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 `OR8C_NMR_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> HEADER ANTIVIRAL PROTEIN 29-JUN-09 2KKZ > ReadCoordsPdb(): >> TITLE SOLUTION NMR STRUCTURE OF THE MONOMERIC W187R MUTANT OF > ReadCoordsPdb(): >> TITLE 2 A/UDORN NS1 EFFECTOR DOMAIN. NORTHEAST STRUCTURAL GENOMICS > ReadCoordsPdb(): >> TITLE 3 TARGET OR8C[W187R]. > ReadCoordsPdb(): >> COMPND MOL_ID: 1; 1 > ReadCoordsPdb(): Counting models in file `OR8C_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 OR8C_NMR_em_bcr3.pdb MODEL 1 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 2137 ATOM records read from file > ReadCoordsPdb(): --> 2137 Regular IUPAC Atoms > ReadCoordsPdb(): --> 0 Pseudo-atoms (DISMAN type) > ReadCoordsPdb(): --> 0 Lone pairs > ReadCoordsPdb(): Bye ... > =============================== INFO ================================ > INFO_mol: # atoms: 2137 (672 C, 1080 H, 197 O, 181 N, 7 S, 0 Q, 0 Metals) > INFO_mol: # residues: 134 (Avg. mol. weight: 112.5) > INFO_mol: # -- M.W. : 15071.2 g/mol. (15.07 kD) Estimated RoG : 14.15 > INFO_mol: CenterMass() -- Working PDB model 1 in file, model no. 1 > INFO_mol: CenterMass() -- Molecule `OR8C_NMR_em_bcr3.pdb' model #1, TOTAL RESIDUES: 134 > INFO_mol: Radius of Gyration : 14.8547 angstroms > INFO_mol: Center of Masses: x_cm(-0.622), y_cm(0.347), z_cm(1.067) > INFO_res: MPASRYITDM TIEELSRDWF MLMPKQKVEG PLCIRIDQAI MDKNIMLKAN > INFO_res: FSVIFDRLET LILLRAFTEE GAIVGEISPL PSFPGHTIED VKNAIGVLIG > INFO_res: GLERNDNTVR VSKTLQRFAW GSSNENGRPP LTLE > INFO_res: > INFO_res: MET PRO ALA SER ARG TYR ILE THR ASP MET THR ILE > INFO_res: GLU GLU LEU SER ARG ASP TRP PHE MET LEU MET PRO > INFO_res: LYS GLN LYS VAL GLU GLY PRO LEU CYS ILE ARG ILE > INFO_res: ASP GLN ALA ILE MET ASP LYS ASN ILE MET LEU LYS > INFO_res: ALA ASN PHE SER VAL ILE PHE ASP ARG LEU GLU THR > INFO_res: LEU ILE LEU LEU ARG ALA PHE THR GLU GLU GLY ALA > INFO_res: ILE VAL GLY GLU ILE SER PRO LEU PRO SER PHE PRO > INFO_res: GLY HIS THR ILE GLU ASP VAL LYS ASN ALA ILE GLY > INFO_res: VAL LEU ILE GLY GLY LEU GLU ARG ASN ASP ASN THR > INFO_res: VAL ARG VAL SER LYS THR LEU GLN ARG PHE ALA TRP > INFO_res: GLY SER SER ASN GLU ASN GLY ARG PRO PRO LEU THR > INFO_res: LEU GLU > INFO_res: > INFO_res: 7 ALA 9 ARG 7 ASN 7 ASP 1 CYS 3 GLN > INFO_res: 11 GLU 9 GLY 1 HIS 13 ILE 14 LEU 6 LYS > INFO_res: 6 MET 6 PHE 8 PRO 8 SER 8 THR 1 TYR > INFO_res: 2 TRP 7 VAL > INFO_res: DISULFIDE: ** NO INFO FOR DISULFIDES IN FILE > ===================================================================== > ReadCoordsPdb(): *** monomer, 1 [1] chains *** PdbStat> > locate_file(): file `OR8C_NMR_em_bcr3.upl' opened