phenix --debug XML-RPC server started on port 35461 parse_command_line_phil_args (App.py:770): parsing file /Volumes/RAID1/Jeong/Phenix/PKG_CBDA/APO/.phenix/project_data/refine_2.eff __init__ (PhilLayout.py:230): started setup_app (MainWindow.py:986): started setup_app (MainWindow.py:513): started update_widget_value (PhilInterface.py:426): widget not found: refinement.input.xray_data.r_free_flags.test_flag_value update_widget_value (PhilInterface.py:426): widget not found: refinement.input.neutron_data.r_free_flags.test_flag_value update_widget_value (PhilInterface.py:426): widget not found: refinement.input.neutron_data.r_free_flags.test_flag_value Restoring results from /Volumes/RAID1/Jeong/Phenix/PKG_CBDA/APO/Refine_2 add_result_file (Templates.py:612): /Volumes/RAID1/Jeong/Phenix/PKG_CBDA/APO/Refine_2/PKG_CBDA_APO_refine_2.eff Effective parameters for this run add_file (AdvancedWidgets.py:337): /Volumes/RAID1/Jeong/Phenix/PKG_CBDA/APO/Refine_2/PKG_CBDA_APO_refine_2.eff add_result_file (Templates.py:612): /Volumes/RAID1/Jeong/Phenix/PKG_CBDA/APO/Refine_2/PKG_CBDA_APO_refine_2.geo Geometry restraints before refinement add_file (AdvancedWidgets.py:337): /Volumes/RAID1/Jeong/Phenix/PKG_CBDA/APO/Refine_2/PKG_CBDA_APO_refine_2.geo _add_any_file (AdvancedWidgets.py:357): /Volumes/RAID1/Jeong/Phenix/PKG_CBDA/APO/Refine_2/PKG_CBDA_APO_refine_2.geo add_result_file (Templates.py:612): /Volumes/RAID1/Jeong/Phenix/PKG_CBDA/APO/Refine_2/PKG_CBDA_APO_refine_2.log phenix.refine log file add_file (AdvancedWidgets.py:337): /Volumes/RAID1/Jeong/Phenix/PKG_CBDA/APO/Refine_2/PKG_CBDA_APO_refine_2.log _add_any_file (AdvancedWidgets.py:357): /Volumes/RAID1/Jeong/Phenix/PKG_CBDA/APO/Refine_2/PKG_CBDA_APO_refine_2.log add_result_file (Templates.py:612): /Volumes/RAID1/Jeong/Phenix/PKG_CBDA/APO/Refine_2/PKG_CBDA_APO_refine_2_2mFo-DFc.map SigmaA-weighted 2Fo-Fc map add_file (AdvancedWidgets.py:337): /Volumes/RAID1/Jeong/Phenix/PKG_CBDA/APO/Refine_2/PKG_CBDA_APO_refine_2_2mFo-DFc.map _add_any_file (AdvancedWidgets.py:357): /Volumes/RAID1/Jeong/Phenix/PKG_CBDA/APO/Refine_2/PKG_CBDA_APO_refine_2_2mFo-DFc.map add_result_file (Templates.py:612): /Volumes/RAID1/Jeong/Phenix/PKG_CBDA/APO/Refine_2/PKG_CBDA_APO_refine_2_2mFo-DFc_no_fill.map SigmaA-weighted 2Fo-Fc map add_file (AdvancedWidgets.py:337): /Volumes/RAID1/Jeong/Phenix/PKG_CBDA/APO/Refine_2/PKG_CBDA_APO_refine_2_2mFo-DFc_no_fill.map _add_any_file (AdvancedWidgets.py:357): /Volumes/RAID1/Jeong/Phenix/PKG_CBDA/APO/Refine_2/PKG_CBDA_APO_refine_2_2mFo-DFc_no_fill.map add_result_file (Templates.py:612): /Volumes/RAID1/Jeong/Phenix/PKG_CBDA/APO/Refine_2/PKG_CBDA_APO_refine_2_info.txt Run summary in text format add_file (AdvancedWidgets.py:337): /Volumes/RAID1/Jeong/Phenix/PKG_CBDA/APO/Refine_2/PKG_CBDA_APO_refine_2_info.txt _add_any_file (AdvancedWidgets.py:357): /Volumes/RAID1/Jeong/Phenix/PKG_CBDA/APO/Refine_2/PKG_CBDA_APO_refine_2_info.txt add_result_file (Templates.py:612): /Volumes/RAID1/Jeong/Phenix/PKG_CBDA/APO/Refine_2/PKG_CBDA_APO_refine_2_map_coeffs.mtz Map coefficients