testing with greg testing with greg currently we are here: /home/paule/autobuild/building/emsley-vm-suse_2017-03-05__T11_00_02/test-tar/coot-Linux-x86_64-openSUSE-12.3-pre-release-gtk2-python Sun Mar 5 11:17:56 GMT 2017 WARNING:: ccp4 setup file setup-ccp4 does not exist. /home/paule/autobuild/Linux-emsley-vm-suse-pre-release-gtk2-python/bin/coot --no-graphics --script command-line-greg.scm INFO:: Using Standard CCP4 Refmac dictionary from CLIBD_MON: /home/paule/ccp4/ccp4-6.3.0/lib/data/monomers/ INFO:: Reading coordinate file: /home/paule/autobuild/Linux-emsley-vm-suse-pre-release-gtk2-python/share/coot/standard-residues.pdb PDB file /home/paule/autobuild/Linux-emsley-vm-suse-pre-release-gtk2-python/share/coot/standard-residues.pdb has been read. Spacegroup: P 1 initalize graphics molecules...done. (filter-fileselection-filenames-state) (get-active-map-drag-flag) (use-graphics-interface-state) INFO:: coot.py imported Running python script /home/paule/autobuild/Linux-emsley-vm-suse-pre-release-gtk2-python/lib/python2.7/site-packages/coot/coot_load_modules.py Good Morning Paul, Welcome to Coot version 0.8.8-pre (set-display-intro-string "Good Morning Paul, Welcome to Coot version 0.8.8-pre") (use-graphics-interface-state) (filter-fileselection-filenames-state) (get-active-map-drag-flag) (use-graphics-interface-state) (set-display-intro-string "Good morning Paul. Welcome to Coot 0.8.8-pre") (set-display-lists-for-maps 0) (filter-fileselection-filenames-state) (get-active-map-drag-flag) INFO:: There are 1 command line scripts to run command-line-greg.scm INFO:: Reading coordinate file: /home/paule/data/greg-data/tutorial-modern.pdb PDB file /home/paule/data/greg-data/tutorial-modern.pdb has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule INFO:: NCS chain comparison 93/93 INFO:: fill_ghost_info Constructed 1 ghosts Ghost 0 name: "NCS found from matching Chain B onto Chain A" Molecule 0 read successfully DEBUG:: there were 0 types with no dictionary Molecule number -5 is not a valid model molecule INFO:: Reading coordinate file: /home/paule/data/greg-data/2WF6.cif mmCIF file /home/paule/data/greg-data/2WF6.cif has been read. Spacegroup: P 21 21 21 INFO:: Found 1 models Model 1 had 0 links Symmetry available for this molecule Molecule 1 read successfully DEBUG:: there were 3 types with no dictionary in new_molecule_by_atom_selection Something bad happened - No atoms selected INFO:: Reading coordinate file: /home/paule/data/greg-data/ins-code-fragment-pre.pdb PDB file /home/paule/data/greg-data/ins-code-fragment-pre.pdb has been read. No Spacegroup found for this PDB file INFO:: Found 1 models Model 1 had 0 links !! Warning:: No symmetry available for this molecule No Symmetry for this model Molecule 2 read successfully DEBUG:: there were 0 types with no dictionary INFO:: Creating directory coot-backup INFO:: backup file coot-backup/_home_paule_data_greg-data_ins-code-fragment-pre.pdb_Sun_Mar__5_11:17:57_2017_modification_0.pdb.gz INFO:: backup file coot-backup/_home_paule_data_greg-data_ins-code-fragment-pre.pdb_Sun_Mar__5_11:17:57_2017_modification_1.pdb.gz INFO:: backup file coot-backup/_home_paule_data_greg-data_ins-code-fragment-pre.pdb_Sun_Mar__5_11:17:57_2017_modification_2.pdb.gz WARNING:: Error reading bogus.map Read map bogus.map failed WARNING:: Can't find file bogus.mtz INFO:: making map from mtz filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.8 INFO grid sampling...Nuvw = ( 128, 160, 80) INFO:: 0.042 seconds to read MTZ file INFO:: 0.02 seconds to initialize map INFO:: 0.022 seconds for FFT INFO:: 0.004 seconds for statistics Map mean: ........ 8.55445e-10 Map sigma: ....... 0.311501 Map maximum: ..... 