*** ODBMAN *** ODBMAN *** ODBMAN *** ODBMAN *** ODBMAN *** ODBMAN *** Version - 010807/2.2 (C) 1992-2001 Gerard J. Kleywegt, Dept. Cell Mol. Biol., Uppsala (S) User I/O - routines courtesy of Rolf Boelens, Univ. of Utrecht (NL) Others - T.A. Jones, G. Bricogne, Rams, W.A. Hendrickson Others - W. Kabsch, CCP4, PROTEIN, E. Dodson, etc. etc. Started - Tue Nov 13 20:23:28 2001 User - A. Nonymous Mode - interactive Host - sarek ProcID - 10659 Not using a tty as input device *** ODBMAN *** ODBMAN *** ODBMAN *** ODBMAN *** ODBMAN *** ODBMAN *** Reference(s) for this program: * 1 * G.J. Kleywegt (1997). Les amis d"O. CCP4/ESF-EACBM Newsletter on Protein Crystallography 34, September 1997, pp. 5-8. [http://xray.bmc.uu.se/usf/factory_8.html] * 2 * Kleywegt, G.J., Zou, J.Y., Kjeldgaard, M. & Jones, T.A. (2001). Around O. In: "International Tables for Crystallography, Vol. F. Crystallography of Biological Macromolecules" (Rossmann, M.G. & Arnold, E., Editors). Chapter 17.1, pp. 353-356, 366-367. Dordrecht: Kluwer Academic Publishers, The Netherlands. ==> For manuals and up-to-date references, visit: ==> http://xray.bmc.uu.se/usf ==> For downloading up-to-date versions, visit: ==> ftp://xray.bmc.uu.se/pub/gerard *** ODBMAN *** ODBMAN *** ODBMAN *** ODBMAN *** ODBMAN *** ODBMAN *** Max nr of O data blocks (odb) : ( 100) Total nr of O data blocks : ( 400) Max nr of elements per odb : ( 11000) Max length of text odbs : ( 72) Symbol START_TIME : (Tue Nov 13 20:23:28 2001) Symbol USERNAME : ( ) ODBMAN options : ? (list options) ! (comment) QUit $ shell_command & symbol value & ? (list symbols) @ macro_file ECho on_off # parameter(s) (command history) REad filename WRite odb* filename DElete odb* TYpe odb* FOrmat RIC_odb* new_format NAme odb new_name CReate name type nr_elements format DUplicate old_odb new_odb LIst odb* STats RI_odb* HIsto RI_odb* x1 x2 x3 [...] BOxcar R_odb* window_size SImilarity RI_odb1 RI_odb2* [min] [max] [how] ALl_correlations [min] [max] [how] NOn_parametric RI_odb1 RI_odb2* [min] [max] [how] PLot_file RI_odb file [y_lo y_hi label_x label-y] SCatter RI_odb1 RI_odb2 file [label_x label_y] 3D_odl_file RI_odb1 RI_odb2 RI_odb3 file [colour] CGraph_file RI_odb* file CHaracter_function CT_odb function INteger_func I_odb function value FLoat_func R_odb function value SEt ALl odb value SEt MAny odb first last value SEt INdiv odb first last [values] SEt ONe odb index value SEt IF odb other_odb operator value SEt KEep odb first last [step] COmbine RI_odb1 RI_odb2 operator EXtract FIeld odb type file head_skip line_skip field_nr EXtract FOrmat odb type file head_skip line_skip format EXtract MUltiple odb type file head_skip format EXtract PRocheck mol_name file Max nr of O data blocks (odb) : ( 100) Total nr of O data blocks : ( 400) Max nr of elements