Dear all, I am using coot on Mac OS X 10.5.6 and have a problem. I used coot for a year without a problem. Recently I updated to coot-0.6-pre-1-1876 using fink apparently something went wrong during the update. Now I can startup coot but it behaves very badly, displaying no or wrong bonds and it had problems opening every file. I tried to install an other version of coot but I still have the problems. It seems there are muliple versions of some files or something like that. This is what is when when I start coot:
Kind regards and thank you in advance for your help Robert Floor robertfloor% /usr/local/xtal/coot/bin/coot Acquiring application resources from /usr/local/xtal/coot/share/coot/cootrc INFO:: splash_screen_pixmap_dir /usr/local/xtal/coot/share/coot/pixmaps INFO:: Colours file: /usr/local/xtal/coot/share/coot/colours.def loaded There are 117 data in /usr/local/xtal/coot/share/coot/lib/data/monomers/list/mon_lib_list.cif problem reading bond mmCIFLoop problem reading bond mmCIFLoop problem reading bond mmCIFLoop problem reading bond mmCIFLoop problem reading link plane mmCIFLoop problem reading link plane mmCIFLoop problem reading link plane mmCIFLoop problem reading link plane mmCIFLoop problem reading link plane mmCIFLoop problem reading link plane mmCIFLoop problem reading link plane mmCIFLoop problem reading link plane mmCIFLoop problem reading bond mmCIFLoop problem reading link plane mmCIFLoop problem reading link plane mmCIFLoop problem reading link plane mmCIFLoop problem reading link plane mmCIFLoop problem reading link plane mmCIFLoop problem reading link plane mmCIFLoop problem reading link plane mmCIFLoop problem reading link plane mmCIFLoop problem reading bond mmCIFLoop problem reading link plane mmCIFLoop problem reading link plane mmCIFLoop problem reading link plane mmCIFLoop problem reading link plane mmCIFLoop problem reading link plane mmCIFLoop problem reading link plane mmCIFLoop problem reading link plane mmCIFLoop problem reading link plane mmCIFLoop problem reading bond mmCIFLoop problem reading link torsion mmCIFLoop problem reading link plane mmCIFLoop problem reading link plane mmCIFLoop problem reading link plane mmCIFLoop problem reading link plane mmCIFLoop problem reading link plane mmCIFLoop problem reading link plane mmCIFLoop problem reading link plane mmCIFLoop problem reading link plane mmCIFLoop problem reading bond mmCIFLoop problem reading link torsion mmCIFLoop problem reading link plane mmCIFLoop problem reading link plane mmCIFLoop problem reading link plane mmCIFLoop problem reading link plane mmCIFLoop problem reading link plane mmCIFLoop problem reading link plane mmCIFLoop problem reading link plane mmCIFLoop problem reading link plane mmCIFLoop problem reading bond mmCIFLoop problem reading link torsion mmCIFLoop problem reading link plane mmCIFLoop problem reading link plane mmCIFLoop problem reading link plane mmCIFLoop problem reading link plane mmCIFLoop problem reading link plane mmCIFLoop problem reading link plane mmCIFLoop problem reading link plane mmCIFLoop problem reading link plane mmCIFLoop problem reading bond mmCIFLoop problem reading bond mmCIFLoop problem reading link torsion mmCIFLoop problem reading bond mmCIFLoop problem reading bond mmCIFLoop problem reading bond mmCIFLoop problem reading bond mmCIFLoop problem reading bond mmCIFLoop problem reading bond mmCIFLoop problem reading bond mmCIFLoop problem reading bond mmCIFLoop problem reading bond mmCIFLoop problem reading bond mmCIFLoop problem reading bond mmCIFLoop problem reading bond mmCIFLoop problem reading bond mmCIFLoop problem reading bond mmCIFLoop problem reading bond mmCIFLoop problem reading bond mmCIFLoop problem reading bond mmCIFLoop problem reading bond mmCIFLoop problem reading bond mmCIFLoop problem reading bond mmCIFLoop problem reading bond mmCIFLoop problem reading link torsion mmCIFLoop problem reading link torsion mmCIFLoop problem reading link torsion mmCIFLoop problem reading bond mmCIFLoop problem reading link torsion mmCIFLoop problem reading link