id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3073 empty surfaces slow things down Tristan Croll Tom Goddard "{{{ The following bug report has been submitted: Platform: Linux-3.10.0-1062.9.1.el7.x86_64-x86_64-with-centos-7.7.1908-Core ChimeraX Version: 0.93 (2020-04-03) Description If I do ""surface selAtoms"" followed by ""~surface"", the empty surface object hangs around and continues to run callbacks, making coordinate changes *really* slow. Log: UCSF ChimeraX version: 0.93 (2020-04-03) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open Atval.pdb Chain information for Atval.pdb #1 --- Chain | Description D E H I L M P Q | No description available F J N R | No description available G K O S | No description available > toolshed show Shell /opt/UCSF/ChimeraX/lib/python3.7/site-packages/IPython/core/history.py:226: UserWarning: IPython History requires SQLite, your history will not be saved warn(""IPython History requires SQLite, your history will not be saved"") > select ~protein 704 atoms, 752 bonds, 1 model selected > style sel stick Changed 704 atom styles > show sel cartoons > hide sel atoms > select clear > show cartoons > hide atoms > style stick Changed 46072 atom styles > show cartoons > dssp > show ~protein > select ~protein 704 atoms, 752 bonds, 1 model selected > select zone sel 3 Selected 216 atoms > show sel > select up 1068 atoms, 980 bonds, 1 model selected > show sel > select clear > view sel > color byhetero > select clear > view sel > select clear > view sel > select clear > view sel > select clear > view sel Expected an objects specifier or a keyword > select ~protein 704 atoms, 752 bonds, 1 model selected > hide sel cartoons > select clear > hide cartoons > show > addh Summary of feedback from adding hydrogens to Atval.pdb #1 --- warnings | Not adding hydrogens to /H LYS 390 CB because it is missing heavy- atom bond partners Not adding hydrogens to /H GLU 431 CB because it is missing heavy-atom bond partners Not adding hydrogens to /H LYS 434 CB because it is missing heavy-atom bond partners Not adding hydrogens to /H LYS 450 CB because it is missing heavy-atom bond partners Not adding hydrogens to /I LYS 390 CB because it is missing heavy-atom bond partners 27 messages similar to the above omitted notes | No usable SEQRES records for Atval.pdb (#1) chain D; guessing termini instead No usable SEQRES records for Atval.pdb (#1) chain E; guessing termini instead No usable SEQRES records for Atval.pdb (#1) chain F; guessing termini instead No usable SEQRES records for Atval.pdb (#1) chain G; guessing termini instead No usable SEQRES records for Atval.pdb (#1) chain H; guessing termini instead 11 messages similar to the above omitted Chain-initial residues that are actual N termini: /D THR 86, /E THR 86, /F HIS 87, /G LEU 317, /H THR 86, /I THR 86, /J HIS 87, /K LEU 317, /L THR 86, /M THR 86, /N HIS 87, /O LEU 317, /P THR 86, /Q THR 86, /R HIS 87, /S LEU 317 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /D ARG 667, /E ARG 667, /F MET 241, /G SER 475, /H ARG 667, /I ARG 667, /J MET 241, /K SER 475, /L ARG 667, /M ARG 667, /N MET 241, /O SER 475, /P ARG 667, /Q ARG 667, /R MET 241, /S SER 475 3580 hydrogen bonds /D ARG 667 is not terminus, removing H atom from 'C' /E ARG 667 is not terminus, removing H atom from 'C' /F MET 241 is not terminus, removing H atom from 'C' /G SER 475 is not terminus, removing H atom from 'C' /H ARG 667 is not terminus, removing H atom from 'C' 11 messages similar to the above omitted 46152 hydrogens added > select /I:416@CA 1 atom, 1 model selected > select /I:416@CA 1 atom, 1 model selected > select up 22 atoms, 21 bonds, 1 model selected > select clear > select /B:729@C47 1 atom, 1 model selected > select up 85 atoms, 90 bonds, 1 model selected > select ~protein 1176 atoms, 1224 bonds, 1 model selected > select clear > view sel > hide H > select clear Expected an objects specifier or a view name or a keyword > view sel > close > open2 > /run/media/tic20/storage/structure_dump/aus/brisbane/guddat/ahas/RealSpaceRefine_12/working_noh_ligand_atoms_renamed_real_space_refined.pdb Chain information for working_noh_ligand_atoms_renamed_real_space_refined.pdb #1 --- Chain | Description D E H I L M P Q | No description available F J N R | No description available G K O S | No description available V | No description available > isolde start > set selectionWidth 4 Chain information for working_noh_ligand_atoms_renamed_real_space_refined.pdb --- Chain | Description 1.2/D 1.2/E 1.2/H 1.2/I 1.2/L 1.2/M 1.2/P 1.2/Q | No description available 1.2/F 1.2/J 1.2/N 1.2/R | No description available 1.2/G 1.2/K 1.2/O 1.2/S | No description available 1.2/V | No description available Done loading forcefield > hide #!1 models > open2 > /run/media/tic20/storage/structure_dump/aus/brisbane/guddat/ahas/RealSpaceRefine_12/working_noh_ligand_atoms_renamed_real_space_refined.pdb Chain information for