per odb : ( 11000) Max length of text odbs : ( 72) Execute initialisation macro : (/home/gerard/odbman.init) ... Opened macro file : (/home/gerard/odbman.init) ... On unit : ( 61) Command > (! ODBMAN initialisation macro) Command > (echo on) 1 @ /home/gerard/odbman.init 2 ! ODBMAN initialisation macro 3 echo on ... End of macro file ... Control returned to terminal ODBMAN > Command > (read rvrf.odb) ! Created by RVAL V. 011113/0.8 at Tue Nov 13 20:23:20 2001 for gerard ! ! Resolution Read : (RESOLUTION R 6560 (10F8.3)) ! ! Year Read : (YEAR I 6560 (16I5)) ! ! R-value Read : (RVALUE R 6560 (10F8.4)) ! ! Rfree Read : (RFREE R 6560 (10F8.4)) ! ! Rfree minus Rvalue Read : (RFMINUSR R 6560 (10F8.4)) ! ! Has OMAP in EDS flag Read : (HASMAP I 6560 (40I2)) Nr of datablocks read : ( 6) Nr of header/comments : ( 19) Datablock read okay ODBMAN > Command > (list *) Datablock name Type Nr Alt? Format RESOLUTION R 6560 F (10F8.3) RVALUE R 6560 F (10F8.4) RFREE R 6560 F (10F8.4) RFMINUSR R 6560 F (10F8.4) YEAR I 6560 F (16I5) HASMAP I 6560 F (40I2) ODBMAN > Command > (stats *) Stats : (RESOLUTION) Nr of elements : ( 6560) Minimum : ( 5.400E-01) Maximum : ( 4.000E+00) Sum : ( 1.427E+04) Average : ( 2.175E+00) St-devn : ( 4.662E-01) Variance : ( 2.173E-01) Stats : (RVALUE) Nr of elements : ( 6560) Minimum : ( 5.750E-02) Maximum : ( 4.000E-01) Sum : ( 1.308E+03) Average : ( 1.994E-01) St-devn : ( 2.913E-02) Variance : ( 8.488E-04) Stats : (RFREE) Nr of elements : ( 6560) Minimum : ( 6.760E-02) Maximum : ( 4.650E-01) Sum : ( 1.663E+03) Average : ( 2.535E-01) St-devn : ( 3.819E-02) Variance : ( 1.459E-03) Stats : (RFMINUSR) Nr of elements : ( 6560) Minimum : ( 2.000E-04) Maximum : ( 2.200E-01) Sum : ( 3.550E+02) Average : ( 5.412E-02) St-devn : ( 2.424E-02) Variance : ( 5.874E-04) Stats : (YEAR) Nr of elements : ( 6560) Minimum : ( 1.993E+03) Maximum : ( 2.000E+03) Sum : ( 1.311E+07) Average : ( 1.998E+03) St-devn : ( 1.473E+00) Variance : ( 2.169E+00) Stats : (HASMAP) Nr of elements : ( 6560) Minimum : ( 0.000E+00) Maximum : ( 1.000E+00) Sum : ( 2.147E+03) Average : ( 3.273E-01) St-devn : ( 4.692E-01) Variance : ( 2.202E-01) ODBMAN > Command > (histo year 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000) Histrogram limits : ( 1.991E+03 1.992E+03 1.993E+03 1.994E+03 1.995E+03 1.996E+03 1.997E+03 1.998E+03 1.999E+03 2.000E+03) Histogram : (YEAR) Nr < 1991.0000 : 0 ( 0.00 %; Cum 0.00 %) Nr >= 1993.0000 and < 1994.0000 : 6 ( 0.09 %; Cum 0.09 %) Nr >= 1994.0000 and < 1995.0000 : 55 ( 0.84 %; Cum 0.93 %) Nr >= 1995.0000 and < 1996.0000 : 289 ( 4.41 %; Cum 5.34 %) Nr >= 1996.0000 and < 1997.0000 : 528 ( 8.05 %; Cum 13.38 %) Nr >= 1997.0000 and < 1998.0000 : 1022 ( 15.58 %; Cum 28.96 %) Nr >= 1998.0000 and < 1999.0000 : 1413 ( 21.54 %; Cum 50.50 %) Nr >= 1999.0000 