Re: [ccp4bb] Refmac5.scripts error -

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

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Subject: Re: mapping sequence conservation metrics on the B factor column ...
From: Miguel Ortiz Lombardia miguel {- dot -} ortiz-lombardia {- at -} AFMB {- dot -} UNIV-MRS {- dot -} FR
Date: 2009-01-31

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Subject: Re: X-ray photon correlation length
From: "Nave, C (Colin)" colin {- dot -} nave {- at -} DIAMOND {- dot -} AC {- dot -} UK
Date: 2009-01-31

Subject: Re: Refmac5.scripts error -
From: "Stein, ND (Norman)" norman {- dot -} stein {- at -} STFC {- dot -} AC {- dot -} UK
Date: 2009-01-31

Hi Jon

There's no point applying the patch; it should have been incorporated
into all versions of CCP4 subsequent to 5.0.2 already. The problem
seems to be that a spacegroup has not been set in your input mtz file. I
would try editing the file to set the spacegroup, using the SFTOOLS
program included in CCP4.

Norman

-----Original Message-----
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Jonathan Marvin Caruthers
Sent: 31 January 2009 00:08
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Refmac5.scripts error -

All:

I'm trying to get the latest version of Refmac up and running - the one
bundled into ccp4 6.1.0 - and have come across an error I've never seen
before:

#CCP4I TERMINATION STATUS 0 Error from script
/usr/local/ccp4-6.1.0/ccp4-6.1.0/ccp4i/scripts/refmac5.script: can't
read "space_group": no such variable #CCP4I TERMINATION TIME 29 Jan 2009
18:23:02 #CCP4I TERMINATION OUTPUT_FILES
/home/caruthej/bo3/ccp4/bo3A_71_Unspecified.refmac.cif bo3A #CCP4I
MESSAGE Task failed

I found that this error is mentioned on the problems page for ccp4
version 5.0 - 5.0.2 and the suggested fix is to apply the following
patch:

ftp://ftp.ccp4.ac.uk/ccp4/5.0.2/patches/CCP4_utils-25Aug2004.tcl.diff

to the scripts directory.

Does anyone know if the same patch can be used to fix this error for the
latest version of Refmac5 that's bundled into ccp4 6.1.0 as well as the
version that was available in 2004 when the patch was created? Sorry
for the simplistic question, but I don't have permission to install or
modify programs on the system I'm using so I can't readily perform the
experiment and the IT guy wants to know if anybody has any experience
using this patch with the latest version of Refmac5 before he starts
monkeying around with it.

thanks,

Jon Caruthers
Stowell Lab
University of Colorado

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

Next message:
Subject: Re: X-ray photon correlation length
From: "Nave, C (Colin)" colin {- dot -} nave {- at -} DIAMOND {- dot -} AC {- dot -} UK
Date: 2009-01-31