Hi
I noticed last week that, although the CCP4 updater for OSX requires 64-bit
(see CCP4 discussions passim), all the executables are 32-bit (or at least in
my current copy, updated a few weeks ago). So there is an inconsistency - no
doubt this will be sorted out shortly.
If you want a 64-bit build of Pointless for OSX then see Phil Evans' ftp site -
ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre
Use the most recent version - it may solve your problem.
On 12 Aug 2013, at 03:28, Bosch, Juergen wrote:
> Hi Sheena,
>
> simple quickfix to your problem:
> a) Run CAD and limit the output resolution on that mtz file so you don't run
> into the memory allocation error of pointless.
> b) try phenix.xtriage also if it is not a CCP4 program
>
> Jürgen
>
> ......................
> Jürgen Bosch
> Johns Hopkins University
> Bloomberg School of Public Health
> Department of Biochemistry & Molecular Biology
> Johns Hopkins Malaria Research Institute
> 615 North Wolfe Street, W8708
> Baltimore, MD 21205
> Office: +1-410-614-4742
> Lab: +1-410-614-4894
> Fax: +1-410-955-2926
> http://lupo.jhsph.edu
>
>
>
>
> On Aug 11, 2013, at 9:54 PM, Sheena McGowan (Med) wrote:
>
>> Dear all
>>
>> We have been trying to run pointless on a large mtz file which seems to be
>> allocating more than 1.5Gb of memory resulting in the following error:
>>
>> The program run with command: /Applications/ccp4-6.3.0/bin/pointless
>> has failed with error message
>> pointless(507) malloc: *** mmap(size=1577435136) failed (error code=12)
>> *** error: can't allocate region
>> *** set a breakpoint in malloc_error_break to debug
>>
>> We are using OSX 10.8.4 and believe that we need a 64bit version of
>> pointless.
>>
>> Looking at the pre release ftp site, we found the latest versions of
>> pointless compiled for OSX 10.8, however they do not run.
>>
>> dyld: Symbol not found: __ZNSt11range_errorD1Ev
>> Referenced from: /Applications/ccp4-6.3.0/bin/pointless-1.8.7.osx10.8
>> Expected in: /usr/lib/libstdc++.6.dylib
>> in /Applications/ccp4-6.3.0/bin/pointless-1.8.7.osx10.8
>>
>> Any help would be greatly appreciated (and any know if there is a upcoming
>> release of a pre-compiled CCP4 OSX-64bit??)
>>
>> Regards
>> Sheena
>>
>>
>>
>> SHEENA McGOWAN | ARC Future Fellow
>> Department of Biochemistry and Molecular Biology
>> MONASH UNIVERSITY
>> Rm 243, Building 77, Wellington Rd, Clayton
>> Victoria, AUSTRALIA 3800
>> T + 61 3 9902 9309 | F + 61 3 9902 9500
>> E sheena.mcgo...@monash.edu | Skype s.mcgowan
>> W http://www.med.monash.edu.au/biochem/staff/mcgowan.html
>>
>> Australian Society for Biochemistry and Molecular Biology (State
>> Representative) http://www.asbmb.org.au/
>>
>> 39th Lorne Conference for Protein Structure and Function
>> http://www.lorneproteins.org
>> February 9-13, 2014. Mantra Lorne, Lorne, AUSTRALIA
>>
>
>
Harry
--
** note change of address **
Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue,
Cambridge Biomedical Campus, Cambridge CB2 0QH
Chairman of European Crystallographic Association SIG9 (Crystallographic
Computing)
