Hi.
Based on your explanation it looks like you want to remove your "RUN 1
REFERENCE" and "EXCLUDE BATCH 400 TO 500" lines from your script. You might
also want to try without the NAME lines on the off chance that the harvesting
stuff is causing the problems.
My best guess is that the "RUN 1 REFERENCE" is conflicting with assigning both
runs the same dataset name, but that's only a guess.
Good luck,
Pete
-----Original Message-----
From: CCP4 bulletin board on behalf of hari jayaram
Sent: Fri 3/14/2008 1:57 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] exclude range within data in scala , discontinuous run in
scala problem
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"
