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 `SR478_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 160 MET SER GLU LEU PHE SER VAL PRO TYR PHE ILE GLU ASN 1 > ReadCoordsPdb(): Counting models in file `SR478_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 SR478_R3_em_bcr3.pdb MODEL 1 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 2660 ATOM records read from file > ReadCoordsPdb(): --> 2660 Regular IUPAC Atoms > ReadCoordsPdb(): --> 0 Pseudo-atoms (DISMAN type) > ReadCoordsPdb(): --> 0 Lone pairs > ReadCoordsPdb(): Bye ... > =============================== INFO ================================ > INFO_mol: # atoms: 2660 (842 C, 1316 H, 248 O, 248 N, 6 S, 0 Q, 0 Metals) > INFO_mol: # residues: 160 (Avg. mol. weight: 119.2) > INFO_mol: # -- M.W. : 19073.1 g/mol. (19.07 kD) Estimated RoG : 15.14 > INFO_mol: CenterMass() -- Working PDB model 1 in file, model no. 1 > INFO_mol: CenterMass() -- Molecule `SR478_R3_em_bcr3.pdb' model #1, TOTAL RESIDUES: 160 > INFO_mol: Radius of Gyration : 16.9784 angstroms > INFO_mol: Center of Masses: x_cm(-0.609), y_cm(0.002), z_cm(1.828) > INFO_res: MSELFSVPYF IENLKQHIEM NQSEDKIHAM NSYYRSVVST LVQDQLTKNA > INFO_res: VVLKRIQHLD EAYNKVKRGE SKLEHHHHHH MSELFSVPYF IENLKQHIEM > INFO_res: NQSEDKIHAM NSYYRSVVST LVQDQLTKNA VVLKRIQHLD EAYNKVKRGE > INFO_res: SKLEHHHHHH > INFO_res: > INFO_res: MET SER GLU LEU PHE SER VAL PRO TYR PHE ILE GLU > INFO_res: ASN LEU LYS GLN HIS ILE GLU MET ASN GLN SER GLU > INFO_res: ASP LYS ILE HIS ALA MET ASN SER TYR TYR ARG SER > INFO_res: VAL VAL SER THR LEU VAL GLN ASP GLN LEU THR LYS > INFO_res: ASN ALA VAL VAL LEU LYS ARG ILE GLN HIS LEU ASP > INFO_res: GLU ALA TYR ASN LYS VAL LYS ARG GLY GLU SER LYS > INFO_res: LEU GLU HIS HIS HIS HIS HIS HIS MET SER GLU LEU > INFO_res: PHE SER VAL PRO TYR PHE ILE GLU ASN LEU LYS GLN > INFO_res: HIS ILE GLU MET ASN GLN SER GLU ASP LYS ILE HIS > INFO_res: ALA MET ASN SER TYR TYR ARG SER VAL VAL SER THR > INFO_res: LEU VAL GLN ASP GLN LEU THR LYS ASN ALA VAL VAL > INFO_res: LEU LYS ARG ILE GLN HIS LEU ASP GLU ALA TYR ASN > INFO_res: LYS VAL LYS ARG GLY GLU SER LYS LEU GLU HIS HIS > INFO_res: HIS HIS HIS HIS > INFO_res: > INFO_res: 6 ALA 6 ARG 10 ASN 6 ASP 10 GLN 14 GLU > INFO_res: 2 GLY 18 HIS 8 ILE 14 LEU 14 LYS 6 MET > INFO_res: 4 PHE 2 PRO 14 SER 4 THR 8 TYR 14 VAL > INFO_res: DISULFIDE: ** NO INFO FOR DISULFIDES IN FILE > ===================================================================== > ReadCoordsPdb(): *** x-mer, 2 [2] chains PdbStat> > locate_file(): file `SR478_R3_em_bcr3.upl' opened for reading 0 SANI-RDC constraints read 870 NOE-distance constraints (0 Ambiguous NOE/s) read 870 TOTAL constraints read PdbStat> -------------- SUMMARY OF RESTRAINTS --------------- TOTAL NUMBER OF NOE RESTRAINTS : 870 INTRA-RESIDUE RESTRAINTS (I=J) : 188 SEQUENTIAL RESTRAINTS (I-J)=1 : 232 BACKBONE-BACKBONE : 62 BACKBONE-SIDE CHAIN : 43 SIDE CHAIN-SIDE CHAIN : 127 MEDIUM RANGE RESTRAINTS 1<(I-J)<5 : 271 BACKBONE-BACKBONE : 75 BACKBONE-SIDE CHAIN : 74 SIDE CHAIN-SIDE CHAIN : 122 LONG RANGE RESTRAINTS (I-J)>=5 : 179 TOTAL HYDROGEN BOND RESTRAINTS : 0 LONG RANGE H-BOND RESTR. (I-J)>=5 : 0 DISULFIDE RESTRAINTS : 0 INTRA-CHAIN RESTRAINTS : 870 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 SER A 2 0 1.5 1.5 0.0 0.0 0.0 GLU A 3 0 4.5 4.5 0.0 0.0 0.0 LEU A 4 9 11.5 3.0 1.0 7.5 0.0 PHE A 5 0 0.0 0.0 0.0 0.0 0.0 SER A 6 0 1.5 0.5 1.0 0.0 0.0 VAL A 7 6 6.5 1.0 2.0 3.5 0.0 PRO A 8 0 5.0 1.0 4.0 0.0 0.0 TYR A 9 1 9.5 3.5 1.0 5.0 0.0 PHE A 10 1 15.5 3.5 2.0 10.0 0.0 ILE A 11 5 19.0 2.5 8.0 8.5 0.0 GLU A 12 3 5.5 3.5 2.0 0.0 0.0 ASN A 13 0 6.0 2.5 2.5 1.0 0.0 LEU A 14 5 22.0 2.0 7.0 13.0 0.0 LYS A 15 1 6.5 2.0 4.5 0.0 0.0 GLN A 16 1 7.5 2.5 2.5 2.5 0.0 HIS A 17 0 7.0 2.0 3.5 1.5 0.0 ILE A 18 5 16.0 2.5 6.0 7.5 0.0 GLU A 19 2 4.5 2.5 1.5 0.5 0.0 MET A 20 1 5.5 1.5 4.0 0.0 0.0 ASN A 21 1 6.5 3.0 2.0 1.5 0.0 GLN A 22 3 6.5 4.5 1.0 1.0 0.0 SER A 23 0 4.0 3.5 0.5 0.0 0.0 GLU A 24 3 9.0 3.0 2.0 4.0 0.0 ASP A 25 0 6.5 3.0 2.0 1.5 0.0 LYS A 26 7 9.5 4.0 2.0 3.5 0.0 ILE A 27 6 15.0 4.0 3.0 8.0 0.0 HIS A 28 0 3.0 1.5 1.5 0.0 0.0 ALA A 29 0 14.5 1.5 7.0 6.0 0.0 MET A 30 0 11.5 2.0 4.0 5.5 