Hi Folks,
If anyone wants to do this on an Intel mac you will need a fortran
compiler, which is not installed by XCode. There is a compatible
gfortran here:
http://r.research.att.com/tools/
which in my experience works fine, though is completely incapable of
producing static binaries.
There are instructions for the source-code build here:
http://www.ccp4wiki.org/~ccp4wiki/wiki/index.php?title=CCP4_6.1_installation#Source_Code_Installation
and here:
http://www.ccp4wiki.org/~ccp4wiki/wiki/index.php?title=CCP4_installation#Source_Code_Installation
Unfortunately, because the CCP4 release is built with the Intel
compilers (not gfortran) for this platform you can't just drop refmac5
onto an existing CCP4 installation and build, so you have to build
everything :o(
Garib: what compilers do you use such that someone building it
themselves will get a version which works, but using your same source
code and your compilers it does not?
Best wishes,
Graeme
2009/2/24 Garib Murshudov <[log in to unmask]>:
> 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: [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]
>>>>
>>>
>>>
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