and < 2000.0000 : 1713 ( 26.11 %; Cum 76.62 %) Nr >= 2000.0000 : 1534 ( 23.38 %; Cum 100.00 %) ODBMAN > Command > (histo rvalue 0.05 0.1 0.15 0.2 0.25 0.3 0.35 0.4 0.45 0.5) Histrogram limits : ( 5.000E-02 1.000E-01 1.500E-01 2.000E-01 2.500E-01 3.000E-01 3.500E-01 4.000E-01 4.500E-01 5.000E-01) Histogram : (RVALUE) Nr < 0.0500 : 0 ( 0.00 %; Cum 0.00 %) Nr >= 0.0500 and < 0.1000 : 13 ( 0.20 %; Cum 0.20 %) Nr >= 0.1000 and < 0.1500 : 236 ( 3.60 %; Cum 3.80 %) Nr >= 0.1500 and < 0.2000 : 3176 ( 48.41 %; Cum 52.21 %) Nr >= 0.2000 and < 0.2500 : 2888 ( 44.02 %; Cum 96.23 %) Nr >= 0.2500 and < 0.3000 : 221 ( 3.37 %; Cum 99.60 %) Nr >= 0.3000 and < 0.3500 : 19 ( 0.29 %; Cum 99.89 %) Nr >= 0.3500 and < 0.4000 : 6 ( 0.09 %; Cum 99.98 %) Nr >= 0.4000 and < 0.4500 : 1 ( 0.02 %; Cum 100.00 %) Nr >= 0.5000 : 0 ( 0.00 %; Cum 100.00 %) ODBMAN > Command > (histo rfree 0.05 0.1 0.15 0.2 0.25 0.3 0.35 0.4 0.45 0.5) Histrogram limits : ( 5.000E-02 1.000E-01 1.500E-01 2.000E-01 2.500E-01 3.000E-01 3.500E-01 4.000E-01 4.500E-01 5.000E-01) Histogram : (RFREE) Nr < 0.0500 : 0 ( 0.00 %; Cum 0.00 %) Nr >= 0.0500 and < 0.1000 : 3 ( 0.05 %; Cum 0.05 %) Nr >= 0.1000 and < 0.1500 : 43 ( 0.66 %; Cum 0.70 %) Nr >= 0.1500 and < 0.2000 : 387 ( 5.90 %; Cum 6.60 %) Nr >= 0.2000 and < 0.2500 : 2580 ( 39.33 %; Cum 45.93 %) Nr >= 0.2500 and < 0.3000 : 2912 ( 44.39 %; Cum 90.32 %) Nr >= 0.3000 and < 0.3500 : 559 ( 8.52 %; Cum 98.84 %) Nr >= 0.3500 and < 0.4000 : 65 ( 0.99 %; Cum 99.83 %) Nr >= 0.4000 and < 0.4500 : 8 ( 0.12 %; Cum 99.95 %) Nr >= 0.4500 and < 0.5000 : 3 ( 0.05 %; Cum 100.00 %) Nr >= 0.5000 : 0 ( 0.00 %; Cum 100.00 %) ODBMAN > Command > (histo rfminusr 0.01 0.025 0.05 0.075 0.1 0.125 0.15 0.2) Histrogram limits : ( 1.000E-02 2.500E-02 5.000E-02 7.500E-02 1.000E-01 1.250E-01 1.500E-01 2.000E-01) Histogram : (RFMINUSR) Nr < 0.0100 : 75 ( 1.14 %; Cum 1.14 %) Nr >= 0.0100 and < 0.0250 : 503 ( 7.67 %; Cum 8.81 %) Nr >= 0.0250 and < 0.0500 : 2464 ( 37.56 %; Cum 46.37 %) Nr >= 0.0500 and < 0.0750 : 2330 ( 35.52 %; Cum 81.89 %) Nr >= 0.0750 and < 0.1000 : 883 ( 13.46 %; Cum 95.35 %) Nr >= 0.1000 and < 0.1250 : 244 ( 3.72 %; Cum 99.07 %) Nr >= 0.1250 and < 0.1500 : 45 ( 0.69 %; Cum 99.76 %) Nr >= 0.1500 and < 0.2000 : 15 ( 0.23 %; Cum 99.98 %) Nr >= 0.2000 : 1 ( 0.02 %; Cum 100.00 %) ODBMAN > Command > (histo resolution 0.5 0.75 1 1.2 1.4 1.6 1.8 2 2.2 2.4 2.6 2.8 3 3.25 3.5 3.75 4) Histrogram limits : ( 5.000E-01 7.500E-01 1.000E+00 1.200E+00 1.400E+00 1.600E+00 1.800E+00 2.000E+00 2.200E+00 2.400E+00 2.600E+00 2.800E+00 3.000E+00 3.250E+00 3.500E+00 3.750E+00 4.000E+00) Histogram : (RESOLUTION) Nr < 0.5000 : 0 ( 0.00 %; Cum 0.00 %) Nr >= 0.5000 and < 0.7500 : 2 ( 0.03 %; Cum 0.03 %) Nr >= 0.7500 and < 1.0000 : 30 ( 0.46 %; Cum 0.49 %) Nr >= 1.0000 and < 1.2000 : 60 ( 0.91 %; Cum 1.40 %) Nr >= 1.2000 and < 1.4000 : 92 ( 1.40 %; Cum 2.80 %) Nr >= 1.4000 and < 1.6000 : 323 ( 4.92 %; Cum 7.73 %) Nr >= 1.6000 and < 1.8000 : 627 ( 9.56 %; Cum 17.29 %) Nr >= 1.8000 and < 2.0000 : 1148 ( 17.50 %; Cum 34.79 %) Nr >= 2.0000 and < 2.2000 : 1160 ( 17.68 %; Cum 52.47 %) Nr >= 2.2000 and < 2.4000 : 963 ( 14.68 %; Cum 67.15 %) Nr >= 2.4000 and < 2.6000 : 830 ( 12.65 %; Cum 79.80 %) Nr >= 2.6000 and < 2.8000 : 503 ( 7.67 %; Cum 87.47 %) Nr >= 2.8000 and < 3.0000 : 422 ( 6.43 %; Cum 93.90 %) Nr >= 3.0000 and < 3.2500 : 312 ( 4.76 %; Cum 98.66 %) Nr >= 3.2500 and < 3.5000 : 44 ( 0.67 %; Cum 99.33 %) Nr >= 3.5000 and < 3.7500 : 33 ( 0.50 %; Cum 99.83 %) Nr >= 3.7500 and < 4.0000 : 7 ( 0.11 %; Cum 99.94 %) Nr >= 4.0000 : 4 ( 0.06 %; Cum 100.00 %) ODBMAN > Command > (all) Hit # #Elem Corr-C RMS Diff --- Datablock 1 --- --- Datablock 2 --- 1 6560 0.452 2.0272E+00 RESOLUTION RVALUE 2 6560 0.557 1.9727E+00 RESOLUTION RFREE 3 6560 0.335 2.1701E+00 RESOLUTION RFMINUSR 4 6560 -0.075 1.9961E+03 RESOLUTION YEAR 5 6560 -0.039 1.9671E+00 RESOLUTION HASMAP 6 6560 0.773 5.9295E-02 RVALUE RFREE 7 6560 0.016 1.5009E-01 RVALUE RFMINUSR 8 6560 0.088 1.9980E+03 RVALUE YEAR 9 6560 -0.069 4.8913E-01 RVALUE HASMAP 10 6560 0.647 2.0154E-01 RFREE RFMINUSR 11 6560 -0.083 1.9980E+03 RFREE YEAR 12 6560 -0.053 4.7851E-01 RFREE HASMAP 13 6560 -0.236 1.9982E+03 RFMINUSR YEAR 14 6560 -0.001 5.4351E-01 RFMINUSR HASMAP 15 6560 -0.207 1.9979E+03 YEAR HASMAP Nr of hits : ( 15) ODBMAN > Command > (non year *) Hit # #Elem Rank-C Prob Z(D) Prob --- Datablock 1 --- --- Datablock 2 --- 1 6560 -0.207 0.0E+00 6.536 6.3E-11 YEAR RESOLUTION 2 6560 -0.009 4.4E-01 -8.597 8.2E-18 YEAR RVALUE 3 6560 -0.193 0.0E+00 5.954 2.6E-09 YEAR RFREE 4 6560 -0.363 0.0E+00 19.364 0.0E+00 YEAR RFMINUSR ERROR --- BETACF - argument too big or ITMAX too small Nr of hits : ( 4) ODBMAN > Command > (non rvalue *) Hit # #Elem Rank-C Prob Z(D) Prob --- Datablock 1 --- --- Datablock 2 --- 1 6560 0.381 0.0E+00 -31.386 0.0E+00 RVALUE RESOLUTION 2 6560 0.735 0.0E+00 -59.543 0.0E+00 RVALUE RFREE 3 6560 0.013 2.8E-01 -1.156 2.5E-01 RVALUE RFMINUSR 4 6560 -0.009 4.4E-01 -8.597 8.2E-18 RVALUE YEAR ERROR --- BETACF - argument too big or ITMAX too small Nr of hits : ( 4) ODBMAN > Command > (non rfree *) Hit # #Elem Rank-C Prob Z(D) Prob --- Datablock 1 --- --- Datablock 2 --- 1 6560 0.530 0.0E+00 -43.391 0.0E+00 RFREE RESOLUTION 2 6560 0.735 0.0E+00 -59.543 0.0E+00 RFREE RVALUE 3 6560 0.640 0.0E+00 -51.907 0.0E+00 RFREE RFMINUSR 4 6560 -0.193 0.0E+00 5.955 2.6E-09 RFREE YEAR ERROR --- BETACF - argument too big or ITMAX too small Nr of hits : ( 4) ODBMAN > Command > (non rfminusr *) Hit # #Elem Rank-C Prob Z(D) Prob --- Datablock 1 --- --- Datablock 2 --- 1 6560 0.350 0.0E+00 -28.885 0.0E+00 RFMINUSR RESOLUTION 2 