for Coot add_file (AdvancedWidgets.py:337): /Volumes/RAID1/Jeong/Phenix/PKG_CBDA/APO/Refine_2/PKG_CBDA_APO_refine_2_map_coeffs.mtz add_result_file (Templates.py:612): /Volumes/RAID1/Jeong/Phenix/PKG_CBDA/APO/Refine_2/PKG_CBDA_APO_refine_2_mFo-DFc.map SigmaA-weighted difference map add_file (AdvancedWidgets.py:337): /Volumes/RAID1/Jeong/Phenix/PKG_CBDA/APO/Refine_2/PKG_CBDA_APO_refine_2_mFo-DFc.map _add_any_file (AdvancedWidgets.py:357): /Volumes/RAID1/Jeong/Phenix/PKG_CBDA/APO/Refine_2/PKG_CBDA_APO_refine_2_mFo-DFc.map launch_coot_server (External.py:21): PHENIX_COOT=/sw64/bin/coot launch_coot_server (External.py:26): coot command: launch_coot_server (External.py:27): phenix.start_coot --no-state-script --script "/usr/local/phenix-1.6.2-431/phenix/wxGUI2/Coot.py" Coot: Acquiring application resources from /sw64/share/coot/cootrc Coot: INFO:: splash_screen_pixmap_dir /sw64/share/coot/pixmaps Coot: INFO:: Colours file: /sw64/share/coot/colours.def loaded Coot: There are 118 data in /sw64/share/coot/lib/data/monomers/list/mon_lib_list.cif Coot: There are 2 data in /sw64/share/coot/lib/data/monomers/a/ALA.cif Coot: There are 2 data in /sw64/share/coot/lib/data/monomers/a/ASP.cif Coot: There are 2 data in /sw64/share/coot/lib/data/monomers/a/ASN.cif Coot: There are 2 data in /sw64/share/coot/lib/data/monomers/c/CYS.cif Coot: There are 2 data in /sw64/share/coot/lib/data/monomers/g/GLN.cif Coot: There are 2 data in /sw64/share/coot/lib/data/monomers/g/GLY.cif Coot: There are 2 data in /sw64/share/coot/lib/data/monomers/g/GLU.cif Coot: There are 2 data in /sw64/share/coot/lib/data/monomers/p/PHE.cif Coot: There are 2 data in /sw64/share/coot/lib/data/monomers/h/HIS.cif Coot: There are 2 data in /sw64/share/coot/lib/data/monomers/i/ILE.cif Coot: There are 2 data in /sw64/share/coot/lib/data/monomers/l/LYS.cif Coot: There are 2 data in /sw64/share/coot/lib/data/monomers/l/LEU.cif Coot: There are 2 data in /sw64/share/coot/lib/data/monomers/m/MET.cif Coot: There are 2 data in /sw64/share/coot/lib/data/monomers/m/MSE.cif Coot: There are 2 data in /sw64/share/coot/lib/data/monomers/p/PRO.cif Coot: There are 2 data in /sw64/share/coot/lib/data/monomers/a/ARG.cif Coot: There are 2 data in /sw64/share/coot/lib/data/monomers/s/SER.cif Coot: There are 2 data in /sw64/share/coot/lib/data/monomers/t/THR.cif Coot: There are 2 data in /sw64/share/coot/lib/data/monomers/v/VAL.cif Coot: There are 2 data in /sw64/share/coot/lib/data/monomers/t/TRP.cif Coot: There are 2 data in /sw64/share/coot/lib/data/monomers/t/TYR.cif Coot: There are 2 data in /sw64/share/coot/lib/data/monomers/p/PO4.cif Coot: There are 2 data in /sw64/share/coot/lib/data/monomers/s/SO4.cif Coot: There are 2 data in /sw64/share/coot/lib/data/monomers/g/GOL.cif Coot: There are 2 data in /sw64/share/coot/lib/data/monomers/e/ETH.cif Coot: There are 2 data in /sw64/share/coot/lib/data/monomers/c/CIT.cif Coot: There are 2 data in /sw64/share/coot/lib/data/monomers/a/AR.cif Coot: There are 2 data in /sw64/share/coot/lib/data/monomers/a/AD.cif Coot: There are 2 data in /sw64/share/coot/lib/data/monomers/c/CR.cif Coot: There are 2 data in /sw64/share/coot/lib/data/monomers/c/CD.cif Coot: There are 2 data in /sw64/share/coot/lib/data/monomers/g/GR.cif Coot: There are 2 data in /sw64/share/coot/lib/data/monomers/g/GD.cif Coot: There are 2 data in /sw64/share/coot/lib/data/monomers/t/TD.cif Coot: There are 2 data in /sw64/share/coot/lib/data/monomers/u/UR.cif Coot: sbase monomer dir: . Coot: sbase files not found in . Coot: Reading coordinate file: /sw64/share/coot/standard-residues.pdb Coot: PDB file /sw64/share/coot/standard-residues.pdb has been read. Coot: Spacegroup: P 1 Coot: Cell: 40.631 109.18 93.243 90 90 90 Coot: initalize graphics molecules...done. Coot: (filter-fileselection-filenames-state) Coot: (get-active-map-drag-flag) Coot: (use-graphics-interface-state) Coot: DEBUG:: stating pydirectory /sw64/share/coot/python Coot: INFO:: importing coot.py from /sw64/share/coot/python/coot.py Coot: Importing python module coot using command from coot import * Coot: INFO:: coot.py imported Coot: INFO:: coot_python initialized Coot: INFO loading coot python modules Coot: Running python script /sw64/share/coot/python/coot_load_modules.py Coot: Loading: coot_utils.py Coot: Loading: filter.py Coot: Loading: coot_lsq.py Coot: Loading: shelx.py Coot: Loading: get_ebi.py Coot: Loading: local_code.py Coot: Loading: hello.py Coot: Good Evening Choelkim, Welcome to Coot. 0.6.2-pre-1 (revision 2965) [with guile 1.8.6 embedded] [with python 2.6.5 embedded] Coot: (set-display-intro-string "Good Evening Choelkim, Welcome to Coot. 0.6.2-pre-1 (revision 2965) [with guile 1.8.6 embedded] [with python 2.6.5 embedded]") Coot: Loading: mutate.py Coot: Loading: refmac.py Coot: Loading: libcheck.py Coot: Loading: gap.py Coot: Loading: fitting.py Coot: Loading: raster3d.py Coot: Loading: povray.py Coot: Loading: remote_control.py Coot: Loading: generic_objects.py Coot: Loading: ncs.py Coot: Loading: parse_pisa_xml.py Coot: Loading: cns2coot.py Coot: Loading: tips.py Coot: Loading: americanisms.py Coot: Loading: group_settings.py Coot: Loading: brute_lsqman.py Coot: Loading: coot_gui.py Coot: Coot Python Scripting GUI code found and loaded. Coot: Loading: tips_gui.py Coot: Loading: check_for_updates.py Coot: Loading: shelx_extensions.py Coot: Loading: clear_backup.py Coot: Loading: coot_toolbuttons.py Coot: INFO:: loading preferences file /Volumes/RAID1/admin/.coot-preferences/coot_preferences.py Coot: Running python script /Volumes/RAID1/admin/.coot-preferences/coot_preferences.py Coot: (set-filter-fileselection-filenames 0) Coot: (unset-sticky-sort-by-date) Coot: (set-colour-map-rotation-on-read-pdb 21.00) Coot: (set-colour-map-rotation-on-read-pdb-c-only-flag 1) Coot: (set-density-size 10.00) Coot: (set-swap-difference-map-colours 1) Coot: (set-active-map-drag-flag 1) Coot: (set-idle-function-rotate-angle 1.00) Coot: (filter-fileselection-filenames-state) Coot: (get-active-map-drag-flag) Coot: (use-graphics-interface-state) Coot: Loading scheme files from /sw64/share/coot/scheme Coot: Coot