for reading 0 SANI-RDC constraints read 2261 NOE-distance constraints (0 Ambiguous NOE/s) read 2261 TOTAL constraints read PdbStat> -------------- SUMMARY OF RESTRAINTS --------------- TOTAL NUMBER OF NOE RESTRAINTS : 2261 INTRA-RESIDUE RESTRAINTS (I=J) : 615 SEQUENTIAL RESTRAINTS (I-J)=1 : 620 BACKBONE-BACKBONE : 134 BACKBONE-SIDE CHAIN : 81 SIDE CHAIN-SIDE CHAIN : 405 MEDIUM RANGE RESTRAINTS 1<(I-J)<5 : 297 BACKBONE-BACKBONE : 59 BACKBONE-SIDE CHAIN : 51 SIDE CHAIN-SIDE CHAIN : 187 LONG RANGE RESTRAINTS (I-J)>=5 : 729 TOTAL HYDROGEN BOND RESTRAINTS : 0 LONG RANGE H-BOND RESTR. (I-J)>=5 : 0 DISULFIDE RESTRAINTS : 0 INTRA-CHAIN RESTRAINTS : 2261 INTER-CHAIN RESTRAINTS : 0 AMBIGUOUS RESTRAINTS : 0 ----------------------------------------------------- ----------------------------------------------------- ----------------------------------------------------- RES # INTRA INTER seq med lng InterChain MET A 1 1 0.0 0.0 0.0 0.0 0.0 PRO A 2 0 2.0 0.0 0.0 2.0 0.0 ALA A 3 0 2.0 1.5 0.0 0.5 0.0 SER A 4 0 6.5 2.5 0.0 4.0 0.0 ARG A 5 11 13.5 5.0 1.5 7.0 0.0 TYR A 6 3 13.5 7.0 1.0 5.5 0.0 ILE A 7 9 21.0 6.5 2.0 12.5 0.0 THR A 8 2 12.0 5.0 2.5 4.5 0.0 ASP A 9 0 9.0 4.5 0.5 4.0 0.0 MET A 10 4 21.0 4.0 2.0 15.0 0.0 THR A 11 2 7.5 3.5 4.0 0.0 0.0 ILE A 12 15 11.5 5.5 6.0 0.0 0.0 GLU A 13 6 7.5 6.0 1.5 0.0 0.0 GLU A 14 4 10.0 5.0 3.5 1.5 0.0 LEU A 15 9 15.5 5.0 4.5 6.0 0.0 SER A 16 3 8.0 5.5 2.5 0.0 0.0 ARG A 17 12 13.0 7.0 1.5 4.5 0.0 ASP A 18 1 7.5 7.0 0.0 0.5 0.0 TRP A 19 2 13.5 5.5 2.0 6.0 0.0 PHE A 20 2 7.5 6.0 1.5 0.0 0.0 MET A 21 6 9.0 3.0 3.0 3.0 0.0 LEU A 22 10 12.5 8.0 1.5 3.0 0.0 MET A 23 5 21.5 9.5 0.0 12.0 0.0 PRO A 24 0 4.0 2.5 1.5 0.0 0.0 LYS A 25 10 15.0 4.5 1.5 9.0 0.0 GLN A 26 8 10.0 6.5 3.5 0.0 0.0 LYS A 27 11 16.0 6.0 2.0 8.0 0.0 VAL A 28 4 12.5 4.5 4.5 3.5 0.0 GLU A 29 2 14.0 4.0 2.0 8.0 0.0 GLY A 30 0 4.0 3.5 0.5 0.0 0.0 PRO A 31 0 7.0 1.0 0.0 6.0 0.0 LEU A 32 9 15.5 2.0 1.0 12.5 0.0 CYS A 33 1 13.5 6.0 0.5 7.0 0.0 ILE A 34 9 19.5 5.0 0.0 14.5 0.0 ARG A 35 4 8.5 3.0 0.0 5.5 0.0 ILE A 36 7 19.5 5.0 3.0 11.5 0.0 ASP A 37 0 10.5 4.5 3.0 3.0 0.0 GLN A 38 4 19.5 4.5 3.0 12.0 0.0 ALA A 39 1 16.0 6.0 0.5 9.5 0.0 ILE A 40 10 20.0 6.5 7.5 6.0 0.0 MET A 41 7 15.5 7.0 1.5 7.0 0.0 ASP A 42 1 9.5 6.0 0.0 3.5 0.0 LYS A 43 10 14.0 6.0 6.5 1.5 0.0 ASN A 44 7 14.5 7.5 0.0 7.0 0.0 ILE A 45 9 27.5 9.0 1.5 17.0 0.0 MET A 46 9 18.0 9.5 2.5 6.0 0.0 LEU A 47 8 12.5 6.0 0.5 6.0 0.0 LYS A 48 4 11.5 3.5 2.5 5.5 0.0 ALA A 49 0 15.0 3.0 0.5 11.5 0.0 ASN A 50 0 22.0 4.5 0.0 17.5 0.0 PHE A 51 2 29.0 5.0 2.0 22.0 0.0 SER A 52 0 12.0 4.5 0.0 7.5 0.0 VAL A 53 5 26.0 6.0 5.0 15.0 0.0 ILE A 54 9 31.0 13.0 3.5 14.5 0.0 PHE A 55 3 14.5 12.5 2.0 