Re: [ccp4bb] SCALA failed message

- Protein crystallography

Main steps:

- Protein purification
- Crystallisation

Special:

- Programs for crystallography
- X-ray detectors

Basic tutorials:

   - Chemistry
   - Protein
   - Peptide
   - Amino Acids

Xtal community:

- CCP4BB

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: protein folds
From: Jayashankar s {- dot -} jayashankar {- at -} GMAIL {- dot -} COM
Date: 2009-02-25

Next message:
Subject: Re: protein folds
From: Paul Emsley paul {- dot -} emsley {- at -} BIOCH {- dot -} OX {- dot -} AC {- dot -} UK
Date: 2009-02-25

Subject: Re: SCALA failed message
From: James Foadi james_foadi {- at -} YAHOO {- dot -} CO {- dot -} UK
Date: 2009-02-25

Thank you Graeme.
I have installed ccp4 6.1.1 and ran the same job on SCALA succesfully.

J

Dr James Foadi PhD
Membrane Protein Laboratory
Diamond Light Source Ltd.
Diamond House
Harwell Science and Innovation Campus
Didcot
Oxfordshire
OX11 0DE
United Kingdom

office email: james.foadi@diamond.ac.uk
alternative email: j.foadi@imperial.ac.uk
web page:

----- Original Message ----
From: Graeme Winter
To: James Foadi
Cc: CCP4BB@jiscmail.ac.uk
Sent: Tuesday, 24 February, 2009 18:51:16
Subject: Re: [ccp4bb] SCALA failed message

Hi James,

You are the victim of an epic command line. This has been fixed in the
6.1.1 release, but you will find that using a shorter path (i.e.
noniso rather than non-isomorphism &c.) will pull the command line
down to something more sensible.

CCP4i writes this out to allow the job to be rerun in a comment, but
the comment is too long for Scala!

Cheers,

Graeme

2009/2/24 James Foadi :
> Dear all,
> I am running SCALA using ccp4i. The generated command file is:
>
>
> ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------
>
>
> *******************************************************************
> /tmp/james/NONISO_insulin_from_liz_6_2_com.tmp
> *******************************************************************
> title Scale merged insulin_from_liz _ Datasets in1, in2, in3, in4, in5
> run 1 -
> INCLUDE batch 1 to 100
> run 2 -
> INCLUDE batch 201 to 380
> run 3 -
> INCLUDE batch 401 to 522
> run 4 -
> INCLUDE batch 601 to 651
> run 5 -
> INCLUDE batch 701 to 720
> RUN 2 reference
> name run 1 project New crystal New dataset New
> name run 2 project New crystal New dataset New
> name run 3 project New crystal New dataset New
> name run 4 project New crystal New dataset New
> name run 5 project New crystal New dataset New
> exclude EMAX -
> 10.0
> partials -
> check -
> test 0.95 1.05 -
> nogap
> intensities INTEGRATED -
> 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
> output AVERAGE
> print brief nooverlap
> RSIZE 80
> ## This script run with the command ##########
> # /home/james/build/ccp4-6.1.0/bin/scala HKLIN "/home/james/gwyndaf/non-isomorphism/data_created/insulin_from_liz/exp_01/in1_in2_in3_in4_in5_MS_1_001.mtz" HKLOUT "/tmp/james/NONISO_insulin_from_liz_6_1_mtz.tmp" SCALES "/home/james/gwyndaf/non-isomorphism/data_created/insulin_from_liz/NONISO_insulin_from_liz_6.scala" ROGUES "/home/james/gwyndaf/non-isomorphism/data_created/insulin_from_liz/NONISO_insulin_from_liz_6_rogues.log" NORMPLOT "/home/james/gwyndaf/non-isomorphism/data_created/insulin_from_liz/NONISO_insulin_from_liz_6_normplot.xmgr" ANOMPLOT "/home/james/gwyndaf/non-isomorphism/data_created/insulin_from_liz/NONISO_insulin_from_liz_6_anomplot.xmgr" PLOT "/home/james/gwyndaf/non-isomorphism/data_created/insulin_from_liz/NONISO_insulin_from_liz_6_surface_plot.plt" CORRELPLOT "/home/james/gwyndaf/non-isomorphism/data_created/insulin_from_liz/NONISO_insulin_from_liz_6_correlplot.xmgr" ROGUEPLOT
> "/home/james/gwyndaf/non-isomorphism/data_created/insulin_from_liz/NONISO_insulin_from_liz_6_rogueplot.xmgr"
> ################################################
> ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------
>
> Unfortunately SCALA stops immediately with the following error message:
>
>
> -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------
> ** Unrecognized keyword **
>
> **** RUN command must come before SCALES definition ****
>
> ** Missing or illegal value **
> -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------
>
> Any idea on what's wrong? I have to say, I had run this before with similar data (up to 4 runs), and had never this problem.
>
> Thank you!
>
> J
>
> Dr James Foadi PhD
> Membrane Protein Laboratory
> Diamond Light Source Ltd.
> Diamond House
> Harwell Science and Innovation Campus
> Didcot
> Oxfordshire
> OX11 0DE
> United Kingdom
>
>
> office email: james.foadi@diamond.ac.uk
> alternative email: j.foadi@imperial.ac.uk
> web page:
>
>
>
>
>

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: protein folds
From: Jayashankar s {- dot -} jayashankar {- at -} GMAIL {- dot -} COM
Date: 2009-02-25

Next message:
Subject: Re: protein folds
From: Paul Emsley paul {- dot -} emsley {- at -} BIOCH {- dot -} OX {- dot -} AC {- dot -} UK
Date: 2009-02-25