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<mailto: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<http://www.lorneproteins.org/> February 9-13, 2014. Mantra Lorne, Lorne, AUSTRALIA
