Quick navigation:        Home   |    Site Map   ||    References   |    Biography   ||    Copyright   |    Other copyright   |    Contact us   |   
Protein structure
 

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

Basic tutorials: 		 
 

CCP4bb navigation

CCP4bb <-- 2008 <-- March 2008 <-- 17 March 2008
Previous message:
Subject: problem installing arp/warp
From: Mario Sanches msanches {- at -} LNLS {- dot -} BR
Date: 2008-03-17 		Next message:
Subject: Re: question about processing data
From: Bart Hazes bart {- dot -} hazes {- at -} UALBERTA {- dot -} CA
Date: 2008-03-17


Subject: Re: exclude range within data in scala , discontinuous run in scala problem
From: hari jayaram harijay {- at -} GMAIL {- dot -} COM
Date: 2008-03-17
Hi Phil,Thanks for your email. I did get it to work with the options you
suggested .
i.e
Toggle ON "Override automatic definition of runs to mark discontinuities in
data
Toggle ON Define Runs
Toggle OFF Use run 1 as reference run.

Setup runs as follows ( intended to exclude batches 200 to 400 from a total
dataset of 1 to 720 )

Run 1 from 1 to 200
Run 2 from 400 to 720

This combination worked as you said it would.
Thank you for your help

Hari Jayaram
Postdoc
Brandeis University







On Sat, Mar 15, 2008 at 3:44 AM, Phil Evans wrote:

> 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
> > 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"
> > >
> >
>
ProteinCrystallography.org: Copyright 2006-2007 by Quid United Ltd