3.0144 Map minimum: ..... -0.895738 INFO:: 0.03 seconds for contour map INFO:: 0.118 seconds in total WARNING:: file xx-missing.mtz does not exist >>>>>> CCP4 library signal library_file:End of File (Error) raised in ccp4_file_raw_read <<<<<< >>>>>> System signal 0:Success (Error) raised in ccp4_file_rarch <<<<<< >>>>>> CCP4 library signal library_file:End of File (Error) raised in ccp4_file_raw_read <<<<<< >>>>>> System signal 0:Success (Error) raised in ccp4_file_readint <<<<<< >>>>>> System signal 0:Success (Error) raised in ccp4_file_read <<<<<< >>>>>> CCP4 library signal library_file:End of File (Error) raised in ccp4_file_raw_read <<<<<< >>>>>> System signal 0:Success (Error) raised in ccp4_file_readchar <<<<<< >>>>>> CCP4 library signal mtz:Read failed (Error) raised in MtzGet <<<<<< CCP4MTZfile: open_read - File missing or corrupted: /home/paule/data/greg-data/broken.mtz INFO:: not an mtz file: /home/paule/data/greg-data/broken.mtz INFO:: making conventional map from MTZ filename /home/paule/data/greg-data/rnasa-1.8-all_refmac1.mtz using FWT PHWT Number of OBSERVED reflections: 17939 INFO:: finding ASU unique map points with sampling rate 1.8 INFO grid sampling...Nuvw = ( 128, 160, 80) INFO:: 0.035 seconds to read MTZ file INFO:: 0 seconds to initialize map INFO:: 0.021 seconds for FFT INFO:: 0.004 seconds for statistics Map mean: ........ 8.55445e-10 Map sigma: ....... 0.311501 Map maximum: ..... 3.0144 Map minimum: ..... -0.895738 INFO:: 0.025 seconds for contour map INFO:: 0.085 seconds in total INFO:: making map from mtz filename /home/paule/data/greg-data/3hfl_sigmaa.mtz Number of OBSERVED reflections: 17920 INFO:: finding ASU unique map points with sampling rate 1.8 INFO grid sampling...Nuvw = ( 80, 108, 108) INFO:: 0.033 seconds to read MTZ file INFO:: 0.011 seconds to initialize map INFO:: 0.019 seconds for FFT INFO:: 0.004 seconds for statistics Map mean: ........ 6.95553e-11 Map sigma: ....... 0.260405 Map maximum: ..... 1.81878 Map minimum: ..... -1.02352 INFO:: 0.006 seconds for contour map INFO:: 0.073 seconds in total >>>>>> CCP4 library signal library_file:Write failed (Error) raised in ccp4_file_raw_write <<<<<< >>>>>> System signal 28:No space left on device (Error) raised in ccp4_file_writefloat <<<<<< >>>>>> System signal 28:No space left on device (Error) raised in ccp4_file_write <<<<<< >>>>>> CCP4 library signal ccp4_map:Write failed (Error) raised in ccp4_cmap_write_section <<<<<< >>>>>> CCP4 library signal library_file:Bad mode (Error) raised in ccp4_file_writefloat <<<<<< >>>>>> System signal 28:No space left on device (Error) raised in ccp4_file_write <<<<<< >>>>>> CCP4 library signal ccp4_map:Write failed (Error) raised in ccp4_cmap_write_section <<<<<< >>>>>> CCP4 library signal library_file:Bad mode (Error) raised in ccp4_file_writefloat <<<<<< >>>>>> System signal 28:No space left on device (Error) raised in ccp4_file_write <<<<<< >>>>>> CCP4 library signal ccp4_map:Write failed (Error) raised in ccp4_cmap_write_section <<<<<< >>>>>> CCP4 library signal library_file:Bad mode (Error) raised in ccp4_file_writefloat <<<<<< >>>>>> System signal 28:No space left on device (Error) raised in ccp4_file_write <<<<<< >>>>>> CCP4 library signal ccp4_map:Write failed (Error) raised in ccp4_cmap_write_section <<<<<< >>>>>> CCP4 library signal library_file:Bad mode (Error) raised in ccp4_file_writefloat <<<<<< >>>>>> System signal 28:No space left on device (Error) raised in ccp4_file_write <<<<<< >>>>>> CCP4 library signal ccp4_map:Write failed (Error) raised in ccp4_cmap_write_section <<<<<< >>>>>> CCP4 library signal library_file:Bad mode (Error) raised in ccp4_file_writefloat <<<<<< >>>>>> System signal 28:No space left on device (Error) raised in ccp4_file_write <<<<<< >>>>>> CCP4 library signal ccp4_map:Write failed (Error) raised in ccp4_cmap_write_section <<<<<< >>>>>> CCP4 library signal library_file:Bad mode (Error) raised in ccp4_file_writefloat <<<<<< >>>>>> System signal 28:No space left on device (Error) raised in ccp4_file_write <<<<<< >>>>>> CCP4 library signal ccp4_ma