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 `SGR42_NMR_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 22-DEC-07 2JZ2 > ReadCoordsPdb(): >> TITLE SOLUTION NMR STRUCTURE OF SSL0352 PROTEIN FROM SYNECHOCYSTIS SP. PCC > ReadCoordsPdb(): >> TITLE 2 6803. NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET SGR42 > ReadCoordsPdb(): >> COMPND MOL_ID: 1; > ReadCoordsPdb(): >> COMPND 2 MOLECULE: SSL0352 PROTEIN; 1 > ReadCoordsPdb(): Counting models in file `SGR42_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 SGR42_NMR_em_bcr3.pdb MODEL 1 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 1072 ATOM records read from file > ReadCoordsPdb(): --> 1072 Regular IUPAC Atoms > ReadCoordsPdb(): --> 0 Pseudo-atoms (DISMAN type) > ReadCoordsPdb(): --> 0 Lone pairs > ReadCoordsPdb(): Bye ... > =============================== INFO ================================ > INFO_mol: # atoms: 1072 (346 C, 530 H, 97 O, 98 N, 1 S, 0 Q, 0 Metals) > INFO_mol: # residues: 66 (Avg. mol. weight: 115.9) > INFO_mol: # -- M.W. : 7646.5 g/mol. (7.65 kD) Estimated RoG : 10.81 > INFO_mol: CenterMass() -- Working PDB model 1 in file, model no. 1 > INFO_mol: CenterMass() -- Molecule `SGR42_NMR_em_bcr3.pdb' model #1, TOTAL RESIDUES: 66 > INFO_mol: Radius of Gyration : 14.6731 angstroms > INFO_mol: Center of Masses: x_cm(-0.159), y_cm(-0.358), z_cm(-0.009) > INFO_res: MIFPGATVRV TNVDDTYYRF EGLVQRVSDG KAAVLFENGN WDKLVTFRLS > INFO_res: ELEAVKPILE HHHHHH > INFO_res: > INFO_res: MET ILE PHE PRO GLY ALA THR VAL ARG VAL THR ASN > INFO_res: VAL ASP ASP THR TYR TYR ARG PHE GLU GLY LEU VAL > INFO_res: GLN ARG VAL SER ASP GLY LYS ALA ALA VAL LEU PHE > INFO_res: GLU ASN GLY ASN TRP ASP LYS LEU VAL THR PHE ARG > INFO_res: LEU SER GLU LEU GLU ALA VAL LYS PRO ILE LEU GLU > INFO_res: HIS HIS HIS HIS HIS HIS > INFO_res: > INFO_res: 4 ALA 4 ARG 3 ASN 4 ASP 1 GLN 5 GLU > INFO_res: 4 GLY 6 HIS 2 ILE 6 LEU 3 LYS 1 MET > INFO_res: 4 PHE 2 PRO 2 SER 4 THR 2 TYR 1 TRP > INFO_res: 8 VAL > INFO_res: DISULFIDE: ** NO INFO FOR DISULFIDES IN FILE > ===================================================================== > ReadCoordsPdb(): *** monomer, 1 [1] chains *** PdbStat> > locate_file(): file `SGR42_NMR_em_bcr3.upl' opened for reading 0 SANI-RDC constraints read 547 NOE-distance constraints (0 Ambiguous NOE/s) read 547 TOTAL constraints read PdbStat> -------------- SUMMARY OF RESTRAINTS --------------- TOTAL NUMBER OF NOE RESTRAINTS : 547 INTRA-RESIDUE RESTRAINTS (I=J) : 119 SEQUENTIAL RESTRAINTS (I-J)=1 : 148 BACKBONE-BACKBONE : 55 BACKBONE-SIDE CHAIN : 9 SIDE CHAIN-SIDE CHAIN : 84 MEDIUM RANGE RESTRAINTS 1<(I-J)<5 : 57 