0.0 0.0 ASP A 56 0 7.5 4.5 3.0 0.0 0.0 ARG A 57 12 18.5 4.5 5.5 8.5 0.0 LEU A 58 5 25.5 5.0 3.5 17.0 0.0 GLU A 59 5 15.5 6.0 0.0 9.5 0.0 THR A 60 3 8.0 3.5 2.5 2.0 0.0 LEU A 61 8 12.0 1.0 5.5 5.5 0.0 ILE A 62 11 17.5 3.5 0.5 13.5 0.0 LEU A 63 7 21.5 4.5 3.5 13.5 0.0 LEU A 64 9 19.0 4.5 2.5 12.0 0.0 ARG A 65 2 14.5 4.5 3.5 6.5 0.0 ALA A 66 0 9.0 4.0 0.5 4.5 0.0 PHE A 67 2 18.0 5.0 2.0 11.0 0.0 THR A 68 2 18.5 5.0 4.0 9.5 0.0 GLU A 69 5 9.5 4.5 0.5 4.5 0.0 GLU A 70 7 7.0 4.0 3.0 0.0 0.0 GLY A 71 0 4.5 2.5 2.0 0.0 0.0 ALA A 72 1 7.0 1.0 5.0 1.0 0.0 ILE A 73 2 16.0 1.5 1.0 13.5 0.0 VAL A 74 4 14.0 3.5 1.0 9.5 0.0 GLY A 75 0 8.0 2.5 1.0 4.5 0.0 GLU A 76 2 15.5 2.5 2.0 11.0 0.0 ILE A 77 9 16.0 3.5 0.0 12.5 0.0 SER A 78 0 9.0 3.0 2.0 4.0 0.0 PRO A 79 0 8.0 2.0 0.0 6.0 0.0 LEU A 80 10 12.5 3.0 2.5 7.0 0.0 PRO A 81 0 3.0 3.0 0.0 0.0 0.0 SER A 82 0 2.5 2.5 0.0 0.0 0.0 PHE A 83 2 12.5 5.5 3.5 3.5 0.0 PRO A 84 0 7.5 7.5 0.0 0.0 0.0 GLY A 85 0 6.0 5.0 1.0 0.0 0.0 HIS A 86 0 6.5 1.5 0.0 5.0 0.0 THR A 87 2 8.5 2.5 6.0 0.0 0.0 ILE A 88 10 23.0 5.5 3.0 14.5 0.0 GLU A 89 6 11.0 7.0 4.0 0.0 0.0 ASP A 90 1 11.5 5.5 4.5 1.5 0.0 VAL A 91 5 16.5 5.0 6.5 5.0 0.0 LYS A 92 13 12.5 7.0 4.0 1.5 0.0 ASN A 93 8 11.0 7.0 2.0 2.0 0.0 ALA A 94 1 19.0 5.5 6.0 7.5 0.0 ILE A 95 15 20.5 6.5 8.0 6.0 0.0 GLY A 96 0 12.5 5.0 3.5 4.0 0.0 VAL A 97 5 17.0 3.5 4.0 9.5 0.0 LEU A 98 11 17.0 6.0 4.5 6.5 0.0 ILE A 99 12 20.0 6.5 9.0 4.5 0.0 GLY A 100 0 5.0 3.5 1.5 0.0 0.0 GLY A 101 0 4.0 0.5 1.0 2.5 0.0 LEU A 102 10 18.0 1.5 5.5 11.0 0.0 GLU A 103 9 10.5 3.0 6.0 1.5 0.0 ARG A 104 14 7.5 5.0 2.5 0.0 0.0 ASN A 105 3 21.0 6.0 5.5 9.5 0.0 ASP A 106 2 8.0 4.0 1.5 2.5 0.0 ASN A 107 4 22.5 4.0 5.0 13.5 0.0 THR A 108 3 11.5 6.0 0.0 5.5 0.0 VAL A 109 5 13.0 6.5 0.5 6.0 0.0 ARG A 110 6 9.0 6.5 0.0 2.5 0.0 VAL A 111 5 21.5 6.0 2.0 13.5 0.0 SER A 112 1 9.0 4.0 1.5 3.5 0.0 LYS A 113 19 5.5 5.0 0.0 0.5 0.0 THR A 114 2 18.0 6.0 7.5 4.5 0.0 LEU A 115 10 20.0 5.0 6.5 8.5 0.0 GLN A 116 10 16.0 4.5 5.5 6.0 0.0 ARG A 117 12 10.5 8.0 2.5 0.0 0.0 PHE A 118 4 26.0 8.0 6.0 12.0 0.0 ALA A 119 0 12.5 4.0 2.5 6.0 0.0 TRP A 120 8 20.5 3.0 4.0 13.5 0.0 GLY A 121 0 2.0 1.0 1.0 0.0 0.0 SER A 122 0 1.5 1.5 0.0 0.0 0.0 SER A 123 0 3.0 3.0 0.0 0.0 0.0 ASN A 124 1 1.5 1.5 0.0 0.0 0.0 GLU A 125 0 0.0 0.0 0.0 0.0 0.0 ASN A 126 0 0.5 0.5 0.0 0.0 0.0 GLY A 127 0 1.5 1.5 0.0 0.0 0.0 ARG A 128 8 3.5 3.5 0.0 0.0 0.0 PRO A 129 0 5.0 5.0 0.0 0.0 0.0 PRO A 130 0 5.0 5.0 0.0 0.0 0.0 LEU A 131 8 5.5 5.5 0.0 0.0 0.0 THR A 132 2 6.5 6.5 0.0 0.0 0.0 LEU A 133 5 6.0 6.0 0.0 0.0 0.0 GLU A 134 6 2.5 2.5 0.0 0.0 0.0 TOTAL 615 1646.0 620.0 297.0 729.0 0.0 > ANALYZE_cns: Do you want a CONS.OUT file [default no] ?_