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 `DHR29B_R3_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> EXPDTA NMR, 21 STRUCTURES > ReadCoordsPdb(): >> REMARK PdbStat -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > ReadCoordsPdb(): >> REMARK PdbStat -- PDB COORDINATES FOR TEMP_BCM_111.PDB, 20 MODEL/S TEMP_BCM_111.PDB > ReadCoordsPdb(): >> REMARK PdbStat -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > ReadCoordsPdb(): >> SEQRES 1 A 96 SER SER GLN THR LEU ASP ARG ASP PRO THR LEU THR LEU 1 > ReadCoordsPdb(): Counting models in file `DHR29B_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 DHR29B_R3_em_bcr3.pdb MODEL 1 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 1515 ATOM records read from file > ReadCoordsPdb(): --> 1515 Regular IUPAC Atoms > ReadCoordsPdb(): --> 0 Pseudo-atoms (DISMAN type) > ReadCoordsPdb(): --> 0 Lone pairs > ReadCoordsPdb(): Bye ... > =============================== INFO ================================ > INFO_mol: # atoms: 1515 (477 C, 756 H, 148 O, 132 N, 2 S, 0 Q, 0 Metals) > INFO_mol: # residues: 96 (Avg. mol. weight: 112.2) > INFO_mol: # -- M.W. : 10772.0 g/mol. (10.77 kD) Estimated RoG : 12.46 > INFO_mol: CenterMass() -- Working PDB model 1 in file, model no. 1 > INFO_mol: CenterMass() -- Molecule `DHR29B_R3_em_bcr3.pdb' model #1, TOTAL RESIDUES: 96 > INFO_mol: Radius of Gyration : 16.5779 angstroms > INFO_mol: Center of Masses: x_cm(1.331), y_cm(-15.591), z_cm(-14.276) > INFO_res: SSQTLDRDPT LTLSLIAKNT PANSMIMTKL PSVRVKTEGY NPSINVNELF > INFO_res: AYVDLSGSEP GEHDYEVKVE PIPNIKIVEI SPRVVTLQLE HHHHHH > INFO_res: > INFO_res: SER SER GLN THR LEU ASP ARG ASP PRO THR LEU THR > INFO_res: LEU SER LEU ILE ALA LYS ASN THR PRO ALA ASN SER > INFO_res: MET ILE MET THR LYS LEU PRO SER VAL ARG VAL LYS > INFO_res: THR GLU GLY TYR ASN PRO SER ILE ASN VAL ASN GLU > INFO_res: LEU PHE ALA TYR VAL ASP LEU SER GLY SER GLU PRO > INFO_res: GLY GLU HIS ASP TYR GLU VAL LYS VAL GLU PRO ILE > INFO_res: PRO ASN ILE LYS ILE VAL GLU ILE SER PRO ARG VAL > INFO_res: VAL THR LEU GLN LEU GLU HIS HIS HIS HIS HIS HIS > INFO_res: > INFO_res: > INFO_res: 3 ALA 3 ARG 6 ASN 4 ASP 2 GLN 8 GLU > INFO_res: 3 GLY 7 HIS 7 ILE 9 LEU 5 LYS 2 MET > INFO_res: 1 PHE 8 PRO 9 SER 7 THR 3 TYR 9 VAL > INFO_res: DISULFIDE: ** NO INFO FOR DISULFIDES IN FILE > ===================================================================== > ReadCoordsPdb(): *** monomer, 1 [1] chains *** PdbStat> > locate_file(): file `DHR29B_R3_em_bcr3.upl' opened for reading 0 SANI-RDC constraints read 793 NOE-distance constraints (0 Ambiguous NOE/s) read 793 TOTAL constraints read PdbStat> -------------- SUMMARY OF RESTRAINTS --------------- TOTAL NUMBER OF NOE RESTRAINTS : 793 INTRA-RESIDUE RESTRAINTS (I=J) : 157 SEQUENTIAL RESTRAINTS (I-J)=1 : 225 BACKBONE-BACKBONE : 83 BACKBONE-SIDE CHAIN : 30 SIDE CHAIN-SIDE CHAIN : 112 MEDIUM RANGE RESTRAINTS 1<(I-J)<5 : 75 BACKBONE-BACKBONE : 14 BACKBONE-SIDE CHAIN : 7 SIDE CHAIN-SIDE CHAIN : 54 LONG RANGE RESTRAINTS (I-J)>=5 : 336 TOTAL HYDROGEN BOND RESTRAINTS : 0 LONG RANGE H-BOND RESTR. (I-J)>=5 : 0 DISULFIDE RESTRAINTS : 0 INTRA-CHAIN RESTRAINTS : 793 INTER-CHAIN RESTRAINTS : 0 AMBIGUOUS RESTRAINTS : 0 ----------------------------------------------------- ----------------------------------------------------- ----------------------------------------------------- RES # INTRA INTER seq med lng InterChain SER A 1 0 0.0 0.0 0.0 0.0 0.0 SER A 2 0 0.0 0.0 0.0 0.0 0.0 GLN A 3 0 0.0 0.0 0.0 0.0 0.0 THR A 4 0 0.0 0.0 0.0 0.0 0.0 LEU A 5 0 0.0 0.0 0.0 0.0 0.0 ASP A 6 0 0.0 0.0 0.0 0.0 0.0 ARG A 7 0 0.5 0.0 0.0 0.5 0.0 ASP A 8 0 1.5 0.5 0.0 1.0 0.0 PRO A 9 0 2.5 1.0 0.0 1.5 0.0 THR A 10 2 8.0 1.5 0.5 6.0 0.0 LEU A 11 6 7.5 2.5 0.0 5.0 0.0 THR A 12 2 6.5 3.0 0.5 3.0 0.0 LEU A 13 4 12.5 3.0 0.0 9.5 0.0 SER A 14 0 4.5 2.5 0.0 2.0 0.0 LEU A 15 6 15.5 3.5 0.0 12.0 0.0 ILE A 16 4 12.0 5.5 0.5 6.0 0.0 ALA A 17 0 12.0 3.0 1.5 7.5 0.0 LYS A 18 4 7.0 1.0 1.0 5.0 0.0 ASN A 19 1 2.5 1.5 0.0 1.0 0.0 THR A 20 1 10.5 1.0 3.5 6.0 0.0 PRO A 21 0 3.5 1.5 0.0 2.0 0.0 ALA A 22 0 3.0 2.0 1.0 0.0 0.0 ASN A 23 1 3.0 2.0 0.0 1.0 0.0 SER A 24 0 7.0 2.0 2.5 2.5 0.0 MET A 25 2 7.5 2.5 0.5 4.5 0.0 ILE A 26 6 18.5 4.5 4.0 10.0 0.0 MET A 27 4 6.0 4.0 0.5 1.5 0.0 THR A 28 2 9.5 3.0 2.0 4.5 0.0 LYS A 29 1 3.0 3.0 0.0 0.0 0.0 LEU A 30 6 10.5 2.5 2.0 6.0 0.0 