working_noh_ligand_atoms_renamed_real_space_refined.pdb #2 --- Chain | Description D E H I L M P Q | No description available F J N R | No description available G K O S | No description available V | No description available > hide #2&~/V > cartoon #2 > ~cartoon #2&~/V > select #2 46216 atoms, 47135 bonds, 45 pseudobonds, 2 models selected > style sel sphere Changed 46216 atom styles > select clear > toolshed show Shell > close #2 > show #!1 models > select /V 64 atoms, 63 bonds, 1 model selected > select clear > ~cartoon /V > addh Summary of feedback from adding hydrogens to working_noh_ligand_atoms_renamed_real_space_refined.pdb #1.2 --- warnings | Not adding hydrogens to /D LYS 390 CB because it is missing heavy- atom bond partners Not adding hydrogens to /D GLU 431 CB because it is missing heavy-atom bond partners Not adding hydrogens to /D LYS 434 CB because it is missing heavy-atom bond partners Not adding hydrogens to /D LYS 450 CB because it is missing heavy-atom bond partners Not adding hydrogens to /E LYS 390 CB because it is missing heavy-atom bond partners 27 messages similar to the above omitted notes | No usable SEQRES records for working_noh_ligand_atoms_renamed_real_space_refined.pdb (#1.2) chain D; guessing termini instead No usable SEQRES records for working_noh_ligand_atoms_renamed_real_space_refined.pdb (#1.2) chain E; guessing termini instead No usable SEQRES records for working_noh_ligand_atoms_renamed_real_space_refined.pdb (#1.2) chain F; guessing termini instead No usable SEQRES records for working_noh_ligand_atoms_renamed_real_space_refined.pdb (#1.2) chain G; guessing termini instead No usable SEQRES records for working_noh_ligand_atoms_renamed_real_space_refined.pdb (#1.2) chain H; guessing termini instead 12 messages similar to the above omitted Chain-initial residues that are actual N termini: /D THR 86, /E THR 86, /F LYS 83, /G LEU 317, /H THR 86, /I THR 86, /J LYS 83, /K LEU 317, /L THR 86, /M THR 86, /N LYS 83, /O LEU 317, /P THR 86, /Q THR 86, /R LYS 83, /S LEU 317, /V VAL 106 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: /V VAL 113 Chain-final residues that are not actual C termini: /D ARG 667, /E ARG 667, /F MET 241, /G SER 475, /H ARG 667, /I ARG 667, /J MET 241, /K SER 475, /L ARG 667, /M ARG 667, /N MET 241, /O SER 475, /P ARG 667, /Q ARG 667, /R MET 241, /S SER 475 5468 hydrogen bonds /D ARG 667 is not terminus, removing H atom from 'C' /E ARG 667 is not terminus, removing H atom from 'C' /F MET 241 is not terminus, removing H atom from 'C' /G SER 475 is not terminus, removing H atom from 'C' /H ARG 667 is not terminus, removing H atom from 'C' 11 messages similar to the above omitted 46342 hydrogens added > hide HC > close #1.2.5 > select /V 152 atoms, 144 bonds, 1 model selected > select /V 152 atoms, 144 bonds, 1 model selected > open2 > /run/media/tic20/storage/structure_dump/aus/brisbane/guddat/ahas/AtAHAS_val.mrc Opened AtAHAS_val.mrc, grid size 512,512,512, pixel 0.82, shown at level 0.128, step 2, values float32 > select /V 152 atoms, 144 bonds, 1 model selected > select clear > ~cartoon /V > select clear > ~cartoon /V > ~cartoon /V > ~cartoon > cartoon > select up 19 atoms, 18 bonds, 1 model selected > select /V 152 atoms, 144 bonds, 1 model selected > select clear > view sel > select up 19 atoms, 18 bonds, 1 model selected > color sel bychain > color sel byhetero No template found for residue K1000 (VAL) Doing nothing Traceback (most recent call last): File ""/home/tic20/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/isolde.py"", line 2685, in _start_sim_or_toggle_pause self.start_sim() File ""/home/tic20/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/isolde.py"", line 2705, in start_sim self.params, self.sim_params, excluded_residues = self.ignored_residues) File ""/home/tic20/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 576, in __init__ self._prepare_validation_managers(mobile_atoms) File ""/home/tic20/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 746, in _prepare_validation_managers rota_a.restrict_to_selected_residues(mobile_res) File ""/home/tic20/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/validation/rota_annotation.py"", line 129, in restrict_to_selected_residues self.update_graphics() File ""/home/tic20/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/validation/rota_annotation.py"", line 191, in update_graphics non_favored_only = self._hide_favored) File ""/home/tic20/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/molobject.py"", line 1543, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) IndexError: _Map_base::at IndexError: _Map_base::at File ""/home/tic20/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/molobject.py"", line 1543, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) See log for complete Python traceback. Traceback (most recent call