Try updating to 1941. I just put that in cvs an hour ago and it seems to behave ok, at least for me.... Bill
On Sat, Mar 28, 2009 at 10:14 AM, Robert <[email protected]> wrote: > 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. > > -- ------------------------------------------------------------------------- William G. Scott contact info: http://chemistry.ucsc.edu/~wgscott Please reply to: [email protected]