PRO A 31 0 7.0 2.5 0.0 4.5 0.0 SER A 32 0 3.0 1.5 0.0 1.5 0.0 VAL A 33 2 11.5 3.5 0.0 8.0 0.0 ARG A 34 3 11.5 5.0 0.0 6.5 0.0 VAL A 35 2 11.5 3.0 0.0 8.5 0.0 LYS A 36 2 10.5 2.5 0.0 8.0 0.0 THR A 37 1 12.5 3.5 0.0 9.0 0.0 GLU A 38 0 8.0 2.5 0.0 5.5 0.0 GLY A 39 0 2.5 1.0 0.0 1.5 0.0 TYR A 40 2 4.5 2.0 0.0 2.5 0.0 ASN A 41 1 6.0 2.0 2.0 2.0 0.0 PRO A 42 0 1.5 1.5 0.0 0.0 0.0 SER A 43 0 3.0 2.5 0.5 0.0 0.0 ILE A 44 4 9.0 4.0 3.0 2.0 0.0 ASN A 45 2 4.5 3.0 1.5 0.0 0.0 VAL A 46 4 9.5 2.5 6.5 0.5 0.0 ASN A 47 2 4.5 2.5 2.0 0.0 0.0 GLU A 48 1 4.0 2.5 1.5 0.0 0.0 LEU A 49 7 10.5 3.5 5.0 2.0 0.0 PHE A 50 2 8.0 2.0 0.0 6.0 0.0 ALA A 51 0 9.0 0.5 0.0 8.5 0.0 TYR A 52 2 11.0 2.5 0.0 8.5 0.0 VAL A 53 2 14.5 4.5 2.0 8.0 0.0 ASP A 54 0 5.0 3.0 0.5 1.5 0.0 LEU A 55 6 15.5 1.5 2.0 12.0 0.0 SER A 56 0 3.5 1.5 0.5 1.5 0.0 GLY A 57 0 1.5 1.5 0.0 0.0 0.0 SER A 58 0 3.0 1.5 0.0 1.5 0.0 GLU A 59 1 1.5 1.5 0.0 0.0 0.0 PRO A 60 0 3.0 1.0 0.0 2.0 0.0 GLY A 61 0 3.0 1.0 0.0 2.0 0.0 GLU A 62 1 5.0 1.5 0.0 3.5 0.0 HIS A 63 0 5.0 1.5 1.0 2.5 0.0 ASP A 64 0 3.5 1.0 0.0 2.5 0.0 TYR A 65 3 11.5 1.0 1.0 9.5 0.0 GLU A 66 2 5.5 2.0 0.0 3.5 0.0 VAL A 67 1 10.5 4.0 0.5 6.0 0.0 LYS A 68 3 5.5 4.0 0.0 1.5 0.0 VAL A 69 2 9.0 3.5 0.5 5.0 0.0 GLU A 70 1 5.5 3.0 0.0 2.5 0.0 PRO A 71 0 3.0 2.0 0.0 1.0 0.0 ILE A 72 3 7.0 1.5 4.0 1.5 0.0 PRO A 73 0 1.5 1.0 0.5 0.0 0.0 ASN A 74 1 1.0 1.0 0.0 0.0 0.0 ILE A 75 5 14.5 2.5 4.5 7.5 0.0 LYS A 76 3 7.5 4.0 1.0 2.5 0.0 ILE A 77 4 13.5 5.5 1.5 6.5 0.0 VAL A 78 2 16.5 6.0 1.0 9.5 0.0 GLU A 79 1 7.5 4.0 1.5 2.0 0.0 ILE A 80 3 5.5 3.5 0.5 1.5 0.0 SER A 81 0 4.5 3.0 0.5 1.0 0.0 PRO A 82 0 7.0 2.5 2.5 2.0 0.0 ARG A 83 4 6.5 5.0 1.0 0.5 0.0 VAL A 84 1 15.0 7.0 2.0 6.0 0.0 VAL A 85 2 14.0 6.5 2.5 5.0 0.0 THR A 86 2 9.0 4.5 1.0 3.5 0.0 LEU A 87 6 14.0 3.0 1.0 10.0 0.0 GLN A 88 2 8.0 2.5 0.0 5.5 0.0 LEU A 89 6 19.0 3.5 0.0 15.5 0.0 GLU A 90 0 6.5 3.0 0.0 3.5 0.0 HIS A 91 1 2.5 1.5 0.0 1.0 0.0 HIS A 92 0 3.5 1.0 0.0 2.5 0.0 HIS A 93 0 0.0 0.0 0.0 0.0 0.0 HIS A 94 0 0.0 0.0 0.0 0.0 0.0 HIS A 95 0 0.0 0.0 0.0 0.0 0.0 HIS A 96 0 0.0 0.0 0.0 0.0 0.0 TOTAL 157 636.0 225.0 75.0 336.0 0.0 > ANALYZE_cns: Do you want a CONS.OUT file [default no] ?_