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 `HR4527E_NMR_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> HEADER TRANSCRIPTION REGULATOR 03-SEP-10 2L33 > ReadCoordsPdb(): >> TITLE SOLUTION NMR STRUCTURE OF DRBM 2 DOMAIN OF INTERLEUKIN ENHANCER- > ReadCoordsPdb(): >> TITLE 2 BINDING FACTOR 3 FROM HOMO SAPIENS, NORTHEAST STRUCTURAL GENOMICS > ReadCoordsPdb(): >> TITLE 3 CONSORTIUM TARGET HR4527E > ReadCoordsPdb(): >> COMPND MOL_ID: 1; 1 > ReadCoordsPdb(): Counting models in file `HR4527E_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 HR4527E_NMR_em_bcr3.pdb MODEL 1 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 1436 ATOM records read from file > ReadCoordsPdb(): --> 1436 Regular IUPAC Atoms > ReadCoordsPdb(): --> 0 Pseudo-atoms (DISMAN type) > ReadCoordsPdb(): --> 0 Lone pairs > ReadCoordsPdb(): Bye ... > =============================== INFO ================================ > INFO_mol: # atoms: 1436 (447 C, 721 H, 129 O, 135 N, 4 S, 0 Q, 0 Metals) > INFO_mol: # residues: 91 (Avg. mol. weight: 111.9) > INFO_mol: # -- M.W. : 10178.5 g/mol. (10.18 kD) Estimated RoG : 12.21 > INFO_mol: CenterMass() -- Working PDB model 1 in file, model no. 1 > INFO_mol: CenterMass() -- Molecule `HR4527E_NMR_em_bcr3.pdb' model #1, TOTAL RESIDUES: 91 > INFO_mol: Radius of Gyration : 15.5690 angstroms > INFO_mol: Center of Masses: x_cm(0.818), y_cm(4.110), z_cm(2.131) > INFO_res: MGHHHHHHSH MLTKHGKNPV MELNEKRRGL KYELISETGG SHDKRFVMEV > INFO_res: EVDGQKFQGA GSNKKVAKAY AALAALEKLF PDTPLALDAN K > INFO_res: > INFO_res: MET GLY HIS HIS HIS HIS HIS HIS SER HIS MET LEU > INFO_res: THR LYS HIS GLY LYS ASN PRO VAL MET GLU LEU ASN > INFO_res: GLU LYS ARG ARG GLY LEU LYS TYR GLU LEU ILE SER > INFO_res: GLU THR GLY GLY SER HIS ASP LYS ARG PHE VAL MET > INFO_res: GLU VAL GLU VAL ASP GLY GLN LYS PHE GLN GLY ALA > INFO_res: GLY SER ASN LYS LYS VAL ALA LYS ALA TYR ALA ALA > INFO_res: LEU ALA ALA LEU GLU LYS LEU PHE PRO ASP THR PRO > INFO_res: LEU ALA LEU ASP ALA ASN LYS > INFO_res: > INFO_res: 9 ALA 3 ARG 4 ASN 4 ASP 2 GLN 7 GLU > INFO_res: 8 GLY 9 HIS 1 ILE 9 LEU 11 LYS 4 MET > INFO_res: 3 PHE 3 PRO 4 SER 3 THR 2 TYR 5 VAL > INFO_res: DISULFIDE: ** NO INFO FOR DISULFIDES IN FILE > ===================================================================== > ReadCoordsPdb(): *** monomer, 1 [1] chains *** PdbStat> > locate_file(): file `HR4527E_NMR_em_bcr3.upl' opened for reading 0 SANI-RDC constraints read 2481 NOE-distance constraints (0 Ambiguous NOE/s) read 2481 TOTAL constraints read PdbStat> -------------- SUMMARY OF RESTRAINTS --------------- TOTAL NUMBER OF NOE RESTRAINTS : 2481 INTRA-RESIDUE RESTRAINTS (I=J) : 559 SEQUENTIAL RESTRAINTS (I-J)=1 : 599 BACKBONE-BACKBONE : 108 BACKBONE-SIDE CHAIN : 104 SIDE CHAIN-SIDE CHAIN : 387 MEDIUM RANGE RESTRAINTS 1<(I-J)<5 : 469 BACKBONE-BACKBONE : 105 BACKBONE-SIDE CHAIN : 101 SIDE CHAIN-SIDE CHAIN : 263 LONG RANGE RESTRAINTS (I-J)>=5 : 854 TOTAL HYDROGEN BOND RESTRAINTS : 0 LONG RANGE H-BOND RESTR. (I-J)>=5 : 0 DISULFIDE RESTRAINTS : 0 INTRA-CHAIN RESTRAINTS : 2481 