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 `HR4435B_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 83 MET GLY HIS HIS HIS HIS HIS HIS SER HIS MET LEU PRO 1 > ReadCoordsPdb(): Counting models in file `HR4435B_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 HR4435B_R3_em_bcr3.pdb MODEL 1 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 1332 ATOM records read from file > ReadCoordsPdb(): --> 1332 Regular IUPAC Atoms > ReadCoordsPdb(): --> 0 Pseudo-atoms (DISMAN type) > ReadCoordsPdb(): --> 0 Lone pairs > ReadCoordsPdb(): Bye ... > =============================== INFO ================================ > INFO_mol: # atoms: 1332 (423 C, 655 H, 121 O, 125 N, 8 S, 0 Q, 0 Metals) > INFO_mol: # residues: 83 (Avg. mol. weight: 116.7) > INFO_mol: # -- M.W. : 9684.0 g/mol. (9.68 kD) Estimated RoG : 11.79 > INFO_mol: CenterMass() -- Working PDB model 1 in file, model no. 1 > INFO_mol: CenterMass() -- Molecule `HR4435B_R3_em_bcr3.pdb' model #1, TOTAL RESIDUES: 83 > INFO_mol: Radius of Gyration : 12.4415 angstroms > INFO_mol: Center of Masses: x_cm(2.918), y_cm(1.724), z_cm(-0.205) > INFO_res: MGHHHHHHSH MLPPEQWSHT TVRNALKDLL KDMNQSSLAK ECPLSQSMIS > INFO_res: SIVNSTYYAN VSAAKCQEFG RWYKHFKKTK DMM > INFO_res: > INFO_res: MET GLY HIS HIS HIS HIS HIS HIS SER HIS MET LEU > INFO_res: PRO PRO GLU GLN TRP SER HIS THR THR VAL ARG ASN > INFO_res: ALA LEU LYS ASP LEU LEU LYS ASP MET ASN GLN SER > INFO_res: SER LEU ALA LYS GLU CYS PRO LEU SER GLN SER MET > INFO_res: ILE SER SER ILE VAL ASN SER THR TYR TYR ALA ASN > INFO_res: VAL SER ALA ALA LYS CYS GLN GLU PHE GLY ARG TRP > INFO_res: TYR LYS HIS PHE LYS LYS THR LYS ASP MET MET > INFO_res: > INFO_res: 5 ALA 2 ARG 4 ASN 3 ASP 2 CYS 4 GLN > INFO_res: 3 GLU 2 GLY 9 HIS 2 ILE 6 LEU 8 LYS > INFO_res: 6 MET 2 PHE 3 PRO 10 SER 4 THR 3 TYR > INFO_res: 2 TRP 3 VAL > INFO_res: DISULFIDE: ** NO INFO FOR DISULFIDES IN FILE > ===================================================================== > ReadCoordsPdb(): *** monomer, 1 [1] chains *** PdbStat> > locate_file(): file `HR4435B_R3_em_bcr3.upl' opened for reading 0 SANI-RDC constraints read 712 NOE-distance constraints (0 Ambiguous NOE/s) read 712 TOTAL constraints read PdbStat> -------------- SUMMARY OF RESTRAINTS --------------- TOTAL NUMBER OF NOE RESTRAINTS : 712 INTRA-RESIDUE RESTRAINTS (I=J) : 80 SEQUENTIAL RESTRAINTS (I-J)=1 : 245 BACKBONE-BACKBONE : 62 BACKBONE-SIDE CHAIN : 13 SIDE CHAIN-SIDE CHAIN : 170 MEDIUM RANGE RESTRAINTS 1<(I-J)<5 : 236 BACKBONE-BACKBONE : 74 BACKBONE-SIDE CHAIN : 73 SIDE CHAIN-SIDE CHAIN : 89 LONG RANGE RESTRAINTS (I-J)>=5 : 