torsion mmCIFLoop problem reading link torsion mmCIFLoop problem reading bond mmCIFLoop problem reading bond mmCIFLoop problem reading link torsion mmCIFLoop problem reading link torsion mmCIFLoop problem reading link torsion mmCIFLoop problem reading bond mmCIFLoop problem reading link torsion mmCIFLoop problem reading link torsion mmCIFLoop problem reading link torsion mmCIFLoop problem reading bond mmCIFLoop problem reading link torsion mmCIFLoop problem reading link torsion mmCIFLoop problem reading link torsion mmCIFLoop problem reading bond mmCIFLoop problem reading link torsion mmCIFLoop problem reading link torsion mmCIFLoop problem reading link torsion mmCIFLoop problem reading bond mmCIFLoop problem reading bond mmCIFLoop problem reading link torsion mmCIFLoop problem reading link torsion mmCIFLoop problem reading link torsion mmCIFLoop problem reading bond mmCIFLoop problem reading link torsion mmCIFLoop problem reading link torsion mmCIFLoop problem reading link torsion mmCIFLoop problem reading bond mmCIFLoop problem reading bond mmCIFLoop problem reading bond mmCIFLoop problem reading bond mmCIFLoop problem reading bond mmCIFLoop problem reading link plane mmCIFLoop problem reading link plane mmCIFLoop problem reading link plane mmCIFLoop problem reading link plane mmCIFLoop problem reading link plane mmCIFLoop problem reading link plane mmCIFLoop problem reading bond mmCIFLoop problem reading link plane mmCIFLoop problem reading link plane mmCIFLoop problem reading link plane mmCIFLoop problem reading link plane mmCIFLoop problem reading link plane mmCIFLoop problem reading link plane mmCIFLoop problem reading bond mmCIFLoop problem reading bond mmCIFLoop problem reading bond mmCIFLoop problem reading link plane mmCIFLoop problem reading link plane mmCIFLoop problem reading link plane mmCIFLoop problem reading link plane mmCIFLoop problem reading link plane mmCIFLoop problem reading link plane mmCIFLoop problem reading bond mmCIFLoop problem reading bond mmCIFLoop problem reading bond mmCIFLoop problem reading bond mmCIFLoop problem reading bond mmCIFLoop problem reading bond mmCIFLoop problem reading bond mmCIFLoop problem reading bond mmCIFLoop problem reading bond mmCIFLoop problem reading bond mmCIFLoop problem reading bond mmCIFLoop problem reading bond mmCIFLoop problem reading bond mmCIFLoop There are 2 data in /usr/local/xtal/coot/share/coot/lib/data/monomers/a/ALA.cif There are 2 data in /usr/local/xtal/coot/share/coot/lib/data/monomers/a/ASP.cif There are 2 data in /usr/local/xtal/coot/share/coot/lib/data/monomers/a/ASN.cif There are 2 data in /usr/local/xtal/coot/share/coot/lib/data/monomers/c/CYS.cif There are 2 data in /usr/local/xtal/coot/share/coot/lib/data/monomers/g/GLN.cif There are 2 data in /usr/local/xtal/coot/share/coot/lib/data/monomers/g/GLY.cif There are 2 data in /usr/local/xtal/coot/share/coot/lib/data/monomers/g/GLU.cif There are 2 data in /usr/local/xtal/coot/share/coot/lib/data/monomers/p/PHE.cif There are 2 data in /usr/local/xtal/coot/share/coot/lib/data/monomers/h/HIS.cif There are 2 data in /usr/local/xtal/coot/share/coot/lib/data/monomers/i/ILE.cif There are 2 data in /usr/local/xtal/coot/share/coot/lib/data/monomers/l/LYS.cif There are 2 data in /usr/local/xtal/coot/share/coot/lib/data/monomers/l/LEU.cif There are 2 data in /usr/local/xtal/coot/share/coot/lib/data/monomers/m/MET.cif There are 2 data in /usr/local/xtal/coot/share/coot/lib/data/monomers/m/MSE.cif There are 2 data in /usr/local/xtal/coot/share/coot/lib/data/monomers/p/PRO.cif There are 2 data in /usr/local/xtal/coot/share/coot/lib/data/monomers/a/ARG.cif There are 2 data in /usr/local/xtal/coot/share/coot/lib/data/monomers/s/SER.cif There are 2 data in /usr/local/xtal/coot/share/coot/lib/data/monomers/t/THR.cif There are 2 data in /usr/local/xtal/coot/share/coot/lib/data/monomers/v/VAL.cif There are 2 data in /usr/local/xtal/coot/share/coot/lib/data/monomers/t/TRP.cif There are 2 data in /usr/local/xtal/coot/share/coot/lib/data/monomers/t/TYR.cif There are 2 data in /usr/local/xtal/coot/share/coot/lib/data/monomers/p/PO4.cif There are 2 data in /usr/local/xtal/coot/share/coot/lib/data/monomers/s/SO4.cif There are 2 data in /usr/local/xtal/coot/share/coot/lib/data/monomers/g/GOL.cif There are 2 data in /usr/local/xtal/coot/share/coot/lib/data/monomers/e/ETH.cif There are 2 data in /usr/local/xtal/coot/share/coot/lib/data/monomers/c/CIT.cif There are 2 data in /usr/local/xtal/coot/share/coot/lib/data/monomers/a/AR.cif There are 2 data in /usr/local/xtal/coot/share/coot/lib/data/monomers/a/AD.cif There are 2 data in /usr/local/xtal/coot/share/coot/lib/data/monomers/c/CR.cif There are 2 data in /usr/local/xtal/coot/share/coot/lib/data/monomers/c/CD.cif There are 2 data in /usr/local/xtal/coot/share/coot/lib/data/monomers/g/GR.cif There are 2 data in /usr/local/xtal/coot/share/coot/lib/data/monomers/g/GD.cif There are 2 data in /usr/local/xtal/coot/share/coot/lib/data/monomers/t/TD.cif There are 2 data in /usr/local/xtal/coot/share/coot/lib/data/monomers/u/UR.cif Reading coordinate file: /usr/local/xtal/coot/share/coot/standard-residues.pdb PDB file /usr/local/xtal/coot/share/coot/standard-residues.pdb has been read. Spacegroup: P 1 Cell: 40 109 93 90 90 90 (coot-real:70225): Pango-WARNING **: Error loading GDEF table 0x6ead (coot-real:70225): Pango-WARNING **: Error loading GSUB table 0x6ead (coot-real:70225): Pango-WARNING **: Error loading GPOS table 0x6ead initalize graphics molecules...done. (filter-fileselection-filenames-state) (get-active-map-drag-flag) (use-graphics-interface-state) DEBUG:: stating pydirectory /usr/local/xtal/coot/share/coot/python INFO:: loading coot.py from /usr/local/xtal/coot/share/coot/python/coot.py Running python script /usr/local/xtal/coot/share/coot/python/coot.py INFO:: coot.py loaded INFO loading coot python modules Running python script /usr/local/xtal/coot/share/coot/python/coot_load_modules.py Loading: coot_utils.py Loading: filter.py Loading: coot_lsq.py Loading: shelx.py Loading: get_ebi.py Loading: local_code.py Loading: hello.py Good Afternoon Robertfloor, Welcome to Coot. (set-display-intro-string "Good Afternoon Robertfloor, Welcome to Coot.") Loading: mutate.py Loading: refmac.py Loading: libcheck.py Loading: gap.py Loading: fitting.py Loading: raster3d.py Loading: povray.py Loading: generic_objects.py Loading: ncs.py Loading: cns2coot.py Loading: tips.py Loading: americanisms.py Loading: group_settings.py Loading: brute_lsqman.py (filter-fileselection-filenames-state) (get-active-map-drag-flag) (use-graphics-interface-state) Loading scheme files from /usr/local/xtal/coot/share/coot/scheme load "filter.scm" load "matrices.scm" load "coot-utils.scm" load "coot-gui.scm" Coot Scheme Scripting GUI code found and loaded. load "coot-lsq.scm" load "shelx.scm" load "get-ebi.scm" WARNING: (net http client): imported module (net http message) overrides core binding `version' load "local-code.scm" load "hello.scm" Good afternoon Robert Floor. Welcome to Coot. (set-display-intro-string "Good afternoon Robert. Welcome to Coot") load "mutate.scm" load "refmac.scm" load "brute-lsqman.scm" load "libcheck.scm" load "gap.scm" load "fitting.scm" load "raster3d.scm" load "povray.scm" load "remote-control.scm" load "generic-objects.scm" load "fascinating-things.scm" load "ncs.scm" load "cns2coot.scm" load "clear-backup.scm" load "tips.scm" load "americanisms.scm" load "group-settings.scm" (set-display-lists-for-maps 0) load "tips-gui.scm" load "extensions.scm" (filter-fileselection-filenames-state) (get-active-map-drag-flag) Loading ~/.coot...(set-add-terminal-residue-do-post-refine 1) done. (use-graphics-interface-state) (coot-checked-exit 0) (clear-backups-maybe) There are 0 old files (0 bytes) (0.0Mb) in "coot-backup" (stereo-mode-state) State file 0-coot.state.scm written. (save-state) State file 0-coot-history.py written. State file 0-coot-history.scm written. Some deprecated features have been used. Set the environment variable GUILE_WARN_DEPRECATED to "detailed" and rerun the program to get more information. Set it to "no" to suppress this message.
