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 `ER382A_NMR_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> HEADER MEMBRANE PROTEIN 15-DEC-06 2JN0 > ReadCoordsPdb(): >> TITLE SOLUTION NMR STRUCTURE OF THE YGDR PROTEIN FROM ESCHERICHIA > ReadCoordsPdb(): >> TITLE 2 COLI. NORTHEAST STRUCTURAL GENOMICS TARGET ER382A. > ReadCoordsPdb(): >> COMPND MOL_ID: 1; > ReadCoordsPdb(): >> COMPND 2 MOLECULE: HYPOTHETICAL LIPOPROTEIN YGDR; 1 > ReadCoordsPdb(): Counting models in file `ER382A_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 ER382A_NMR_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 15360 ATOM records read from file > ReadCoordsPdb(): --> 15360 Regular IUPAC Atoms > ReadCoordsPdb(): --> 0 Pseudo-atoms (DISMAN type) > ReadCoordsPdb(): --> 0 Lone pairs > ReadCoordsPdb(): Bye ... PdbStat> > locate_file(): file `ER382A_NMR_em_bcr3.hbond' opened for reading 20 NOE-distance constraints read 20 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 : 20 LONG RANGE H-BOND RESTR. (I-J)>=5 : 17 DISULFIDE CONSTRAINTS : 0 INTRA-CHAIN CONSTRAINTS : 20 INTER-CHAIN CONSTRAINTS : 0 RES # INTRA INTER seq med lng ASP 1 0 0.0 0.0 0.0 0.0 TYR 2 0 0.0 0.0 0.0 0.0 VAL 3 0 0.0 0.0 0.0 0.0 MET 4 0 0.0 0.0 0.0 0.0 ALA 5 0 0.0 0.0 0.0 0.0 THR 6 0 0.0 0.0 0.0 0.0 LYS 7 0 0.0 0.0 0.0 0.0 ASP 8 0 0.0 0.0 0.0 0.0 GLY 9 0 0.0 0.0 0.0 0.0 ARG 10 0 0.0 0.0 0.0 0.0 MET 11 0 0.0 0.0 0.0 0.0 ILE 12 0 0.0 0.0 0.0 0.0 LEU 13 0 0.0 0.0 0.0 0.0 THR 14 0 0.0 0.0 0.0 0.0 ASP 15 0 0.0 0.0 0.0 0.0 GLY 16 0 0.0 0.0 0.0 0.0 LYS 17 0 0.0 0.0 0.0 0.0 PRO 18 0 0.0 0.0 0.0 0.0 GLU 19 0 0.0 0.0 0.0 0.0 ILE 20 0 0.0 0.0 0.0 0.0 ASP 21 0 0.0 0.0 0.0 0.0 ASP 22 0 0.0 0.0 0.0 0.0 ASP 23 0 0.0 0.0 0.0 0.0 THR 24 0 0.0 0.0 0.0 0.0 GLY 25 0 0.0 0.0 0.0 0.0 LEU 26 0 0.0 0.0 0.0 0.0 VAL 27 0 0.0 0.0 0.0 0.0 SER 28 0 0.0 0.0 0.0 0.0 TYR 29 0 0.0 0.0 0.0 0.0 HIS 30 0 0.0 0.0 0.0 0.0 ASP 31 0 0.0 0.0 0.0 0.0 GLN 32 0 0.0 0.0 0.0 0.0 GLN 33 0 0.0 0.0 0.0 0.0 GLY 34 0 0.0 0.0 0.0 0.0 ASN 35 0 0.0 0.0 0.0 0.0 ALA 36 0 0.0 0.0 0.0 0.0 MET 37 0 0.0 0.0 0.0 0.0 GLN 38 0 0.0 0.0 0.0 0.0 ILE 39 0 0.0 0.0 0.0 0.0 ASN 40 0 0.0 0.0 0.0 0.0 ARG 41 0 0.0 0.0 0.0 0.0 ASP 42 0 0.0 0.0 0.0 0.0 ASP 43 0 0.0 0.0 0.0 0.0 VAL 44 0 0.0 0.0 0.0 0.0 SER 45 0 0.0 0.0 0.0 0.0 GLN 46 0 0.0 0.0 0.0 0.0 ILE 47 0 0.0 0.0 0.0 0.0 ILE 48 0 0.0 0.0 0.0 0.0 GLU 49 0 0.0 0.0 0.0 0.0 ARG 50 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] ?_