Running PDBSTAT from Linux Ayuda is on: /data/PSVS/PdbStat/PdbStat-5.1 (C) (C) Pdbstat -- A program to evaluate some statistics of macromolecules, (C) given the cartesian coordinates. (C) (C) (c) Copyright 1992-2007 Roberto Tejero and Gaetano T. Montelione (C) Center for Advanced Technology and Medicine (CABM) (C) Rutgers University (C) ** VERSION: 5.1-Exp Compiled 2008-08-07 on (europa) ** ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ===============> 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 ... 123 distance records read --> ... Reading/Loading Dihedral Library .. 799 library records read PdbStat> [rea]d [hel]p [his]tory [men]u [phi] [qui]t... PdbStat> leyendo PDB > locate_file(): file `STR65_NMR_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 29-DEC-06 2JN8 > ReadCoordsPdb(): >> TITLE SOLUTION NMR STRUCTURE OF Q8ZRJ2 FROM SALMONELLA > ReadCoordsPdb(): >> TITLE 2 TYPHIMURIUM. NORTHEAST STRUCTURAL GENOMICS TARGET STR65. > ReadCoordsPdb(): >> COMPND MOL_ID: 1; > ReadCoordsPdb(): >> COMPND 2 MOLECULE: PUTATIVE CYTOPLASMIC PROTEIN; 1 > ReadCoordsPdb(): Counting models in file `STR65_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(): Reading *all* models in file STR65_NMR_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 34000 ATOM records read from file > ReadCoordsPdb(): --> 34000 Regular IUPAC Atoms > ReadCoordsPdb(): --> 0 Pseudo-atoms (DISMAN type) > ReadCoordsPdb(): --> 0 Lone pairs > ReadCoordsPdb(): Bye ... PdbStat> > locate_file(): file `STR65_NMR_em_bcr3.hbond' opened for reading 84 NOE-distance constraints read 84 TOTAL constraints read PdbStat> -------------- SUMMARY OF CONSTRAINTS --------------- TOTAL NUMBER OF NOE CONSTRAINTS : 0 INTRA-RESIDUE CONSTRAINTS (I=J) : 0 SEQUENTIAL CONSTRAINTS (I-J)=1 : 0 BACKBONE-BACKBONE : 0 BACKBONE-SIDE CHAIN : 0 SIDE CHAIN-SIDE CHAIN : 0 MEDIUM RANGE CONSTRAINTS 1<(I-J)<5 : 0 BACKBONE-BACKBONE : 0 BACKBONE-SIDE CHAIN : 0 SIDE CHAIN-SIDE CHAIN : 0 LONG RANGE CONSTRAINTS (I-J)>=5 : 0 TOTAL HYDROGEN BOND RESTRAINTS : 84 LONG RANGE H-BOND RESTR. (I-J)>=5 : 0 DISULFIDE CONSTRAINTS : 0 INTRA-CHAIN CONSTRAINTS : 84 INTER-CHAIN CONSTRAINTS : 0 RES # INTRA INTER seq med lng VAL 1 0 0.0 0.0 0.0 0.0 ASN 2 0 0.0 0.0 0.0 0.0 PHE 3 0 0.0 0.0 0.0 0.0 LYS 4 0 0.0 0.0 0.0 0.0 ASP 5 0 0.0 0.0 0.0 0.0 LYS 6 0 0.0 0.0 0.0 0.0 SER 7 0 0.0 0.0 0.0 0.0 MET 8 0 0.0 0.0 0.0 0.0 PRO 9 0 0.0 0.0 0.0 0.0 THR 10 0 0.0 0.0 0.0 0.0 ALA 11 0 0.0 0.0 0.0 0.0 ILE 12 0 0.0 0.0 0.0 0.0 GLU 13 0 0.0 0.0 0.0 