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[ccp4bb] exclude range within data in scala , discontinuous run in scala problem
 

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CCP4bb <-- 2008 <-- March 2008 <-- 14 March 2008
Previous message:
Subject: energy minimise ligand model
From: Thomas Edwards T {- dot -} A {- dot -} Edwards {- at -} LEEDS {- dot -} AC {- dot -} UK
Date: 2008-03-14 		Next message:
Subject: Re: exclude range within data in scala , discontinuous run in scala problem
From: "Meyer, Peter" pameyer {- at -} MCW {- dot -} EDU
Date: 2008-03-14


Subject: exclude range within data in scala , discontinuous run in scala problem
From: hari jayaram harijay {- at -} GMAIL {- dot -} COM
Date: 2008-03-14
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"

CCP4bb navigation

CCP4bb <-- 2008 <-- March 2008 <-- 14 March 2008
Previous message:
Subject: energy minimise ligand model
From: Thomas Edwards T {- dot -} A {- dot -} Edwards {- at -} LEEDS {- dot -} AC {- dot -} UK
Date: 2008-03-14 		Next message:
Subject: Re: exclude range within data in scala , discontinuous run in scala problem
From: "Meyer, Peter" pameyer {- at -} MCW {- dot -} EDU
Date: 2008-03-14


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