6560 0.013 2.8E-01 -1.155 2.5E-01 RFMINUSR RVALUE 3 6560 0.640 0.0E+00 -51.907 0.0E+00 RFMINUSR RFREE 4 6560 -0.363 0.0E+00 19.364 0.0E+00 RFMINUSR YEAR ERROR --- BETACF - argument too big or ITMAX too small Nr of hits : ( 4) ODBMAN > Command > (scatter year rfree rfree_vs_year.plt) X label : (Value of YEAR) Y label : (Value of RFREE) X lower : ( 1.993E+03) X upper : ( 2.000E+03) Y lower : ( 4.773E-02) Y upper : ( 4.849E-01) O2D plot file written ODBMAN > Command > (scatter year rfminusr rfminusr_vs_year.plt) X label : (Value of YEAR) Y label : (Value of RFMINUSR) X lower : ( 1.993E+03) X upper : ( 2.000E+03) Y lower : ( -1.079E-02) Y upper : ( 2.310E-01) O2D plot file written ODBMAN > Command > (scatter rvalue rfree rfree_vs_rvalue.plt) X label : (Value of RVALUE) Y label : (Value of RFREE) X lower : ( 4.038E-02) X upper : ( 4.171E-01) Y lower : ( 4.773E-02) Y upper : ( 4.849E-01) O2D plot file written ODBMAN > Command > (scatter rvalue rfminusr rfminusr_vs_rvalue.plt) X label : (Value of RVALUE) Y label : (Value of RFMINUSR) X lower : ( 4.038E-02) X upper : ( 4.171E-01) Y lower : ( -1.079E-02) Y upper : ( 2.310E-01) O2D plot file written ODBMAN > Command > (scatter rfree rfminusr rfminusr_vs_rfree.plt) X label : (Value of RFREE) Y label : (Value of RFMINUSR) X lower : ( 4.773E-02) X upper : ( 4.849E-01) Y lower : ( -1.079E-02) Y upper : ( 2.310E-01) O2D plot file written ODBMAN > Command > (scatter resolution rfree rfree_vs_resolution.plt) X label : (Value of RESOLUTION) Y label : (Value of RFREE) X lower : ( 3.670E-01) X upper : ( 4.173E+00) Y lower : ( 4.773E-02) Y upper : ( 4.849E-01) O2D plot file written ODBMAN > Command > (scatter resolution rfminusr rfminusr_vs_resolution.plt) X label : (Value of RESOLUTION) Y label : (Value of RFMINUSR) X lower : ( 3.670E-01) X upper : ( 4.173E+00) Y lower : ( -1.079E-02) Y upper : ( 2.310E-01) O2D plot file written ODBMAN > Command > (scatter rfree hasmap hasmap_vs_rfree.plt) X label : (Value of RFREE) Y label : (Value of HASMAP) X lower : ( 4.773E-02) X upper : ( 4.849E-01) Y lower : ( -5.000E-02) Y upper : ( 1.050E+00) O2D plot file written ODBMAN > Command > (quit) STOP ... Toodle pip ... statement executed *** ODBMAN *** ODBMAN *** ODBMAN *** ODBMAN *** ODBMAN *** ODBMAN *** Version - 010807/2.2 Started - Tue Nov 13 20:23:28 2001 Stopped - Tue Nov 13 20:23:32 2001 CPU-time taken : User - 2.9 Sys - 0.6 Total - 3.4 *** ODBMAN *** ODBMAN *** ODBMAN *** ODBMAN *** ODBMAN *** ODBMAN *** >>>>>>>>>>>>>> USF .... Uppsala Software Factory <<<<<<<<<<<<<< >>>>>>>>>> This program: (C) 1992-2001, G J Kleywegt <<<<<<<<<< >>>>>>>>>>>>>>>> E-mail: gerard@xray.bmc.uu.se <<<<<<<<<<<<<<<< >>>>>>>>>>>>>>>>>> http://xray.bmc.uu.se/usf <<<<<<<<<<<<<<<<<< *** ODBMAN *** ODBMAN *** ODBMAN *** ODBMAN *** ODBMAN *** ODBMAN ***