Hi Phil,Thanks for your email. I did get it to work with the options you suggested . i.e Toggle ON "Override automatic definition of runs to mark discontinuities in data Toggle ON Define Runs Toggle OFF Use run 1 as reference run.
Setup runs as follows ( intended to exclude batches 200 to 400 from a total dataset of 1 to 720 ) Run 1 from 1 to 200 Run 2 from 400 to 720 This combination worked as you said it would. Thank you for your help Hari Jayaram Postdoc Brandeis University On Sat, Mar 15, 2008 at 3:44 AM, Phil Evans <[EMAIL PROTECTED]> wrote: > You are right: this is a bug I should fix sometime > > Assigning two runs should work though > > You should not assign a reference run, and you shouldn't need to > reassign the datasets > > Best wishes > Phil > > On 14 Mar 2008, at 21:45, hari jayaram wrote: > > > Hi. > > I did try that beforehand when I tried excluding a "range" of > > batches with the ccp4i gui > > > > But I got an error > > > > Scala: *** Gap in "time" (rotation) *** > > > > Sorry...both versions of the protocol for handling a bad internal > > wedge are giving me either a "gap in rotation" error or a "Run 2 > > has not been assigned to a dataset" error > > > > I am still stuck. > > > > ( error and com file for the "exclude data" range option is attached > > below) > > Thanks for your help. > > > > Hari Jayaram > > > > > > > > ---------------------------- > > Error > > --------------------------- > > > > **** Large gap in "time" (rotation) coordinate: 3.5 **** > > **** See WARNING above **** > > **** Smoothed B-factor impossible **** > > > > > *************************************************************************** > > * Information from CCP4Interface script > > > *************************************************************************** > > The program run with command: scala HKLIN "/Users/hari/aps_feb08/ > > p2-2/p2-2_A1_1_0001_sorted.mtz" HKLOUT "/tmp/hari/p2_2_13_2_mtz.tmp" > > SCALES "/Users/hari/aps_feb08/p2-2/p2_2_13.scala" ROGUES "/Users/ > > hari/aps_feb08/p2-2/p2_2_13_rogues.log" NORMPLOT "/Users/hari/ > > aps_feb08/p2-2/p2_2_13_normplot.xmgr" ANOMPLOT "/Users/hari/ > > aps_feb08/p2-2/p2_2_13_anomplot.xmgr" PLOT "/Users/hari/aps_feb08/ > > p2-2/p2_2_13_surface_plot.plt" CORRELPLOT "/Users/hari/aps_feb08/ > > p2-2/p2_2_13_correlplot.xmgr" > > has failed with error message > > Scala: *** Gap in "time" (rotation) *** > > > *************************************************************************** > > > > > > #CCP4I TERMINATION STATUS 0 " Scala: *** Gap in "time" (rotation) > > ***" > > #CCP4I TERMINATION TIME 14 Mar 2008 17:38:34 > > #CCP4I TERMINATION OUTPUT_FILES /Users/hari/aps_feb08/p2-2/ > > p2-2_A1_1_0001_sorted.mtz p2_2 > > #CCP4I MESSAGE Task failed > > > > ---------------------------- > > The com script was > > ---------------------------- > > ******************************************************************* > > /tmp/hari/p2_2_13_3_com.tmp > > ******************************************************************* > > title Scala anon and deleted batches 200_400b try with two run > > definitions > > name project p2_2 crystal p2-2_A1_1 dataset p2_2 > > exclude EMAX - > > 10.0 > > exclude batch - > > 400 to 540 > > partials - > > check - > > test 0.95 1.05 - > > nogap > > intensities PROFILE - > > PARTIALS > > final PARTIALS > > scales - > > rotation SPACING 5 - > > secondary 6 - > > bfactor ON - > > BROTATION SPACING 20 > > UNFIX V > > FIX A0 > > UNFIX A1 > > initial MEAN > > tie surface 0.001 > > tie bfactor 0.3 > > cycles 10 converge 0.3 reject 2 > > anomalous on > > output AVERAGE > > print cycles nooverlap > > RSIZE 80 > > > > > > ## This script run with the command ########## > > # scala HKLIN "/Users/hari/aps_feb08/p2-2/p2-2_A1_1_0001_sorted.mtz" > > HKLOUT "/tmp/hari/p2_2_13_2_mtz.tmp" SCALES "/Users/hari/aps_feb08/ > > p2-2/p2_2_13.scala" ROGUES "/Users/hari/aps_feb08/p2-2/ > > p2_2_13_rogues.log" NORMPLOT "/Users/hari/aps_feb08/p2-2/ > > p2_2_13_normplot.xmgr" ANOMPLOT "/Users/hari/aps_feb08/p2-2/ > > p2_2_13_anomplot.xmgr" PLOT "/Users/hari/aps_feb08/p2-2/ > > p2_2_13_surface_plot.plt" CORRELPLOT "/Users/hari/aps_feb08/p2-2/ > > p2_2_13_correlplot.xmgr" > > ################################################ > > > > > > On Fri, Mar 14, 2008 at 5:11 PM, Phil Evans <[EMAIL PROTECTED]> > > wrote: > > In ccp4i Scala task, click to open the "Excluded