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 `HR3102A_R3Cons_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> EXPDTA NMR, 21 STRUCTURES > ReadCoordsPdb(): >> REMARK PdbStat -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > ReadCoordsPdb(): >> REMARK PdbStat -- PDB COORDINATES FOR TEMP_BCM_111.PDB, 20 MODEL/S TEMP_BCM_111.PDB > ReadCoordsPdb(): >> REMARK PdbStat -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > ReadCoordsPdb(): >> SEQRES 1 A 86 MET GLY HIS HIS HIS HIS HIS HIS SER HIS PRO ASN GLU 1 > ReadCoordsPdb(): Counting models in file `HR3102A_R3Cons_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 HR3102A_R3Cons_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 27280 ATOM records read from file > ReadCoordsPdb(): --> 27280 Regular IUPAC Atoms > ReadCoordsPdb(): --> 0 Pseudo-atoms (DISMAN type) > ReadCoordsPdb(): --> 0 Lone pairs > ReadCoordsPdb(): Bye ... PdbStat> > locate_file(): file `HR3102A_R3Cons_em_bcr3.upl' opened for reading 2302 NOE-distance constraints read 2302 TOTAL constraints read PdbStat> > DRAW_cntct: from coordinates or constraints (coor/cons) ?:_ > DRAW_cntct: Making PS file for `HR3102A_R3Cons_em_bcr3.upl.ps' > DRAW_maps: Please enter title for plot (up to 4 lines) > DRAW_maps: To finish just type an asterisk '*' by itself PdbStat> > DRAW_cntct: from coordinates or constraints (coor/cons) ?:_ > MAIN_cntct: What model do you want (1-20) or average ?_ : > do_average_coords(): Making average for backbone atoms > do_average_coords(): Calculating center of masses > do_average_coords(): Calling optimal rotation for backbone > do_average_coords(): Calc. average coordinates backbone FindSameAtom(): Atom _NOT_ Found 1 HIS3 HE2 FindSameAtom(): Atom _NOT_ Found 1 HIS3 HE2 FindSameAtom(): Atom _NOT_ Found 1 HIS3 HE2 FindSameAtom(): Atom _NOT_ Found 1 HIS3 HE2 FindSameAtom(): Atom _NOT_ Found 1 HIS3 HE2 FindSameAtom(): Atom _NOT_ Found 1 HIS3 HE2 FindSameAtom(): Atom _NOT_ Found 1 HIS3 HE2 FindSameAtom(): Atom _NOT_ Found 1 HIS3 HE2 FindSameAtom(): Atom _NOT_ Found 1 HIS4 HD1 FindSameAtom(): Atom _NOT_ Found 1 HIS4 HD1 FindSameAtom(): Atom _NOT_ Found 1 HIS4 HD1 FindSameAtom(): Atom _NOT_ Found 1 HIS4 HD1 FindSameAtom(): Atom _NOT_ Found 1 HIS4 HD1 FindSameAtom(): Atom _NOT_ Found 1 HIS4 HD1 FindSameAtom(): Atom _NOT_ Found 1 HIS4 HD1 FindSameAtom(): Atom _NOT_ Found 1 HIS4 HD1 FindSameAtom(): Atom _NOT_ Found 1 HIS4 HD1 FindSameAtom(): Atom _NOT_ Found 1 HIS4 HD1 FindSameAtom(): Atom _NOT_ Found 1 HIS4 HD1 FindSameAtom(): Atom _NOT_ Found 1 HIS4 HD1 FindSameAtom(): Atom _NOT_ Found 1 HIS5 HE2 FindSameAtom(): Atom _NOT_ Found 1 HIS5 HE2 FindSameAtom(): Atom _NOT_ Found 1 HIS5 HE2 FindSameAtom(): Atom _NOT_ Found 1 HIS5 HE2 FindSameAtom(): Atom _NOT_ Found 1 HIS5 HE2 FindSameAtom(): Atom _NOT_ Found 1 HIS5 HE2 FindSameAtom(): Atom _NOT_ Found 1 HIS5 HE2 FindSameAtom(): Atom _NOT_ Found 1 HIS5 HE2 FindSameAtom(): Atom _NOT_ Found 1 HIS5 HE2 FindSameAtom(): Atom _NOT_ Found 1 HIS5 HE2 FindSameAtom(): Atom _NOT_ Found 1 HIS5 HE2 FindSameAtom(): Atom _NOT_ Found 1 HIS6 HD1 FindSameAtom(): Atom _NOT_ Found 1 HIS6 HD1 FindSameAtom(): Atom _NOT_ Found 1 HIS6 HD1 FindSameAtom(): Atom _NOT_ Found 1 HIS6 HD1 FindSameAtom(): Atom _NOT_ Found 1 HIS6 HD1 FindSameAtom(): Atom _NOT_ Found 1 HIS6 HD1 FindSameAtom(): Atom _NOT_ Found 1 HIS6 HD1 FindSameAtom(): Atom _NOT_ Found 1 HIS6 HD1 FindSameAtom(): Atom _NOT_ Found 1 HIS6 HD1 FindSameAtom(): Atom _NOT_ Found 1 HIS6 HD1 FindSameAtom(): Atom _NOT_ Found 1 HIS6 HD1 FindSameAtom(): Atom _NOT_ Found 1 HIS6 HD1 FindSameAtom(): Atom _NOT_ Found 1 HIS7 HE2 FindSameAtom(): Atom _NOT_ Found 1 HIS7 HE2 FindSameAtom(): Atom _NOT_ Found 1 HIS7 HE2 FindSameAtom(): Atom _NOT_ Found 1 HIS7 HE2 FindSameAtom(): Atom _NOT_ Found 1 HIS7 HE2 FindSameAtom(): Atom _NOT_ Found 1 HIS7 HE2 FindSameAtom(): Atom _NOT_ Found 1 HIS7 HE2 FindSameAtom(): Atom _NOT_ Found 1 HIS7 HE2 FindSameAtom(): Atom _NOT_ Found 1 HIS7 HE2 FindSameAtom(): Atom _NOT_ Found 1 HIS8 HE2 FindSameAtom(): Atom _NOT_ Found 1 HIS8 HE2 FindSameAtom(): Atom _NOT_ Found 1 HIS8 HE2 FindSameAtom(): Atom _NOT_ Found 1 HIS8 HE2 FindSameAtom(): Atom _NOT_ Found 1 HIS8 HE2 FindSameAtom(): Atom _NOT_ Found 1 HIS8 HE2 FindSameAtom(): Atom _NOT_ Found 1 HIS8 HE2 FindSameAtom(): Atom _NOT_ Found 1 HIS8 HE2 FindSameAtom(): Atom _NOT_ Found 1 HIS8 HE2 FindSameAtom(): Atom _NOT_ Found 1 HIS8 HE2 FindSameAtom(): Atom _NOT_ Found 1 HIS8 HE2 > MAIN_cntct: distance cutoff ?:_ > MAIN_cntct: atom type (hydr, heavy, all) ?:_ > CLOSE_cntcts: Contacts for 5.00 angs threshold and HYDR atom type > CLOSE_cntcts: 7830 Close contacts written to file `HR3102A_R3Cons_em_bcr3.upl_Close_cntcts_model21' > MAIN_cntct: Making contact map PS file