0.0 ASN A 31 0 4.0 1.5 2.5 0.0 0.0 SER A 32 0 3.0 1.5 1.0 0.5 0.0 TYR A 33 4 19.5 3.0 7.0 9.5 0.0 TYR A 34 4 12.5 2.5 4.5 5.5 0.0 ARG A 35 1 1.5 1.0 0.5 0.0 0.0 SER A 36 0 2.5 1.5 1.0 0.0 0.0 VAL A 37 5 21.5 5.0 8.0 8.5 0.0 VAL A 38 1 15.0 5.5 7.0 2.5 0.0 SER A 39 1 6.5 3.5 3.0 0.0 0.0 THR A 40 2 14.0 6.0 8.0 0.0 0.0 LEU A 41 4 14.5 5.0 7.0 2.5 0.0 VAL A 42 4 14.0 4.5 6.5 3.0 0.0 GLN A 43 1 7.5 4.5 3.0 0.0 0.0 ASP A 44 1 5.5 1.5 4.0 0.0 0.0 GLN A 45 2 5.5 3.5 1.0 1.0 0.0 LEU A 46 10 8.0 5.5 2.0 0.5 0.0 THR A 47 3 12.0 5.5 5.5 1.0 0.0 LYS A 48 2 17.5 6.0 11.5 0.0 0.0 ASN A 49 3 9.0 5.0 4.0 0.0 0.0 ALA A 50 1 10.5 4.5 6.0 0.0 0.0 VAL A 51 6 18.5 5.0 13.0 0.5 0.0 VAL A 52 7 17.0 5.5 7.5 4.0 0.0 LEU A 53 8 13.5 4.5 9.0 0.0 0.0 LYS A 54 6 10.5 2.5 8.0 0.0 0.0 ARG A 55 0 5.5 1.5 3.0 1.0 0.0 ILE A 56 2 16.0 3.5 10.0 2.5 0.0 GLN A 57 0 7.5 3.0 4.5 0.0 0.0 HIS A 58 0 2.5 1.0 1.5 0.0 0.0 LEU A 59 4 17.5 3.5 4.5 9.5 0.0 ASP A 60 0 7.5 4.0 2.5 1.0 0.0 GLU A 61 3 11.5 2.5 2.5 6.5 0.0 ALA A 62 0 14.0 2.5 2.5 9.0 0.0 TYR A 63 3 13.0 4.0 4.5 4.5 0.0 ASN A 64 0 5.0 2.5 2.0 0.5 0.0 LYS A 65 0 4.0 1.0 3.0 0.0 0.0 VAL A 66 6 11.0 3.0 2.5 5.5 0.0 LYS A 67 3 14.0 4.5 5.5 4.0 0.0 ARG A 68 5 8.5 4.5 3.5 0.5 0.0 GLY A 69 1 7.0 4.5 1.5 1.0 0.0 GLU A 70 3 10.0 3.5 4.5 2.0 0.0 SER A 71 1 4.5 3.0 0.5 1.0 0.0 LYS A 72 6 4.5 3.5 1.0 0.0 0.0 LEU A 73 10 6.5 5.0 1.5 0.0 0.0 GLU A 74 5 5.5 4.5 1.0 0.0 0.0 HIS A 75 0 2.0 1.0 1.0 0.0 0.0 HIS A 76 0 0.0 0.0 0.0 0.0 0.0 HIS A 77 0 0.0 0.0 0.0 0.0 0.0 HIS A 78 0 0.0 0.0 0.0 0.0 0.0 HIS A 79 0 0.0 0.0 0.0 0.0 0.0 HIS A 80 0 0.0 0.0 0.0 0.0 0.0 MET B 1 0 0.0 0.0 0.0 0.0 0.0 SER B 2 0 0.0 0.0 0.0 0.0 0.0 GLU B 3 0 0.0 0.0 0.0 0.0 0.0 LEU B 4 0 0.0 0.0 0.0 0.0 0.0 PHE B 5 0 0.0 0.0 0.0 0.0 0.0 SER B 6 0 0.0 0.0 0.0 0.0 0.0 VAL B 7 0 0.0 0.0 0.0 0.0 0.0 PRO B 8 0 0.0 0.0 0.0 0.0 0.0 TYR B 9 0 0.0 0.0 0.0 0.0 0.0 PHE B 10 0 0.0 0.0 0.0 0.0 0.0 ILE B 11 0 0.0 0.0 0.0 0.0 0.0 GLU B 12 0 0.0 0.0 0.0 0.0 0.0 ASN B 13 0 0.0 0.0 0.0 0.0 0.0 LEU B 14 0 0.0 0.0 0.0 0.0 0.0 LYS B 15 0 0.0 0.0 0.0 0.0 0.0 GLN B 16 0 0.0 0.0 0.0 0.0 0.0 HIS B 