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
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> --
> Jan Abendroth
> Emerald BioStructures
> Seattle / Bainbridge Island WA, USA
> home: Jan.Abendroth_at_gmail.com
> work: JAbendroth_at_embios.com
> http://www.emeraldbiostructures.com
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