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 <
[log in to unmask]>
> 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"
> >
>