Re: [ccp4bb] TLS refinement in Refmac gets stuck

[Eleanor Dodson]

Yes - I found that irritating bug; it is a disaster for less experienced 
users..

It doesnt seem to happen with the linux installation..
 Eleanor


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: owner-ccp...@jiscmail.ac.uk 
[mailto:owner-ccp...@jiscmail.ac.uk] On
Behalf Of Anita Lewit-Bentley
Sent: 23 February 2009 15:31
To: CCP4BB@JISCMAIL.AC.UK
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: ale...@pasteur.fr




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