17 0 0.0 0.0 0.0 0.0 0.0 ILE B 18 0 0.0 0.0 0.0 0.0 0.0 GLU B 19 0 0.0 0.0 0.0 0.0 0.0 MET B 20 0 0.0 0.0 0.0 0.0 0.0 ASN B 21 0 0.0 0.0 0.0 0.0 0.0 GLN B 22 0 0.0 0.0 0.0 0.0 0.0 SER B 23 0 0.0 0.0 0.0 0.0 0.0 GLU B 24 0 0.0 0.0 0.0 0.0 0.0 ASP B 25 0 0.0 0.0 0.0 0.0 0.0 LYS B 26 0 0.0 0.0 0.0 0.0 0.0 ILE B 27 0 0.0 0.0 0.0 0.0 0.0 HIS B 28 0 0.0 0.0 0.0 0.0 0.0 ALA B 29 0 0.0 0.0 0.0 0.0 0.0 MET B 30 0 0.0 0.0 0.0 0.0 0.0 ASN B 31 0 0.0 0.0 0.0 0.0 0.0 SER B 32 0 0.0 0.0 0.0 0.0 0.0 TYR B 33 0 0.0 0.0 0.0 0.0 0.0 TYR B 34 0 0.0 0.0 0.0 0.0 0.0 ARG B 35 0 0.0 0.0 0.0 0.0 0.0 SER B 36 0 0.0 0.0 0.0 0.0 0.0 VAL B 37 0 0.0 0.0 0.0 0.0 0.0 VAL B 38 0 0.0 0.0 0.0 0.0 0.0 SER B 39 0 0.0 0.0 0.0 0.0 0.0 THR B 40 0 0.0 0.0 0.0 0.0 0.0 LEU B 41 0 0.0 0.0 0.0 0.0 0.0 VAL B 42 0 0.0 0.0 0.0 0.0 0.0 GLN B 43 0 0.0 0.0 0.0 0.0 0.0 ASP B 44 0 0.0 0.0 0.0 0.0 0.0 GLN B 45 0 0.0 0.0 0.0 0.0 0.0 LEU B 46 0 0.0 0.0 0.0 0.0 0.0 THR B 47 0 0.0 0.0 0.0 0.0 0.0 LYS B 48 0 0.0 0.0 0.0 0.0 0.0 ASN B 49 0 0.0 0.0 0.0 0.0 0.0 ALA B 50 0 0.0 0.0 0.0 0.0 0.0 VAL B 51 0 0.0 0.0 0.0 0.0 0.0 VAL B 52 0 0.0 0.0 0.0 0.0 0.0 LEU B 53 0 0.0 0.0 0.0 0.0 0.0 LYS B 54 0 0.0 0.0 0.0 0.0 0.0 ARG B 55 0 0.0 0.0 0.0 0.0 0.0 ILE B 56 0 0.0 0.0 0.0 0.0 0.0 GLN B 57 0 0.0 0.0 0.0 0.0 0.0 HIS B 58 0 0.0 0.0 0.0 0.0 0.0 LEU B 59 0 0.0 0.0 0.0 0.0 0.0 ASP B 60 0 0.0 0.0 0.0 0.0 0.0 GLU B 61 0 0.0 0.0 0.0 0.0 0.0 ALA B 62 0 0.0 0.0 0.0 0.0 0.0 TYR B 63 0 0.0 0.0 0.0 0.0 0.0 ASN B 64 0 0.0 0.0 0.0 0.0 0.0 LYS B 65 0 0.0 0.0 0.0 0.0 0.0 VAL B 66 0 0.0 0.0 0.0 0.0 0.0 LYS B 67 0 0.0 0.0 0.0 0.0 0.0 ARG B 68 0 0.0 0.0 0.0 0.0 0.0 GLY B 69 0 0.0 0.0 0.0 0.0 0.0 GLU B 70 0 0.0 0.0 0.0 0.0 0.0 SER B 71 0 0.0 0.0 0.0 0.0 0.0 LYS B 72 0 0.0 0.0 0.0 0.0 0.0 LEU B 73 0 0.0 0.0 0.0 0.0 0.0 GLU B 74 0 0.0 0.0 0.0 0.0 0.0 HIS B 75 0 0.0 0.0 0.0 0.0 0.0 HIS B 76 0 0.0 0.0 0.0 0.0 0.0 HIS B 77 0 0.0 0.0 0.0 0.0 0.0 HIS B 78 0 0.0 0.0 0.0 0.0 0.0 HIS B 79 0 0.0 0.0 0.0 0.0 0.0 HIS B 80 0 0.0 0.0 0.0 0.0 0.0 TOTAL 188 682.0 232.0 271.0 179.0 0.0 > ANALYZE_cns: Do you want a CONS.OUT file [default no] ?_