151 TOTAL HYDROGEN BOND RESTRAINTS : 0 LONG RANGE H-BOND RESTR. (I-J)>=5 : 0 DISULFIDE RESTRAINTS : 0 INTRA-CHAIN RESTRAINTS : 712 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 0 0.0 0.0 0.0 0.0 0.0 MET A 11 0 0.0 0.0 0.0 0.0 0.0 LEU A 12 1 3.0 1.0 0.0 2.0 0.0 PRO A 13 0 2.0 2.0 0.0 0.0 0.0 PRO A 14 0 3.5 2.0 1.5 0.0 0.0 GLU A 15 0 1.5 1.5 0.0 0.0 0.0 GLN A 16 0 3.0 2.5 0.5 0.0 0.0 TRP A 17 3 13.0 3.0 3.5 6.5 0.0 SER A 18 0 4.0 1.0 3.0 0.0 0.0 HIS A 19 1 3.0 1.0 1.0 1.0 0.0 THR A 20 0 7.0 3.0 4.0 0.0 0.0 THR A 21 0 10.0 4.0 6.0 0.0 0.0 VAL A 22 0 21.0 4.5 5.5 11.0 0.0 ARG A 23 1 13.0 4.5 5.5 3.0 0.0 ASN A 24 1 6.5 3.0 3.5 0.0 0.0 ALA A 25 0 8.5 2.0 4.5 2.0 0.0 LEU A 26 0 25.5 3.5 12.5 9.5 0.0 LYS A 27 2 9.0 5.0 4.0 0.0 0.0 ASP A 28 0 7.5 4.0 3.5 0.0 0.0 LEU A 29 1 12.5 3.5 6.5 2.5 0.0 LEU A 30 1 15.0 3.5 5.5 6.0 0.0 LYS A 31 6 5.5 2.5 3.0 0.0 0.0 ASP A 32 0 5.0 4.0 1.0 0.0 0.0 MET A 33 5 13.5 6.5 3.0 4.0 0.0 ASN A 34 0 7.5 5.0 2.5 0.0 0.0 GLN A 35 1 13.0 2.5 2.5 8.0 0.0 SER A 36 0 5.5 2.0 2.5 1.0 0.0 SER A 37 1 6.0 2.0 4.0 0.0 0.0 LEU A 38 1 21.0 4.5 3.0 13.5 0.0 ALA A 39 0 12.5 4.5 4.5 3.5 0.0 LYS A 40 3 3.5 1.5 2.0 0.0 0.0 GLU A 41 0 5.5 2.5 1.0 2.0 0.0 CYS A 42 0 8.0 3.5 2.5 2.0 0.0 PRO A 43 0 10.5 5.5 0.0 5.0 0.0 LEU A 44 0 22.0 6.0 3.5 12.5 0.0 SER A 45 0 6.5 3.0 3.0 0.5 0.0 GLN A 46 0 12.5 3.0 5.0 4.5 0.0 SER A 47 0 4.0 2.5 1.5 0.0 0.0 MET A 48 4 14.5 3.5 11.0 0.0 0.0 ILE A 49 2 23.5 6.5 8.0 9.0 0.0 SER A 50 0 11.0 4.5 5.5 1.0 0.0 SER A 51 0 9.5 4.0 5.5 0.0 0.0 ILE A 52 0 15.0 6.0 4.0 5.0 0.0 VAL A 53 0 12.5 6.0 6.0 0.5 0.0 ASN A 54 0 6.0 4.0 2.0 0.0 0.0 SER A 55 0 4.5 2.0 2.5 0.0 0.0 THR A 56 0 3.5 3.0 0.5 0.0 0.0 TYR A 57 2 5.5 4.5 1.0 0.0 0.0 TYR A 58 2 4.5 3.5 0.5 0.5 0.0 ALA A 59 0 1.5 1.5 0.0 0.0 0.0 ASN A 60 2 2.5 2.5 0.0 0.0 0.0 VAL A 61 0 9.5 3.5 3.5 2.5 0.0 SER A 62 0 5.5 2.5 3.0 0.0 0.0 ALA A 63 0 2.5 1.5 1.0 0.0 0.0 ALA A 64 0 5.5 1.0 4.5 0.0 0.0 LYS A 65 7 12.0 3.5 6.5 2.0 0.0 CYS A 66 0 8.0 4.5 2.0 1.5 0.0 GLN A 67 4 7.0 4.0 3.0 0.0 0.0 GLU A 68 0 9.5 3.5 4.5 1.5 0.0 PHE A 69 1 25.0 4.0 5.5 15.5 0.0 GLY A 70 0 7.0 3.5 3.0 0.5 0.0 ARG A 71 6 5.0 2.0 3.0 0.0 0.0 TRP A 72 2 18.0 4.0 6.5 7.5 0.0 TYR A 73 1 15.5 4.5 9.0 2.0 0.0 LYS A 74 4 7.5 4.5 3.0 0.0 0.0 HIS A 75 0 7.5 4.0 3.5 0.0 0.0 PHE A 76 1 9.5 4.5 4.5 0.5 0.0 LYS A 77 4 11.0 5.0 4.5 1.5 0.0 LYS A 78 4 5.0 3.0 2.0 0.0 0.0 THR A 79 0 3.0 2.5 0.5 0.0 0.0 LYS A 80 1 5.0 4.0 1.0 0.0 0.0 ASP A 81 0 4.0 4.0 0.0 0.0 0.0 MET A 82 2 3.5 3.0 0.5 0.0 0.0 MET A 83 3 1.5 1.5 0.0 0.0 0.0 TOTAL 80 632.0 245.0 236.0 151.0 0.0 > ANALYZE_cns: Do you want a CONS.OUT file [default no] ?_