Scheme Scripting GUI code found and loaded. Coot: (set-display-intro-string "Good evening Choel. Welcome to Coot") Coot: (set-display-lists-for-maps 0) Coot: INFO:: loading preferences file /Volumes/RAID1/admin/.coot-preferences/coot-preferences.scm Coot: (set-filter-fileselection-filenames 0) Coot: (unset-sticky-sort-by-date) Coot: (set-colour-map-rotation-on-read-pdb 21.00) Coot: (set-colour-map-rotation-on-read-pdb-c-only-flag 1) Coot: (set-density-size 10.00) Coot: (set-swap-difference-map-colours 1) Coot: (set-active-map-drag-flag 1) Coot: (set-idle-function-rotate-angle 1.00) Coot: (filter-fileselection-filenames-state) Coot: (get-active-map-drag-flag) Coot: Loading ~/.coot...done. Coot: Running python script /usr/local/phenix-1.6.2-431/phenix/wxGUI2/Coot.py Coot: Loading PHENIX Coot extensions. . . Coot: xml-rpc server running on port 46712 Coot: INFO:: Command: (set-find-hydrogen-torsion 1) Coot: INFO:: Command: (use-graphics-interface-state) Coot: coot_phenix_interface.close_tmp_model() Coot: coot_phenix_interface.close_all() Coot: coot_phenix_interface.load_phenix_refine_final_files(/Volumes/RAID1/Jeong/Phenix/PKG_CBDA/APO/Refine_2, PKG_CBDA_APO_refine_2) Coot: INFO:: Command: (handle-read-draw-molecule-with-recentre "/Volumes/RAID1/Jeong/Phenix/PKG_CBDA/APO/Refine_2/PKG_CBDA_APO_refine_2.pdb" 1) Coot: Reading coordinate file: /Volumes/RAID1/Jeong/Phenix/PKG_CBDA/APO/Refine_2/PKG_CBDA_APO_refine_2.pdb Coot: PDB file /Volumes/RAID1/Jeong/Phenix/PKG_CBDA/APO/Refine_2/PKG_CBDA_APO_refine_2.pdb has been read. Coot: Spacegroup: P 43 Coot: Cell: 62.584 62.584 199.518 90 90 90 Coot: INFO:: Found 1 models Coot: Model 1 had 0 links Coot: Symmetry available for this molecule Coot: INFO:: NCS chain comparison 123/128 Coot: INFO:: NCS chain comparison 123/128 Coot: INFO:: NCS chain comparison 122/128 Coot: INFO:: NCS chain comparison 0/128 Coot: INFO:: NCS chain comparison 0/128 Coot: INFO:: NCS chain comparison 0/128 Coot: INFO:: NCS chain comparison 0/128 Coot: INFO:: NCS chain comparison 1/1 Coot: INFO:: NCS chain comparison 0/1 Coot: INFO:: NCS chain comparison 0/1 Coot: INFO:: NCS chain comparison 1/1 Coot: INFO:: fill_ghost_info Constructed 5 ghosts Coot: Ghost 0 name: "NCS found from matching Chain B onto Chain A" Coot: Ghost 1 name: "NCS found from matching Chain C onto Chain A" Coot: Ghost 2 name: "NCS found from matching Chain D onto Chain A" Coot: Ghost 3 name: "NCS found from matching Chain H onto Chain G" Coot: Ghost 4 name: "NCS found from matching Chain F onto Chain E" Coot: Molecule 0 read successfully Coot: INFO:: Command: (set-molecule-bonds-colour-map-rotation 0 30.00) Coot: coot_phenix_interface.auto_load_maps(/Volumes/RAID1/Jeong/Phenix/PKG_CBDA/APO/Refine_2/PKG_CBDA_APO_refine_2_map_coeffs.mtz, phi=PH) Coot: INFO:: Command: (set-colour-map-rotation-for-maps 0.00) Coot: valid_labels(/Volumes/RAID1/Jeong/Phenix/PKG_CBDA/APO/Refine_2/PKG_CBDA_APO_refine_2_map_coeffs.mtz,2FOFCWT,PH2FOFCWT,,0) returns 1 Coot: INFO:: Command: (make-and-draw-map "/Volumes/RAID1/Jeong/Phenix/PKG_CBDA/APO/Refine_2/PKG_CBDA_APO_refine_2_map_coeffs.mtz" "2FOFCWT" "PH2FOFCWT" "" 0 0) Coot: INFO:: making map from mtz filename /Volumes/RAID1/Jeong/Phenix/PKG_CBDA/APO/Refine_2/PKG_CBDA_APO_refine_2_map_coeffs.mtz Coot: Number of OBSERVED reflections: 25085 Coot: INFO:: finding ASU unique map points with sampling rate 1.5 Coot: INFO grid sampling...Nuvw = ( 80, 80, 240) Coot: INFO:: 0.395 seconds to read MTZ file Coot: INFO:: 0.857 seconds to initialize map Coot: INFO:: 0.152 seconds for FFT Coot: INFO:: 0.049 seconds for statistics Coot: Map mean: ........ -9.54107e-11 Coot: Map sigma: ....... 0.118475 Coot: Map maximum: ..... 0.915382 Coot: Map minimum: ..... -0.497048 Coot: INFO:: 0.015 seconds for contour map Coot: INFO:: 1.468 seconds in total Coot: valid_labels(/Volumes/RAID1/Jeong/Phenix/PKG_CBDA/APO/Refine_2/PKG_CBDA_APO_refine_2_map_coeffs.mtz,FOFCWT,PHFOFCWT,,0) returns 1 Coot: INFO:: Command: (make-and-draw-map "/Volumes/RAID1/Jeong/Phenix/PKG_CBDA/APO/Refine_2/PKG_CBDA_APO_refine_2_map_coeffs.mtz" "FOFCWT" "PHFOFCWT" "" 0 1) Coot: INFO:: making map from mtz filename /Volumes/RAID1/Jeong/Phenix/PKG_CBDA/APO/Refine_2/PKG_CBDA_APO_refine_2_map_coeffs.mtz Coot: Number of OBSERVED reflections: 20657 Coot: INFO:: finding ASU unique map points with sampling rate 1.5 Coot: INFO grid sampling...Nuvw = ( 80, 80, 240) Coot: INFO:: 0.143 seconds to read MTZ file Coot: INFO:: 0.004 seconds to initialize map Coot: INFO:: 0.137 seconds for FFT Coot: INFO:: 0.049 seconds for statistics Coot: Map mean: ........ -1.5539e-11 Coot: Map sigma: ....... 0.0481121 Coot: Map maximum: ..... 0.317881 Coot: Map minimum: ..... -0.318594 Coot: INFO:: 0.005 seconds for contour map Coot: INFO:: 0.338 seconds in total Coot: INFO:: Command: (set-colour-map-rotation-for-maps 0.00) Coot: coot_phenix_interface.load_probe_results(/Volumes/RAID1/Jeong/Phenix/PKG_CBDA/APO/Refine_2/.comm/probe.txt) Coot: coot_phenix_interface.show_probe_dots(True, True) Coot: coot_phenix_interface.show_probe_dots(False, True) Coot: coot_phenix_interface.close_tmp_model() Coot: coot_phenix_interface.close_all() Coot: INFO:: Command: (close-molecule 0) Coot: coot_phenix_interface.load_phenix_refine_final_files(/Volumes/RAID1/Jeong/Phenix/PKG_CBDA/APO/Refine_2, PKG_CBDA_APO_refine_2) Coot: INFO:: Command: (handle-read-draw-molecule-with-recentre "/Volumes/RAID1/Jeong/Phenix/PKG_CBDA/APO/Refine_2/PKG_CBDA_APO_refine_2.pdb" 1) Coot: Reading coordinate file: /Volumes/RAID1/Jeong/Phenix/PKG_CBDA/APO/Refine_2/PKG_CBDA_APO_refine_2.pdb Coot: PDB file /Volumes/RAID1/Jeong/Phenix/PKG_CBDA/APO/Refine_2/PKG_CBDA_APO_refine_2.pdb has been read. Coot: Spacegroup: P 43 Coot: Cell: 62.584 62.584 199.518 90 90 90 Coot: INFO:: Found 1 models Coot: Model 1 had 0 links Coot: Symmetry available for this molecule Coot: INFO:: NCS chain comparison 123/128 Coot: INFO:: NCS chain comparison 123/128 Coot: INFO:: NCS chain comparison 122/128 Coot: INFO:: NCS chain comparison 0/128 Coot: INFO:: NCS chain comparison 0/128 Coot: INFO:: NCS chain comparison 0/128 Coot: INFO:: NCS chain comparison 