BACKBONE-BACKBONE : 6 BACKBONE-SIDE CHAIN : 10 SIDE CHAIN-SIDE CHAIN : 41 LONG RANGE RESTRAINTS (I-J)>=5 : 223 TOTAL HYDROGEN BOND RESTRAINTS : 0 LONG RANGE H-BOND RESTR. (I-J)>=5 : 0 DISULFIDE RESTRAINTS : 0 INTRA-CHAIN RESTRAINTS : 547 INTER-CHAIN RESTRAINTS : 0 AMBIGUOUS RESTRAINTS : 0 ----------------------------------------------------- ----------------------------------------------------- ----------------------------------------------------- RES # INTRA INTER seq med lng InterChain MET A 1 0 1.0 0.0 1.0 0.0 0.0 ILE A 2 1 4.5 1.5 1.5 1.5 0.0 PHE A 3 2 5.0 3.0 1.5 0.5 0.0 PRO A 4 0 7.0 2.0 0.5 4.5 0.0 GLY A 5 0 2.5 1.0 0.0 1.5 0.0 ALA A 6 0 6.5 1.5 3.0 2.0 0.0 THR A 7 1 8.0 3.5 0.0 4.5 0.0 VAL A 8 2 13.0 4.0 0.5 8.5 0.0 ARG A 9 4 10.5 2.5 1.0 7.0 0.0 VAL A 10 3 14.5 2.0 2.0 10.5 0.0 THR A 11 1 7.0 1.5 1.0 4.5 0.0 ASN A 12 0 8.0 1.5 3.5 3.0 0.0 VAL A 13 1 6.5 2.5 0.0 4.0 0.0 ASP A 14 3 2.0 2.0 0.0 0.0 0.0 ASP A 15 2 4.0 1.0 2.0 1.0 0.0 THR A 16 2 3.0 3.0 0.0 0.0 0.0 TYR A 17 1 10.5 3.5 1.5 5.5 0.0 TYR A 18 3 12.0 3.0 1.0 8.0 0.0 ARG A 19 5 4.0 2.5 0.0 1.5 0.0 PHE A 20 3 6.5 2.0 2.0 2.5 0.0 GLU A 21 1 6.0 2.5 0.0 3.5 0.0 GLY A 22 0 7.0 2.0 0.0 5.0 0.0 LEU A 23 3 6.0 1.5 0.5 4.0 0.0 VAL A 24 1 10.5 1.5 1.0 8.0 0.0 GLN A 25 5 9.5 2.5 0.5 6.5 0.0 ARG A 26 1 9.0 4.0 1.0 4.0 0.0 VAL A 27 2 9.5 5.0 0.0 4.5 0.0 SER A 28 0 4.0 3.5 0.5 0.0 0.0 ASP A 29 1 2.5 2.5 0.0 0.0 0.0 GLY A 30 0 3.5 2.0 0.0 1.5 0.0 LYS A 31 4 8.5 2.0 0.5 6.0 0.0 ALA A 32 0 7.0 2.5 0.0 4.5 0.0 ALA A 33 0 8.5 2.0 0.0 6.5 0.0 VAL A 34 2 11.0 2.0 1.5 7.5 0.0 LEU A 35 4 14.5 2.5 1.0 11.0 0.0 PHE A 36 2 16.5 3.5 1.5 11.5 0.0 GLU A 37 2 6.5 3.0 1.5 2.0 0.0 ASN A 38 2 3.5 1.5 2.0 0.0 0.0 GLY A 39 0 1.0 1.0 0.0 0.0 0.0 ASN A 40 1 2.5 2.5 0.0 0.0 0.0 TRP A 41 5 10.0 3.0 4.0 3.0 0.0 ASP A 42 1 6.0 2.5 0.0 3.5 0.0 LYS A 43 4 7.5 2.5 3.0 2.0 0.0 LEU A 44 4 6.5 3.0 0.0 3.5 0.0 VAL A 45 1 10.5 3.0 3.0 4.5 0.0 THR A 46 2 7.5 2.5 0.0 5.0 0.0 PHE A 47 2 16.5 3.0 2.5 11.0 0.0 ARG A 48 5 8.0 2.5 2.5 3.0 0.0 LEU A 49 6 7.0 3.0 1.0 3.0 0.0 SER A 50 3 4.0 2.5 1.5 0.0 0.0 GLU A 51 1 8.0 2.5 3.0 2.5 0.0 LEU A 52 5 12.5 3.5 1.0 8.0 0.0 GLU A 53 1 9.5 3.0 1.0 5.5 0.0 ALA A 54 0 7.0 2.5 0.0 4.5 0.0 VAL A 55 3 11.0 2.5 1.0 7.5 0.0 LYS A 56 4 3.5 3.5 0.0 0.0 0.0 PRO A 57 0 3.5 3.5 0.0 0.0 0.0 ILE A 58 5 3.0 3.0 0.0 0.0 0.0 LEU A 59 1 2.0 2.0 0.0 0.0 0.0 GLU A 60 1 1.0 1.0 0.0 0.0 0.0 HIS A 61 0 0.5 0.5 0.0 0.0 0.0 HIS A 62 0 0.0 0.0 0.0 0.0 0.0 HIS A 63 0 0.0 0.0 0.0 0.0 0.0 HIS A 64 0 0.0 0.0 0.0 0.0 0.0 HIS A 65 0 0.0 0.0 0.0 0.0 0.0 HIS A 66 0 0.0 0.0 0.0 0.0 0.0 TOTAL 119 428.0 148.0 57.0 223.0 0.0 > ANALYZE_cns: Do you want a CONS.OUT file [default no] ?_