Running PDBSTAT from Linux Ayuda is on: /farm/software/PdbStat/PdbStat-5.9 (C) (C) Pdbstat -- A program to evaluate some statistics of macromolecules, (C) given the cartesian coordinates. (C) (C) (c) Copyright 1992-2013 Roberto Tejero and Gaetano T. Montelione (C) Center for Advanced Technology and Medicine (CABM) (C) Rutgers University (C) ** VERSION: 5.9-exp mar may 14 00:20:00 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 ...) 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 `CSR4_R3_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> EXPDTA NMR, 21 STRUCTURES > ReadCoordsPdb(): >> REMARK PdbStat -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > ReadCoordsPdb(): >> REMARK PdbStat -- PDB COORDINATES FOR 2JR2_R3EM.PDB, 20 MODEL/S 2JR2_R3EM.PDB > ReadCoordsPdb(): >> REMARK PdbStat -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > ReadCoordsPdb(): >> SEQRES 1 A 76 MET PRO ILE VAL SER LYS TYR SER ASN GLU ARG VAL GLU > ReadCoordsPdb(): Counting models in file `CSR4_R3_em_bcr3.pdb'; Model: > 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 CSR4_R3_em_bcr3.pdb MODEL 1 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 2448 ATOM records read from file > ReadCoordsPdb(): --> 2448 Regular IUPAC Atoms > ReadCoordsPdb(): --> 0 Pseudo-atoms (DISMAN type) > ReadCoordsPdb(): --> 0 Lone pairs > ReadCoordsPdb(): Bye ... > =============================== INFO ================================ > INFO_mol: # atoms: 2448 (762 C, 1242 H, 224 O, 214 N, 6 S, 0 Q, 0 Metals) > INFO_mol: # residues: 152 (Avg. mol. weight: 113.0) > INFO_mol: # -- M.W. : 17177.5 g/mol. (17.18 kD) Estimated RoG : 14.84 > INFO_mol: CenterMass() -- Working PDB model 1 in file, model no. 1 > INFO_mol: CenterMass() -- Molecule `CSR4_R3_em_bcr3.pdb' model #1, TOTAL RESIDUES: 152 > INFO_mol: Radius of Gyration : 16.1472 angstroms > INFO_mol: Center of Masses: x_cm(-0.662), y_cm(-0.408), z_cm(1.109) > INFO_res: MPIVSKYSNE RVEKIIQDLL DVLVKEEVTP DLALMCLGNA VTNIIAQVPE > INFO_res: SKRVAVVDNF TKALKQSVLE HHHHHHMPIV SKYSNERVEK IIQDLLDVLV > INFO_res: KEEVTPDLAL MCLGNAVTNI IAQVPESKRV AVVDNFTKAL KQSVLEHHHH > INFO_res: HH > INFO_res: > INFO_res: MET PRO ILE VAL SER LYS TYR SER ASN GLU ARG VAL > INFO_res: GLU LYS ILE ILE GLN ASP LEU LEU ASP VAL LEU VAL > INFO_res: LYS GLU GLU VAL THR PRO ASP LEU ALA LEU MET CYS > INFO_res: LEU GLY ASN ALA VAL THR ASN ILE ILE ALA GLN VAL > INFO_res: PRO GLU SER LYS ARG VAL ALA VAL VAL ASP ASN PHE > INFO_res: THR LYS ALA LEU LYS GLN SER VAL LEU GLU HIS HIS > INFO_res: HIS HIS HIS HIS MET PRO ILE VAL SER LYS TYR SER > INFO_res: ASN GLU ARG VAL GLU LYS ILE ILE GLN ASP LEU LEU > INFO_res: ASP VAL LEU VAL LYS GLU GLU VAL THR PRO ASP LEU > INFO_res: ALA LEU MET CYS LEU GLY ASN ALA VAL THR ASN ILE > INFO_res: ILE ALA GLN VAL PRO GLU SER LYS ARG VAL ALA VAL > INFO_res: VAL ASP ASN PHE THR LYS ALA LEU LYS GLN SER VAL > INFO_res: LEU GLU HIS HIS HIS HIS HIS HIS > INFO_res: > INFO_res: 10 ALA 4 ARG 8 ASN 8 ASP 2 CYS 6 GLN > INFO_res: 12 GLU 2 GLY 12 HIS 10 ILE 16 LEU 12 LYS > INFO_res: 4 MET 2 PHE 6 PRO 8 SER 6 THR 2 TYR > INFO_res: 22 VAL > INFO_res: DISULFIDE: ** NO INFO FOR DISULFIDES IN FILE > ===================================================================== > ReadCoordsPdb(): *** x-mer, 2 [2] chains PdbStat> > locate_file(): file `CSR4_R3_em_bcr3.upl' opened for reading 0 SANI-RDC constraints read 1384 NOE-distance constraints (0 Ambiguous NOE/s) read 1384 TOTAL constraints read PdbStat> -------------- SUMMARY OF RESTRAINTS --------------- TOTAL NUMBER OF NOE RESTRAINTS : 1384 INTRA-RESIDUE RESTRAINTS (I=J) : 0 SEQUENTIAL RESTRAINTS (I-J)=1 : 220 BACKBONE-BACKBONE : 92 BACKBONE-SIDE CHAIN : 72 SIDE CHAIN-SIDE CHAIN : 56 MEDIUM RANGE RESTRAINTS 1<(I-J)<5 : 774 BACKBONE-BACKBONE : 296 BACKBONE-SIDE CHAIN : 200 SIDE CHAIN-SIDE CHAIN : 278 LONG RANGE RESTRAINTS (I-J)>=5 : 390 TOTAL HYDROGEN BOND RESTRAINTS : 0 LONG RANGE H-BOND RESTR. (I-J)>=5 : 0 DISULFIDE RESTRAINTS : 0 INTRA-CHAIN RESTRAINTS : 1018 INTER-CHAIN RESTRAINTS : 366 AMBIGUOUS RESTRAINTS : 0 ----------------------------------------------------- ----------------------------------------------------- ----------------------------------------------------- RES # INTRA INTER seq med lng InterChain MET A 1 0 0.0 0.0 0.0 0.0 0.0 PRO A 2 0 0.0 0.0 0.0 0.0 0.0 ILE A 3 0 0.0 0.0 0.0 0.0 0.0 VAL A 4 0 0.0 0.0 0.0 0.0 0.0 SER A 5 0 1.0 0.0 1.0 0.0 0.0 LYS A 6 0 0.0 0.0 0.0 0.0 0.0 TYR A 7 0 10.0 0.5 1.5 8.0 5.5 SER A 8 0 6.0 1.0 5.0 0.0 0.0 ASN A 9 0 4.0 1.0 3.0 0.0 0.0 GLU A 10 0 4.0 1.0 3.0 0.0 0.0 ARG A 