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: [log in to unmask]
>>> [mailto:[log in to unmask]] On
>>> Behalf Of Anita Lewit-Bentley
>>> Sent: 23 February 2009 15:31
>>> To: [log in to unmask]
>>> 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: [log in to unmask]
>>>
>>
>>
>>
>> Disclaimer
>> This communication is confidential and may contain privileged
>> information intended solely for the named addressee(s). It may not be
>> used or disclosed except for the purpose for which it has been sent.
>> If you are not the intended recipient you must not review, use,
>> disclose, copy, distribute or take any action in reliance upon it. If
>> you have received this communication in error, please notify Astex
>> Therapeutics Ltd by emailing [log in to unmask] and
>> destroy all copies of the message and any attached documents.
>> Astex Therapeutics Ltd monitors, controls and protects all its
>> messaging traffic in compliance with its corporate email policy. The
>> Company accepts no liability or responsibility for any onward
>> transmission or use of emails and attachments having left the Astex
>> Therapeutics domain. Unless expressly stated, opinions in this
>> message are those of the individual sender and not of Astex
>> Therapeutics Ltd. The recipient should check this email and any
>> attachments for the presence of computer viruses. Astex Therapeutics
>> Ltd accepts no liability for damage caused by any virus transmitted
>> by this email. E-mail is susceptible to data corruption,
>> interception, unauthorized amendment, and tampering, Astex
>> Therapeutics Ltd only send and receive e-mails on the basis that the
>> Company is not liable for any such alteration or any consequences
>> thereof.
>> Astex Therapeutics Ltd., Registered in England at 436 Cambridge
>> Science Park, Cambridge CB4 0QA under number 3751674
>>
>>
>
>
>
|