Child killing and/or wrong bus seems to be related with static
compilation on Mac intel OS 10.5. Existence of this bug is the reason
why the version with bug fixes was not announced.
If you build from source code then this bug can be overcomed
Download source files and copy them to ccp4 source file directory and
build from source.
Source codes can be found www.ysbl.york.ac.uk/refmac/latest_refmac.html
After gunzipping and untarring (it will work if you have build ccp4
from source)
cp *.f $CPROG/refmac5_/
cp *.fh $CPROG/refmac5_/
cp *.c $CPROG/refmac5_/
cp *.cpp $CPROG/refmac5_/
cp *.h $CPROG/refmac5_/
cd $CPROG
rm *.o
make refmac5
cp refmac5 $CBIN/
After this procedure bus should be fine and child will also be safe.
Garib
On 24 Feb 2009, at 14:16, Anita Lewit-Bentley wrote:
Hi Ian,
A bug was reported with that version of Refmac, though I've no idea
if that would cause your problem: you should upgrade to the latest
version from the York website.
Done - and here is what happens:
1) the latest CCP4 package (6.1.1) runs the same version of Refmac
(5.5.0066) and, predictably, crashes the same way;
2) on the Refmac webside there are much more recent versions of
Refmac, not yet incorporated into the CCP4 package. Versions 72 and
higher have a bug fix for TLS refinement.
3) included version 5.5.0086 (the precompiled version for Mac -
intel) in CCP4 6.1 - and that runs fine ....
....except that it exits with a "bus error, child killed"!!!!
I HATE seeing a child killed ....
but anyway, the output pdb and mtz files exist in the "scratch"
directory with a .tmp extension, but otherwise perfectly useable.
So I can scrape along if I remember to copy the .tmp files accross
to my working directory. Better than nothing!
Thanks for your hint.
Cheers,
Anita
-----Original Message-----
From: [email protected] [mailto:[email protected]
] On
Behalf Of Anita Lewit-Bentley
Sent: 23 February 2009 15:31
To: [email protected]
Subject: TLS refinement in Refmac gets stuck
Dear ccp4 folks,
I am refining a structure in several crystal forms, with several
molecules
in the asymmetric unit. The structure is rather flexible, so I am
using
TLS refinement, having first submitted the coordinates to the
TLSMD server
(http://skuld.bmsc.washington.edu/~tlsmd/
<http://skuld.bmsc.washington.edu/~tlsmd/jobs/TLSMD7413_IBXkmSis/ANALYSIS/
index.html> ).
The TLS refinement worked OK with REFMAC 5.2.0019 (CCP4 6.0.2) for 3
molecules in the asu, but not for crystal forms with 6 molecules/
asu (it
just got hung).
For the latter crystal forms I have switched to CCP4 6.1.0 with
REFMAC
5.5.0066, where it worked fine for two crystals - and now plays up
for the
third crystal!
It is not exactly crashing, so I don't know what is going on. This
is the
last part of the logfile:
"Problem
xyz 1230 5.6147661 -5.1691742 2.8234024 -
1.55429840E-02 9.35771316E-02 0.17803398 0.23723726
-0.13626081
5.39243035E-02 -0.14011805 -1.55429840E-02 0.11864197
0.40574944
0.71992165 0.57164854 -0.39361250
**************************************************************************
*
* Information from CCP4Interface script
**************************************************************************
*
Writing final coordinates (XYZOUT) to
/Users/anita/work/Integ/SOLEIL_09_08/3MSe_NTLS9_8_6_refmac1.pdb
**************************************************************************
*
**************************************************************************
*
* Information from CCP4Interface script
**************************************************************************
*
Writing final phases (HKLOUT) to
/Users/anita/work/Integ/SOLEIL_09_08/3M_Se_TLS_refmac1.mtz
**************************************************************************
*
**************************************************************************
*
* Information from CCP4Interface script
**************************************************************************
*
Writing final TLS (TLSOUT) to
/Users/anita/work/Integ/SOLEIL_09_08/3MSe_NTLS9_8_6_refmac1.tls
**************************************************************************
*
"
Unfortunately, there are NO files written out! There is no real
error
message either, the CCP4i interface says the job has finished
normally.
I have already tried to vary the number of TLS fragments, with no
better
result. The older Refmac just gets hung....
Any help will be appreciated!
Thanks,
Anita
Anita Lewit-Bentley
Unité d'Immunologie Structurale
CNRS URA 2185
Département de Biologie Structurale & Chimie
Institut Pasteur
25 rue du Dr. Roux
75724 Paris cedex 15
FRANCE
Tel: 33- (0)1 45 68 88 95
FAX: 33-(0)1 40 61 30 74
email: [email protected]
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