0/128 Coot: INFO:: NCS chain comparison 1/1 Coot: INFO:: NCS chain comparison 0/1 Coot: INFO:: NCS chain comparison 0/1 Coot: INFO:: NCS chain comparison 1/1 Coot: INFO:: fill_ghost_info Constructed 5 ghosts Coot: Ghost 0 name: "NCS found from matching Chain B onto Chain A" Coot: Ghost 1 name: "NCS found from matching Chain C onto Chain A" Coot: Ghost 2 name: "NCS found from matching Chain D onto Chain A" Coot: Ghost 3 name: "NCS found from matching Chain H onto Chain G" Coot: Ghost 4 name: "NCS found from matching Chain F onto Chain E" Coot: Molecule 3 read successfully Coot: INFO:: Command: (set-molecule-bonds-colour-map-rotation 3 30.00) Coot: coot_phenix_interface.auto_load_maps(/Volumes/RAID1/Jeong/Phenix/PKG_CBDA/APO/Refine_2/PKG_CBDA_APO_refine_2_map_coeffs.mtz, phi=PH) Coot: INFO:: Command: (set-colour-map-rotation-for-maps 0.00) Coot: valid_labels(/Volumes/RAID1/Jeong/Phenix/PKG_CBDA/APO/Refine_2/PKG_CBDA_APO_refine_2_map_coeffs.mtz,2FOFCWT,PH2FOFCWT,,0) returns 1 Coot: INFO:: Command: (make-and-draw-map "/Volumes/RAID1/Jeong/Phenix/PKG_CBDA/APO/Refine_2/PKG_CBDA_APO_refine_2_map_coeffs.mtz" "2FOFCWT" "PH2FOFCWT" "" 0 0) Coot: INFO:: making map from mtz filename /Volumes/RAID1/Jeong/Phenix/PKG_CBDA/APO/Refine_2/PKG_CBDA_APO_refine_2_map_coeffs.mtz Coot: Number of OBSERVED reflections: 25085 Coot: INFO:: finding ASU unique map points with sampling rate 1.5 Coot: INFO grid sampling...Nuvw = ( 80, 80, 240) Coot: INFO:: 0.142 seconds to read MTZ file Coot: INFO:: 0.004 seconds to initialize map Coot: INFO:: 0.149 seconds for FFT Coot: INFO:: 0.048 seconds for statistics Coot: Map mean: ........ -9.54107e-11 Coot: Map sigma: ....... 0.118475 Coot: Map maximum: ..... 0.915382 Coot: Map minimum: ..... -0.497048 Coot: INFO:: 0.014 seconds for contour map Coot: INFO:: 0.357 seconds in total Coot: valid_labels(/Volumes/RAID1/Jeong/Phenix/PKG_CBDA/APO/Refine_2/PKG_CBDA_APO_refine_2_map_coeffs.mtz,FOFCWT,PHFOFCWT,,0) returns 1 Coot: INFO:: Command: (make-and-draw-map "/Volumes/RAID1/Jeong/Phenix/PKG_CBDA/APO/Refine_2/PKG_CBDA_APO_refine_2_map_coeffs.mtz" "FOFCWT" "PHFOFCWT" "" 0 1) Coot: INFO:: making map from mtz filename /Volumes/RAID1/Jeong/Phenix/PKG_CBDA/APO/Refine_2/PKG_CBDA_APO_refine_2_map_coeffs.mtz Coot: Number of OBSERVED reflections: 20657 Coot: INFO:: finding ASU unique map points with sampling rate 1.5 Coot: INFO grid sampling...Nuvw = ( 80, 80, 240) Coot: INFO:: 0.142 seconds to read MTZ file Coot: INFO:: 0.003 seconds to initialize map Coot: INFO:: 0.138 seconds for FFT Coot: INFO:: 0.048 seconds for statistics Coot: Map mean: ........ -1.5539e-11 Coot: Map sigma: ....... 0.0481121 Coot: Map maximum: ..... 0.317881 Coot: Map minimum: ..... -0.318594 Coot: INFO:: 0.005 seconds for contour map Coot: INFO:: 0.336 seconds in total Coot: INFO:: Command: (set-colour-map-rotation-for-maps 0.00) Coot: coot_phenix_interface.load_probe_results(/Volumes/RAID1/Jeong/Phenix/PKG_CBDA/APO/Refine_2/.comm/probe.txt) Coot: coot_phenix_interface.show_probe_dots(False, True) Coot: coot_phenix_interface.is_alive()