11 0 10.5 0.5 9.5 0.5 0.5 VAL A 12 0 14.0 1.0 5.5 7.5 5.0 GLU A 13 0 8.0 1.5 6.5 0.0 0.0 LYS A 14 0 7.0 1.5 5.5 0.0 0.0 ILE A 15 0 19.0 1.0 10.0 8.0 8.0 ILE A 16 0 15.0 0.0 6.5 8.5 8.5 GLN A 17 0 6.0 0.5 5.5 0.0 0.0 ASP A 18 0 10.5 1.0 9.5 0.0 2.5 LEU A 19 0 13.0 1.0 10.0 2.0 7.0 LEU A 20 0 13.5 1.5 6.5 5.5 5.5 ASP A 21 0 11.0 3.0 8.0 0.0 0.0 VAL A 22 0 15.5 4.0 10.5 1.0 6.5 LEU A 23 0 13.5 2.5 6.0 5.0 4.0 VAL A 24 0 6.0 1.0 5.0 0.0 0.0 LYS A 25 0 6.5 1.5 5.0 0.0 0.0 GLU A 26 0 9.5 2.0 5.0 2.5 2.5 GLU A 27 0 3.5 1.5 2.0 0.0 0.0 VAL A 28 0 10.5 1.0 6.0 3.5 1.5 THR A 29 0 9.0 4.0 4.0 1.0 1.0 PRO A 30 0 9.5 3.5 3.0 3.0 3.0 ASP A 31 0 4.5 1.0 3.5 0.0 0.0 LEU A 32 0 23.0 2.0 13.0 8.0 8.0 ALA A 33 0 14.5 2.5 5.5 6.5 3.5 LEU A 34 0 13.0 2.5 3.0 7.5 7.5 MET A 35 0 14.0 2.0 9.0 3.0 3.0 CYS A 36 0 12.5 1.5 5.0 6.0 6.0 LEU A 37 0 9.0 0.5 8.5 0.0 2.5 GLY A 38 0 10.0 1.0 5.0 4.0 4.5 ASN A 39 0 15.0 2.5 8.5 4.0 4.0 ALA A 40 0 13.0 3.0 5.5 4.5 5.5 VAL A 41 0 23.5 2.5 12.5 8.5 8.0 THR A 42 0 9.0 2.0 3.5 3.5 3.5 ASN A 43 0 6.5 1.0 3.5 2.0 2.0 ILE A 44 0 17.5 0.5 7.5 9.5 9.5 ILE A 45 0 24.5 2.0 6.5 16.0 5.0 ALA A 46 0 8.5 4.0 3.5 1.0 0.5 GLN A 47 0 11.0 3.5 6.5 1.0 1.0 VAL A 48 0 14.0 5.0 4.5 4.5 1.0 PRO A 49 0 8.5 4.0 4.5 0.0 0.0 GLU A 50 0 9.0 1.0 8.0 0.0 0.0 SER A 51 0 4.5 2.0 2.5 0.0 0.0 LYS A 52 0 10.0 1.5 8.5 0.0 0.0 ARG A 53 0 21.5 1.5 11.0 9.0 1.5 VAL A 54 0 8.0 3.0 3.5 1.5 1.0 ALA A 55 0 7.5 2.5 5.0 0.0 0.0 VAL A 56 0 9.5 1.0 5.5 3.0 0.0 VAL A 57 0 14.5 1.5 6.0 7.0 3.5 ASP A 58 0 9.0 1.5 6.5 1.0 1.0 ASN A 59 0 8.0 1.0 7.0 0.0 0.0 PHE A 60 0 23.5 2.5 11.0 10.0 11.0 THR A 61 0 13.0 3.0 10.0 0.0 4.5 LYS A 62 0 9.0 2.0 7.0 0.0 0.0 ALA A 63 0 5.0 1.0 4.0 0.0 0.0 LEU A 64 0 19.0 0.0 11.0 8.0 12.5 LYS A 65 0 8.5 0.0 6.0 2.5 4.5 GLN A 66 0 4.0 0.5 3.5 0.0 0.0 SER A 67 0 5.0 1.5 3.5 0.0 0.0 VAL A 68 0 9.0 1.0 2.0 6.0 6.0 LEU A 69 0 3.0 0.0 2.0 1.0 1.0 GLU A 70 0 2.5 1.0 1.5 0.0 0.0 HIS A 71 0 1.5 1.0 0.0 0.5 0.5 HIS A 72 0 0.0 0.0 0.0 0.0 0.0 HIS A 73 0 0.0 0.0 0.0 0.0 0.0 HIS A 74 0 0.0 0.0 0.0 0.0 0.0 HIS A 75 0 0.0 0.0 0.0 0.0 0.0 HIS A 76 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 PRO B 2 0 0.0 0.0 0.0 0.0 0.0 ILE B 3 0 0.0 0.0 0.0 0.0 0.0 VAL B 4 0 0.0 0.0 0.0 0.0 0.0 SER B 5 0 1.0 0.0 1.0 0.0 0.0 LYS B 6 0 0.0 0.0 0.0 0.0 0.0 TYR