0.0 LYS 14 0 0.0 0.0 0.0 0.0 ALA 15 0 0.0 0.0 0.0 0.0 LEU 16 0 0.0 0.0 0.0 0.0 ASP 17 0 0.0 0.0 0.0 0.0 PHE 18 0 0.0 0.0 0.0 0.0 ILE 19 0 0.0 0.0 0.0 0.0 GLY 20 0 0.0 0.0 0.0 0.0 GLY 21 0 0.0 0.0 0.0 0.0 MET 22 0 0.0 0.0 0.0 0.0 ASN 23 0 0.0 0.0 0.0 0.0 THR 24 0 0.0 0.0 0.0 0.0 SER 25 0 0.0 0.0 0.0 0.0 ALA 26 0 0.0 0.0 0.0 0.0 SER 27 0 0.0 0.0 0.0 0.0 VAL 28 0 0.0 0.0 0.0 0.0 PRO 29 0 0.0 0.0 0.0 0.0 HIS 30 0 0.0 0.0 0.0 0.0 SER 31 0 0.0 0.0 0.0 0.0 MET 32 0 0.0 0.0 0.0 0.0 ASP 33 0 0.0 0.0 0.0 0.0 GLU 34 0 0.0 0.0 0.0 0.0 SER 35 0 0.0 0.0 0.0 0.0 THR 36 0 0.0 0.0 0.0 0.0 ALA 37 0 0.0 0.0 0.0 0.0 LYS 38 0 0.0 0.0 0.0 0.0 GLY 39 0 0.0 0.0 0.0 0.0 ILE 40 0 0.0 0.0 0.0 0.0 LEU 41 0 0.0 0.0 0.0 0.0 LYS 42 0 0.0 0.0 0.0 0.0 TYR 43 0 0.0 0.0 0.0 0.0 LEU 44 0 0.0 0.0 0.0 0.0 HIS 45 0 0.0 0.0 0.0 0.0 ASP 46 0 0.0 0.0 0.0 0.0 LEU 47 0 0.0 0.0 0.0 0.0 GLY 48 0 0.0 0.0 0.0 0.0 VAL 49 0 0.0 0.0 0.0 0.0 PRO 50 0 0.0 0.0 0.0 0.0 VAL 51 0 0.0 0.0 0.0 0.0 SER 52 0 0.0 0.0 0.0 0.0 PRO 53 0 0.0 0.0 0.0 0.0 GLU 54 0 0.0 0.0 0.0 0.0 VAL 55 0 0.0 0.0 0.0 0.0 VAL 56 0 0.0 0.0 0.0 0.0 VAL 57 0 0.0 0.0 0.0 0.0 ALA 58 0 0.0 0.0 0.0 0.0 ARG 59 0 0.0 0.0 0.0 0.0 GLY 60 0 0.0 0.0 0.0 0.0 GLU 61 0 0.0 0.0 0.0 0.0 GLN 62 0 0.0 0.0 0.0 0.0 GLU 63 0 0.0 0.0 0.0 0.0 GLY 64 0 0.0 0.0 0.0 0.0 TRP 65 0 0.0 0.0 0.0 0.0 ASN 66 0 0.0 0.0 0.0 0.0 PRO 67 0 0.0 0.0 0.0 0.0 GLU 68 0 0.0 0.0 0.0 0.0 PHE 69 0 0.0 0.0 0.0 0.0 THR 70 0 0.0 0.0 0.0 0.0 LYS 71 0 0.0 0.0 0.0 0.0 LYS 72 0 0.0 0.0 0.0 0.0 VAL 73 0 0.0 0.0 0.0 0.0 ALA 74 0 0.0 0.0 0.0 0.0 GLY 75 0 0.0 0.0 0.0 0.0 TRP 76 0 0.0 0.0 0.0 0.0 ALA 77 0 0.0 0.0 0.0 0.0 GLU 78 0 0.0 0.0 0.0 0.0 LYS 79 0 0.0 0.0 0.0 0.0 VAL 80 0 0.0 0.0 0.0 0.0 ALA 81 0 0.0 0.0 0.0 0.0 SER 82 0 0.0 0.0 0.0 0.0 GLY 83 0 0.0 0.0 0.0 0.0 ASN 84 0 0.0 0.0 0.0 0.0 ARG 85 0 0.0 0.0 0.0 0.0 ILE 86 0 0.0 0.0 0.0 0.0 LEU 87 0 0.0 0.0 0.0 0.0 ILE 88 0 0.0 0.0 0.0 0.0 LYS 89 0 0.0 0.0 0.0 0.0 ASN 90 0 0.0 0.0 0.0 0.0 PRO 91 0 0.0 0.0 0.0 0.0 GLU 92 0 0.0 0.0 0.0 0.0 TYR 93 0 0.0 0.0 0.0 0.0 PHE 94 0 0.0 0.0 0.0 0.0 SER 95 0 0.0 0.0 0.0 0.0 THR 96 0 0.0 0.0 0.0 0.0 TYR 97 0 0.0 0.0 0.0 0.0 MET 98 0 0.0 0.0 0.0 0.0 GLN 99 0 0.0 0.0 0.0 0.0 GLU 100 0 0.0 0.0 0.0 0.0 GLN 101 0 0.0 0.0 0.0 0.0 LEU 102 0 0.0 0.0 0.0 0.0 LYS 103 0 0.0 0.0 0.0 0.0 GLU 104 0 0.0 0.0 0.0 0.0 LEU 105 0 0.0 0.0 0.0 0.0 VAL 106 0 0.0 0.0 0.0 0.0 LEU 107 0 0.0 0.0 0.0 0.0 GLU 108 0 0.0 0.0 0.0 0.0 HIS 109 0 0.0 0.0 0.0 0.0 TOTAL 0 0.0 0.0 0.0 0.0 > ANALYZE_cns: Do you want a CONS.OUT file [default no] ?_