0 0.5 0.5 0.0 0.0 0.0 THR A 68 1 4.0 2.0 0.0 2.0 0.0 PHE A 69 0 7.5 4.5 1.0 2.0 0.0 GLU A 70 2 7.0 6.0 0.0 1.0 0.0 VAL A 71 0 12.5 5.0 1.0 6.5 0.0 GLU A 72 0 2.5 2.0 0.0 0.5 0.0 PHE A 73 0 1.0 0.0 0.0 1.0 0.0 GLY A 74 0 0.0 0.0 0.0 0.0 0.0 PHE A 75 0 6.0 0.0 0.0 6.0 0.0 PRO A 76 0 5.5 2.5 0.0 3.0 0.0 VAL A 77 0 16.0 4.5 2.0 9.5 0.0 GLU A 78 2 6.0 5.0 1.0 0.0 0.0 GLY A 79 0 4.5 3.0 1.5 0.0 0.0 GLY A 80 0 0.5 0.5 0.0 0.0 0.0 VAL A 81 1 20.0 3.0 3.5 13.5 0.0 GLU A 82 3 11.5 6.5 0.0 5.0 0.0 GLY A 83 0 14.0 4.5 0.0 9.5 0.0 SER A 84 0 7.5 1.0 2.0 4.5 0.0 GLY A 85 0 0.5 0.5 0.0 0.0 0.0 ARG A 86 0 2.0 0.5 0.0 1.5 0.0 VAL A 87 1 11.5 3.5 2.0 6.0 0.0 VAL A 88 0 7.5 4.5 0.0 3.0 0.0 THR A 89 1 8.0 3.0 0.0 5.0 0.0 GLY A 90 0 4.0 3.0 0.0 1.0 0.0 LEU A 91 1 11.5 5.0 0.0 6.5 0.0 THR A 92 0 5.0 3.5 0.0 1.5 0.0 PRO A 93 0 2.5 2.0 0.0 0.5 0.0 SER A 94 0 6.0 4.0 0.0 2.0 0.0 GLY A 95 0 4.5 3.5 0.0 1.0 0.0 LYS A 96 13 9.0 6.0 0.0 3.0 0.0 ALA A 97 0 11.0 5.0 0.5 5.5 0.0 ALA A 98 0 8.0 1.0 0.0 7.0 0.0 SER A 99 0 4.0 1.0 0.5 2.5 0.0 SER A 100 0 8.5 1.0 0.0 7.5 0.0 LEU A 101 3 4.0 2.0 0.0 2.0 0.0 TYR A 102 0 9.0 2.5 0.0 6.5 0.0 ILE A 103 1 4.5 2.0 0.0 2.5 0.0 GLY A 104 0 1.5 1.0 0.0 0.5 0.0 PRO A 105 0 0.0 0.0 0.0 0.0 0.0 TYR A 106 0 1.0 0.0 0.0 1.0 0.0 GLY A 107 0 0.0 0.0 0.0 0.0 0.0 GLU A 108 2 2.0 2.0 0.0 0.0 0.0 ILE A 109 1 13.5 3.5 6.0 4.0 0.0 GLU A 110 3 5.5 4.0 1.5 0.0 0.0 ALA A 111 0 4.5 3.0 1.0 0.5 0.0 VAL A 112 1 14.0 1.5 3.5 9.0 0.0 TYR A 113 2 9.5 3.0 5.0 1.5 0.0 ASP A 114 3 4.5 4.0 0.5 0.0 0.0 ALA A 115 0 5.5 2.5 1.5 1.5 0.0 LEU A 116 4 11.0 1.5 1.5 8.0 0.0 MET A 117 3 3.0 3.0 0.0 0.0 0.0 LYS A 118 6 6.0 4.0 2.0 0.0 0.0 TRP A 119 1 14.0 4.5 3.0 6.5 0.0 VAL A 120 1 11.0 4.5 1.0 5.5 0.0 ASP A 121 2 6.0 4.0 2.0 0.0 0.0 ASP A 122 3 4.5 4.0 0.5 0.0 0.0 ASN A 123 6 4.0 2.5 1.5 0.0 0.0 GLY A 124 0 1.0 0.5 0.5 0.0 0.0 PHE A 125 2 9.5 1.5 0.0 8.0 0.0 ASP A 126 0 4.0 3.0 0.0 1.0 0.0 LEU A 127 1 5.5 4.0 1.0 0.5 0.0 SER A 128 0 3.0 3.0 0.0 0.0 0.0 GLY A 129 0 2.0 1.0 1.0 0.0 0.0 GLU A 130 2 0.5 0.5 0.0 0.0 0.0 ALA A 131 0 5.5 0.5 0.0 5.0 0.0 TYR A 132 0 6.0 1.5 0.5 4.0 0.0 GLU A 133 2 4.0 1.5 0.0 2.5 0.0 ILE A 134 1 6.5 2.0 0.5 4.0 0.0 TYR A 135 1 4.5 1.5 0.0 3.0 0.0 LEU A 136 1 2.5 1.5 0.0 1.0 0.0 ASP A 137 0 4.5 2.5 0.0 2.0 0.0 ASN A 138 3 1.5 1.0 0.5 0.0 0.0 PRO A 139 0 3.0 0.5 0.0 2.5 0.0 ALA A 140 0 3.5 1.5 1.5 0.5 0.0 GLU A 141 5 3.5 3.0 0.5 0.0 0.0 THR A 142 1 8.5 3.5 2.0 3.0 0.0 ALA A 143 0 4.0 1.5 2.5 0.0 0.0 PRO A 144 0 4.5 3.5 1.0 0.0 0.0 ASP A 145 3 5.0 4.0 0.5 0.5 0.0 GLN A 146 5 4.5 1.5 2.0 1.0 0.0 LEU A 147 4 10.5 2.5 1.5 6.5 0.0 ARG A 148 0 4.0 2.0 0.0 2.0 0.0 THR A 149 0 7.0 1.5 0.0 5.5 0.0 ARG A 150 2 4.0 2.5 0.0 1.5 0.0 VAL A 151 1 8.5 2.5 0.0 6.0 0.0 SER A 152 0 5.0 1.5 0.0 3.5 0.0 LEU A 153 3 7.0 2.0 0.5 4.5 0.0 MET A 154 6 4.0 2.5 0.0 1.5 0.0 LEU A 155 1 12.5 3.5 0.5 8.5 0.0 HIS A 156 3 3.5 3.5 0.0 0.0 0.0 GLU A 157 2 2.0 2.0 0.0 0.0 0.0 SER A 158 0 1.0 1.0 0.0 0.0 0.0 LEU A 159 1 1.5 0.5 0.0 1.0 0.0 GLU A 160 1 1.0 1.0 0.0 0.0 0.0 HIS A 161 0 0.5 0.5 0.0 0.0 0.0 HIS A 162 0 0.0 0.0 0.0 0.0 0.0 HIS A 163 0 0.0 0.0 0.0 0.0 0.0 HIS A 164 0 0.0 0.0 0.0 0.0 0.0 HIS A 165 0 0.0 0.0 0.0 0.0 0.0 HIS A 166 0 0.0 0.0 0.0 0.0 0.0 TOTAL 211 895.0 406.0 105.0 384.0 0.0 > ANALYZE_cns: Do you want a CONS.OUT file [default no] ?_