B 7 0 10.0 0.5 1.5 8.0 5.5 SER B 8 0 6.0 1.0 5.0 0.0 0.0 ASN B 9 0 4.0 1.0 3.0 0.0 0.0 GLU B 10 0 4.0 1.0 3.0 0.0 0.0 ARG B 11 0 10.5 0.5 9.5 0.5 0.5 VAL B 12 0 14.0 1.0 5.5 7.5 5.0 GLU B 13 0 8.0 1.5 6.5 0.0 0.0 LYS B 14 0 7.0 1.5 5.5 0.0 0.0 ILE B 15 0 19.0 1.0 10.0 8.0 8.0 ILE B 16 0 15.0 0.0 6.5 8.5 8.5 GLN B 17 0 6.0 0.5 5.5 0.0 0.0 ASP B 18 0 10.5 1.0 9.5 0.0 2.5 LEU B 19 0 13.0 1.0 10.0 2.0 7.0 LEU B 20 0 13.5 1.5 6.5 5.5 5.5 ASP B 21 0 11.0 3.0 8.0 0.0 0.0 VAL B 22 0 15.5 4.0 10.5 1.0 6.5 LEU B 23 0 13.5 2.5 6.0 5.0 4.0 VAL B 24 0 6.0 1.0 5.0 0.0 0.0 LYS B 25 0 6.5 1.5 5.0 0.0 0.0 GLU B 26 0 9.5 2.0 5.0 2.5 2.5 GLU B 27 0 3.5 1.5 2.0 0.0 0.0 VAL B 28 0 10.5 1.0 6.0 3.5 1.5 THR B 29 0 9.0 4.0 4.0 1.0 1.0 PRO B 30 0 9.5 3.5 3.0 3.0 3.0 ASP B 31 0 4.5 1.0 3.5 0.0 0.0 LEU B 32 0 23.0 2.0 13.0 8.0 8.0 ALA B 33 0 14.5 2.5 5.5 6.5 3.5 LEU B 34 0 13.0 2.5 3.0 7.5 7.5 MET B 35 0 14.0 2.0 9.0 3.0 3.0 CYS B 36 0 12.5 1.5 5.0 6.0 6.0 LEU B 37 0 9.0 0.5 8.5 0.0 2.5 GLY B 38 0 10.0 1.0 5.0 4.0 4.5 ASN B 39 0 15.0 2.5 8.5 4.0 4.0 ALA B 40 0 13.0 3.0 5.5 4.5 5.5 VAL B 41 0 23.5 2.5 12.5 8.5 8.0 THR B 42 0 9.0 2.0 3.5 3.5 3.5 ASN B 43 0 6.5 1.0 3.5 2.0 2.0 ILE B 44 0 17.5 0.5 7.5 9.5 9.5 ILE B 45 0 24.5 2.0 6.5 16.0 5.0 ALA B 46 0 8.5 4.0 3.5 1.0 0.5 GLN B 47 0 11.0 3.5 6.5 1.0 1.0 VAL B 48 0 14.0 5.0 4.5 4.5 1.0 PRO B 49 0 8.5 4.0 4.5 0.0 0.0 GLU B 50 0 9.0 1.0 8.0 0.0 0.0 SER B 51 0 4.5 2.0 2.5 0.0 0.0 LYS B 52 0 10.0 1.5 8.5 0.0 0.0 ARG B 53 0 21.5 1.5 11.0 9.0 1.5 VAL B 54 0 8.0 3.0 3.5 1.5 1.0 ALA B 55 0 7.5 2.5 5.0 0.0 0.0 VAL B 56 0 9.5 1.0 5.5 3.0 0.0 VAL B 57 0 14.5 1.5 6.0 7.0 3.5 ASP B 58 0 9.0 1.5 6.5 1.0 1.0 ASN B 59 0 8.0 1.0 7.0 0.0 0.0 PHE B 60 0 23.5 2.5 11.0 10.0 11.0 THR B 61 0 13.0 3.0 10.0 0.0 4.5 LYS B 62 0 9.0 2.0 7.0 0.0 0.0 ALA B 63 0 5.0 1.0 4.0 0.0 0.0 LEU B 64 0 19.0 0.0 11.0 8.0 12.5 LYS B 65 0 8.5 0.0 6.0 2.5 4.5 GLN B 66 0 4.0 0.5 3.5 0.0 0.0 SER B 67 0 5.0 1.5 3.5 0.0 0.0 VAL B 68 0 9.0 1.0 2.0 6.0 6.0 LEU B 69 0 3.0 0.0 2.0 1.0 1.0 GLU B 70 0 2.5 1.0 1.5 0.0 0.0 HIS B 71 0 1.5 1.0 0.0 0.5 0.5 HIS B 72 0 0.0 0.0 0.0 0.0 0.0 HIS B 73 0 0.0 0.0 0.0 0.0 0.0 HIS 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 TOTAL 0 1384.0 220.0 774.0 390.0 366.0 > ANALYZE_cns: Do you want a CONS.OUT file [default no] ?_