data" panel, click on > > "Exclude selected batches" > > > > There you can define one or more ranges of batches or lists to exclude > > > > If you just want to exclude the last part you can define a range eg > > 301 to 999 > > > > You don't need to explicitly define runs > > > > Phil > > > > On 14 Mar 2008, at 18:57, hari jayaram wrote: > > > > > Hi I am trying to exclude a bad wedge of data during scaling in > > > scala in the newest ccp4 > > > > > > ( fink install this morning from W.G Scotts sage.ucsc Binaries ..so > > > they should be version 6) > > > > > > The batches I need are > > > 1 to 200 and 400-720 > > > I have clicked the "Override automatic definition of runs to mark > > > discontinuities in data" button as well as created two runs to > > > contain the required data > > > > > > But I get a "Run 2 has not been assigned to a dataset" error. > > > How I can exclude a bad wedge in the middle of my data from within > > > scala without going through the split and sort route in mtzutils. I > > > have attached the com file generated by ccp4i and the error text > > below > > > > > > Thanks for your help > > > Hari Jayaram > > > Postdoc , Miller Lab > > > Brandeis University > > > > > > > > > ----------------------------- > > > The error I get is > > > ----------------------------- > > > 13 714 715 716 > > > 717 718 719 720 > > > > > > **** Run 2 has not been assigned to a dataset **** > > > > > > > > > *************************************************************************** > > > * Information from CCP4Interface script > > > > > > *************************************************************************** > > > The program run with command: scala HKLIN "/Users/hari/aps_feb08/ > > > p2-2/p2-2_A1_1_0001_sorted.mtz" HKLOUT "/tmp/hari/p2_2_12_2_mtz.tmp" > > > SCALES "/Users/hari/aps_feb08/p2-2/p2_2_12.scala" ROGUES "/Users/ > > > hari/aps_feb08/p2-2/p2_2_12_rogues.log" NORMPLOT "/Users/hari/ > > > aps_feb08/p2-2/p2_2_12_normplot.xmgr" ANOMPLOT "/Users/hari/ > > > aps_feb08/p2-2/p2_2_12_anomplot.xmgr" PLOT "/Users/hari/aps_feb08/ > > > p2-2/p2_2_12_surface_plot.plt" CORRELPLOT "/Users/hari/aps_feb08/ > > > p2-2/p2_2_12_correlplot.xmgr" > > > has failed with error message > > > Scala: ***** Error in input ***** > > > > > > *************************************************************************** > > > > > > > > > In the GUI and the com file I can see that Run 2 has been > > > correctly assigned to the correct dataset , i.e the same as Run 1 , > > > but I still see this error > > > > > > ------------------------------------------------------------------------- > > > The ccp4i generated com files is attached here > > > > > ------------------------------------------------------------------------ > > > > > > ******************************************************************* > > > /tmp/hari/p2_2_12_3_com.tmp > > > ******************************************************************* > > > title Scala anon and deleted batches 200_400b try with two run > > > definitions > > > run 1 - > > > INCLUDE batch 1 to 200 > > > run 2 - > > > INCLUDE batch 400 to 720 > > > RUN 1 reference > > > name run 1 project p2_2 crystal p2-2_A1_1 dataset p2_2 > > > name run 2 project p2_2 crystal p2-2_A1_1 dataset p2_2 > > > exclude EMAX - > > > 10.0 > > > exclude batch - > > > 400 to 540 > > > partials - > > > check - > > > test 0.95 1.05 - > > > nogap > > > intensities PROFILE - > > > PARTIALS > > > final PARTIALS > > > scales - > > > rotation SPACING 5 - > > > secondary 6 - > > > bfactor ON - > > > BROTATION SPACING 20 > > > UNFIX V > > > FIX A0 > > > UNFIX A1 > > > initial MEAN > > > tie surface 0.001 > > > tie bfactor 0.3 > > > cycles 10 converge 0.3 reject 2 > > > anomalous on > > > output AVERAGE > > > print cycles nooverlap > > > RSIZE 80 > > > ## This script run with the command ########## > > > # scala HKLIN "/Users/hari/aps_feb08/p2-2/p2-2_A1_1_0001_sorted.mtz" > > > HKLOUT "/tmp/hari/p2_2_12_2_mtz.tmp" SCALES "/Users/hari/aps_feb08/ > > > p2-2/p2_2_12.scala" ROGUES "/Users/hari/aps_feb08/p2-2/ > > > p2_2_12_rogues.log" NORMPLOT "/Users/hari/aps_feb08/p2-2/ > > > p2_2_12_normplot.xmgr" ANOMPLOT "/Users/hari/aps_feb08/p2-2/ > > > p2_2_12_anomplot.xmgr" PLOT "/Users/hari/aps_feb08/p2-2/ > > > p2_2_12_surface_plot.plt" CORRELPLOT "/Users/hari/aps_feb08/p2-2/ > > > p2_2_12_correlplot.xmgr" > > > > > >
