Are you using the 32-bit or 64-bit coot? I have to confess only having checked the 64-bit version (which worked ok in my hands).
On Jan 7, 2010, at 9:31 PM, Jan Abendroth wrote: > Hi all, > I am trying to update coot on osx 10.6 from a 0.6-pre version to the current > fink version (0.6.1-pre). Doing the usual fink spiel (fink selfupdate, fink > index ...) I ran into some issues during 'fink update-all': a few packages > that are dbus and dbus-dependent would not install. All the rest of the core > packages could be installed manually. > > Coot now would install just fine (fink install coot) after I removed the old > installation (fink remove coot). > > Now coot starts up fine as 0.6.1, coordinates can be read, analyzed and > modified. However, I cannot read in maps from mtz files, see message from the > xterminal below. Coot actually totally freezes in this process. Similarly, > ccp4 maps cannot be read in either due to a issue with space groups. > > Any ideas would be highly welcome > > Jan > > reading in mtz file > ... > initalize graphics molecules...done. > (handle-read-draw-molecule-with-recentre > "204964c6_2009-10-26_als503_i213_xds_refmac21-coot-Ab31.pdb" 1) > Reading coordinate file: > 204964c6_2009-10-26_als503_i213_xds_refmac21-coot-Ab31.pdb > PDB file 204964c6_2009-10-26_als503_i213_xds_refmac21-coot-Ab31.pdb has been > read. > Spacegroup: I 21 3 > Cell: 135.38 135.38 135.38 90 90 90 > INFO:: Found 1 models > Model 1 had 0 links > Symmetry available for this molecule > INFO:: NCS chain comparison 170/172 > INFO:: fill_ghost_info Constructed 1 ghosts > Ghost 0 name: "NCS found from matching Chain B onto Chain A" > Molecule 0 read successfully > coot-real(86853,0xa01cd500) malloc: *** error for object 0x2650a00: pointer > being freed was not allocated > *** set a breakpoint in malloc_error_break to debug > > [... same message many times over ...] > > Spacegroup_registry: ASU warning, LGhash=0x > Spacegroup_registry: ASU fail > INFO:: not an mtz file: 204964c6_2009-10-26_als503_i213_xds_refmac21.mtz > > reading in a ccp4 style map: > saved directory name: /Users/jan/deCODE/ssgcid/AnphA.01382.a/ccp4/ > CCP4 map filename: > /Users/jan/deCODE/ssgcid/AnphA.01382.a/ccp4/204964c6_2009-10-26_als503_i213_xds_refmac21_2Fofc.map > INFO:: map file type was determined to be CCP4 type > allocating space in read_ccp4_map > attempting to read CCP4 map: > /Users/jan/deCODE/ssgcid/AnphA.01382.a/ccp4/204964c6_2009-10-26_als503_i213_xds_refmac21_2Fofc.map > Spgr_cacheobj: symops fail > > -- > Jan Abendroth > Emerald BioStructures > Seattle / Bainbridge Island WA, USA > home: Jan.Abendroth_at_gmail.com > work: JAbendroth_at_embios.com > http://www.emeraldbiostructures.com > > > > > > -- > Jan Abendroth > Emerald BioStructures > Seattle / Bainbridge Island WA, USA > home: Jan.Abendroth_at_gmail.com > work: JAbendroth_at_embios.com > http://www.emeraldbiostructures.com > > > > > >
