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 `PSR293_NMR_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 24-FEB-09 2KFP > ReadCoordsPdb(): >> TITLE SOLUTION NMR STRUCTURE OF PSPTO_3016 FROM PSEUDOMONAS > ReadCoordsPdb(): >> TITLE 2 SYRINGAE. NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET > ReadCoordsPdb(): >> TITLE 3 PSR293. > ReadCoordsPdb(): >> COMPND MOL_ID: 1; 1 > ReadCoordsPdb(): Counting models in file `PSR293_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 PSR293_NMR_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 41420 ATOM records read from file > ReadCoordsPdb(): --> 41420 Regular IUPAC Atoms > ReadCoordsPdb(): --> 0 Pseudo-atoms (DISMAN type) > ReadCoordsPdb(): --> 0 Lone pairs > ReadCoordsPdb(): Bye ... > ReadCoordsPdb(): ** monomer, 1 [1] chains ** PdbStat> > RMSD_coords : Enter ranges [3-20,25,30-67] ?_ : > RMSD_coords : Reference structure (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 onto model 1 > do_average_coords(): Calc. average coordinates backbone > RMSD_coords : File name for RMSDs (def. `rmsd.pdbstat')?_ : > Kabsch RMSD of backb atoms in res. *[1..125],for model 1 is: 1.231 > Kabsch RMSD of backb atoms in res. *[1..125],for model 2 is: 1.611 > Kabsch RMSD of backb atoms in res. *[1..125],for model 3 is: 1.919 > Kabsch RMSD of backb atoms in res. *[1..125],for model 4 is: 1.770 > Kabsch RMSD of backb atoms in res. *[1..125],for model 5 is: 1.660 > Kabsch RMSD of backb atoms in res. *[1..125],for model 6 is: 1.459 > Kabsch RMSD of backb atoms in res. *[1..125],for model 7 is: 2.331 > Kabsch RMSD of backb atoms in res. *[1..125],for model 8 is: 1.598 > Kabsch RMSD of backb atoms in res. *[1..125],for model 9 is: 1.039 (*) > Kabsch RMSD of backb atoms in res. *[1..125],for model 10 is: 1.519 > Kabsch RMSD of backb atoms in res. *[1..125],for model 11 is: 1.237 > Kabsch RMSD of backb atoms in res. *[1..125],for model 12 is: 1.618 > Kabsch RMSD of backb atoms in res. *[1..125],for model 13 is: 2.548 > Kabsch RMSD of backb atoms in res. *[1..125],for model 14 is: 1.603 > Kabsch RMSD of backb atoms in res. *[1..125],for model 15 is: 1.904 > Kabsch RMSD of backb atoms in res. *[1..125],for model 16 is: 1.294 > Kabsch RMSD of backb atoms in res. *[1..125],for model 17 is: 2.395 > Kabsch RMSD of backb atoms in res. *[1..125],for model 18 is: 1.573 > Kabsch RMSD of backb atoms in res. *[1..125],for model 19 is: 1.880 > Kabsch RMSD of backb atoms in res. *[1..125],for model 20 is: 1.071 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[1..125], is: 1.663 > Range of RMSD values to reference struct. is 1.039 to 2.548 PdbStat> > RMSD_coords : Enter ranges [3-20,25,30-67] ?_ : > RMSD_coords : Reference structure (1-20) or (average) ?_ > do_average_coords(): Making average for heavy atoms > do_average_coords(): Calculating center of masses > do_average_coords(): Calling optimal rotation for heavy onto model 1 > do_average_coords(): Calc. average coordinates heavy > RMSD_coords : File name for RMSDs (def. `rmsd.pdbstat')?_ : > Kabsch RMSD of heavy atoms in res. *[1..125],for model 1 is: 1.854 > Kabsch RMSD of heavy atoms in res. *[1..125],for model 2 is: 2.252 > Kabsch RMSD of heavy atoms in res. *[1..125],for model 3 is: 2.528 > Kabsch RMSD of heavy atoms in res. *[1..125],for model 4 is: 2.359 > Kabsch RMSD of heavy atoms in res. *[1..125],for model 5 is: 2.331 > Kabsch RMSD of heavy atoms in res. *[1..125],for model 6 is: 2.175 > Kabsch RMSD of heavy atoms in res. *[1..125],for model 7 is: 3.002 > Kabsch RMSD of heavy atoms in res. *[1..125],for model 8 is: 2.368 > Kabsch RMSD of heavy atoms in res. *[1..125],for model 9 is: 1.722 (*) > Kabsch RMSD of heavy atoms in res. *[1..125],for model 10 is: 2.169 > Kabsch RMSD of heavy atoms in res. *[1..125],for model 11 is: 1.893 > Kabsch RMSD of heavy atoms in res. *[1..125],for model 12 is: 2.212 > Kabsch RMSD of heavy atoms in res. *[1..125],for model 13 is: 3.165 > Kabsch RMSD of heavy atoms in res. *[1..125],for model 14 is: 2.230 > Kabsch RMSD of heavy atoms in res. *[1..125],for model 15 is: 2.443 > Kabsch RMSD of heavy atoms in res. *[1..125],for model 16 is: 2.063 > Kabsch RMSD of heavy atoms in res. *[1..125],for model 17 is: 2.828 > Kabsch RMSD of heavy atoms in res. *[1..125],for model 18 is: 2.087 > Kabsch RMSD of heavy atoms in res. *[1..125],for model 19 is: 2.367 > Kabsch RMSD of heavy atoms in res. *[1..125],for model 20 is: 1.758 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[1..125], is: 2.290 > Range of RMSD values to reference struct. is 1.722 to 3.165 PdbStat> PdbStat> *END* of program detected, BYE! ...