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
