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

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CCP4bb <-- 2008 <-- March 2008 <-- 14 March 2008

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Subject: Re: exclude range within data in scala , discontinuous run in scala problem
From: Phil Evans pre {- at -} MRC-LMB {- dot -} CAM {- dot -} AC {- dot -} UK
Date: 2008-03-14

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Subject: Tricks to solubilize protein
From: Ju He julie {- dot -} he {- at -} GMAIL {- dot -} COM
Date: 2008-03-14

Subject: Re: 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 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 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"
> >
>

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CCP4bb <-- 2008 <-- March 2008 <-- 14 March 2008

Next message:
Subject: Tricks to solubilize protein
From: Ju He julie {- dot -} he {- at -} GMAIL {- dot -} COM
Date: 2008-03-14