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"
>