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 GLY A 2 0 0.0 0.0 0.0 0.0 0.0 HIS A 3 0 0.0 0.0 0.0 0.0 0.0 HIS A 4 0 0.0 0.0 0.0 0.0 0.0 HIS A 5 0 0.0 0.0 0.0 0.0 0.0 HIS A 6 0 0.0 0.0 0.0 0.0 0.0 HIS A 7 0 0.0 0.0 0.0 0.0 0.0 HIS A 8 0 0.0 0.0 0.0 0.0 0.0 SER A 9 0 0.0 0.0 0.0 0.0 0.0 HIS A 10 1 5.0 2.0 3.0 0.0 0.0 MET A 11 10 14.0 7.5 0.0 6.5 0.0 LEU A 12 10 26.5 11.0 8.0 7.5 0.0 THR A 13 2 18.5 6.5 1.5 10.5 0.0 LYS A 14 13 4.0 4.0 0.0 0.0 0.0 HIS A 15 1 6.5 4.5 2.0 0.0 0.0 GLY A 16 0 8.0 3.0 5.0 0.0 0.0 LYS A 17 23 16.0 6.5 4.5 5.0 0.0 ASN A 18 5 23.5 9.5 11.0 3.0 0.0 PRO A 19 0 41.5 9.0 4.5 28.0 0.0 VAL A 20 5 40.0 12.0 11.5 16.5 0.0 MET A 21 10 26.0 11.5 14.5 0.0 0.0 GLU A 22 8 32.5 7.0 13.0 12.5 0.0 LEU A 23 12 35.5 6.5 12.5 16.5 0.0 ASN A 24 7 19.0 6.5 9.0 3.5 0.0 GLU A 25 7 14.0 8.5 5.5 0.0 0.0 LYS A 26 29 28.5 8.5 9.5 10.5 0.0 ARG A 27 12 30.0 8.5 7.5 14.0 0.0 ARG A 28 8 13.0 11.0 2.0 0.0 0.0 GLY A 29 0 9.0 9.0 0.0 0.0 0.0 LEU A 30 8 31.5 9.0 9.0 13.5 0.0 LYS A 31 15 18.5 11.5 4.0 3.0 0.0 TYR A 32 6 47.0 10.0 2.5 34.5 0.0 GLU A 33 5 21.0 9.0 7.0 5.0 0.0 LEU A 34 11 38.5 12.5 7.0 19.0 0.0 ILE A 35 11 46.5 14.0 3.0 29.5 0.0 SER A 36 1 19.0 9.5 3.0 6.5 0.0 GLU A 37 5 15.5 7.5 3.5 4.5 0.0 THR A 38 2 13.5 7.0 0.5 6.0 0.0 GLY A 39 0 3.5 3.0 0.0 0.5 0.0 GLY A 40 0 2.0 0.5 1.5 0.0 0.0 SER A 41 0 0.0 0.0 0.0 0.0 0.0 HIS A 42 1 2.5 2.5 0.0 0.0 0.0 ASP A 43 0 5.5 5.0 0.5 0.0 0.0 LYS A 44 29 14.0 2.5 8.5 3.0 0.0 ARG A 45 4 6.5 0.0 1.0 5.5 0.0 PHE A 46 2 35.0 3.0 8.0 24.0 0.0 VAL A 47 4 35.0 6.5 2.0 26.5 0.0 MET A 48 11 61.5 7.0 0.5 54.0 0.0 GLU A 49 6 46.5 10.5 1.0 35.0 0.0 VAL A 50 5 48.5 11.0 3.5 34.0 0.0 GLU A 51 9 40.5 10.0 6.5 24.0 0.0 VAL A 52 4 41.0 9.5 11.5 20.0 0.0 ASP A 53 2 17.0 6.0 5.0 6.0 0.0 GLY A 54 0 12.0 5.5 6.5 0.0 0.0 GLN A 55 14 29.5 8.0 16.0 5.5 0.0 LYS A 56 20 37.5 10.0 4.0 23.5 0.0 PHE A 57 5 58.5 8.5 5.5 44.5 0.0 GLN A 58 15 39.0 7.5 2.0 29.5 0.0 GLY A 59 0 21.5 8.0 0.0 13.5 0.0 ALA A 60 1 20.5 7.5 0.5 12.5 0.0 GLY A 61 0 16.0 4.0 1.5 10.5 0.0 SER A 62 0 4.0 1.5 1.5 1.0 0.0 ASN A 63 4 20.5 3.0 14.0 3.5 0.0 LYS A 64 20 27.5 6.0 2.5 19.0 0.0 LYS A 65 31 20.0 10.5 8.0 1.5 0.0 VAL A 66 5 34.5 10.5 19.5 4.5 0.0 ALA A 67 1 31.0 5.5 9.0 16.5 0.0 LYS A 68 23 47.5 4.5 9.5 33.5 0.0 ALA A 69 1 25.0 6.5 9.5 9.0 0.0 TYR A 70 6 38.0 8.0 18.0 12.0 0.0 ALA A 71 1 39.0 6.0 10.0 23.0 0.0 ALA A 72 1 30.5 3.5 9.5 17.5 0.0 LEU A 73 11 37.5 6.0 20.0 11.5 0.0 ALA A 74 1 24.0 7.0 12.0 5.0 0.0 ALA A 75 1 27.5 7.0 11.0 9.5 0.0 LEU A 76 12 44.0 8.5 18.0 17.5 0.0 GLU A 77 6 19.0 7.0 11.5 0.5 0.0 LYS A 78 19 30.5 14.5 7.0 9.0 0.0 LEU A 79 12 44.5 21.5 6.0 17.0 0.0 PHE A 80 6 42.0 14.0 12.5 15.5 0.0 PRO A 81 0 14.0 9.0 5.0 0.0 0.0 ASP A 82 2 7.5 7.0 0.5 0.0 0.0 THR A 83 3 12.5 9.5 3.0 0.0 0.0 PRO A 84 0 11.0 11.0 0.0 0.0 0.0 LEU A 85 10 9.0 8.0 1.0 0.0 0.0 ALA A 86 1 6.5 6.0 0.5 0.0 0.0 LEU A 87 11 6.5 6.5 0.0 0.0 0.0 ASP A 88 3 7.5 7.0 0.5 0.0 0.0 ALA A 89 1 3.5 3.5 0.0 0.0 0.0 ASN A 90 2 1.5 1.5 0.0 0.0 0.0 LYS A 91 6 0.5 0.5 0.0 0.0 0.0 TOTAL 559 1922.0 599.0 469.0 854.0 0.0 > ANALYZE_cns: Do you want a CONS.OUT file [default no] ?_