last): File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/home/tic20/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/isolde.py"", line 1060, in _selection_changed self._enable_rebuild_residue_frame(r) File ""/home/tic20/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/isolde.py"", line 1664, in _enable_rebuild_residue_frame self._update_selected_residue_info_live(None, None) File ""/home/tic20/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/isolde.py"", line 2217, in _update_selected_residue_info_live score = rot.score File ""/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/atomic/molc.py"", line 93, in get_prop cget(self._c_pointer_ref, 1, v_ref) IndexError: _Map_base::at Error processing trigger ""selection changed"": IndexError: _Map_base::at File ""/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/atomic/molc.py"", line 93, in get_prop cget(self._c_pointer_ref, 1, v_ref) See log for complete Python traceback. > close #1.2.2 Traceback (most recent call last): File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/home/tic20/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/isolde.py"", line 1027, in _update_model_list self._update_sim_control_button_states() File ""/home/tic20/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/isolde.py"", line 1127, in _update_sim_control_button_states self._selection_changed() File ""/home/tic20/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/isolde.py"", line 1060, in _selection_changed self._enable_rebuild_residue_frame(r) File ""/home/tic20/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/isolde.py"", line 1664, in _enable_rebuild_residue_frame self._update_selected_residue_info_live(None, None) File ""/home/tic20/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/isolde.py"", line 2217, in _update_selected_residue_info_live score = rot.score File ""/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/atomic/molc.py"", line 93, in get_prop cget(self._c_pointer_ref, 1, v_ref) IndexError: _Map_base::at Error processing trigger ""remove models"": IndexError: _Map_base::at File ""/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/atomic/molc.py"", line 93, in get_prop cget(self._c_pointer_ref, 1, v_ref) See log for complete Python traceback. > close #1.2.3 Traceback (most recent call last): File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/home/tic20/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/isolde.py"", line 1027, in _update_model_list self._update_sim_control_button_states() File ""/home/tic20/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/isolde.py"", line 1127, in _update_sim_control_button_states self._selection_changed() File ""/home/tic20/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/isolde.py"", line 1060, in _selection_changed self._enable_rebuild_residue_frame(r) File ""/home/tic20/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/isolde.py"", line 1664, in _enable_rebuild_residue_frame self._update_selected_residue_info_live(None, None) File ""/home/tic20/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/isolde.py"", line 2217, in _update_selected_residue_info_live score = rot.score File ""/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/atomic/molc.py"", line 93, in get_prop cget(self._c_pointer_ref, 1, v_ref) IndexError: _Map_base::at Error processing trigger ""remove models"": IndexError: _Map_base::at File ""/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/atomic/molc.py"", line 93, in get_prop cget(self._c_pointer_ref, 1, v_ref) See log for complete Python traceback. > select clear Traceback (most recent call last): File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/home/tic20/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/isolde.py"", line 1060, in _selection_changed self._enable_rebuild_residue_frame(r) File ""/home/tic20/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/isolde.py"", line 1664, in _enable_rebuild_residue_frame self._update_selected_residue_info_live(None, None) File ""/home/tic20/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/isolde.py"", line 2217, in _update_selected_residue_info_live score = rot.score File ""/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/atomic/molc.py"", line 93, in get_prop cget(self._c_pointer_ref, 1, v_ref) IndexError: _Map_base::at Error processing trigger ""selection changed"": IndexError: _Map_base::at File ""/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/atomic/molc.py"", line 93, in get_prop cget(self._c_pointer_ref, 1, v_ref) See log for complete Python traceback. Traceback (most recent call last): File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/home/tic20/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/isolde.py"", line 1060, in _selection_changed self._enable_rebuild_residue_frame(r) File ""/home/tic20/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/isolde.py"", line 1664, in _enable_rebuild_residue_frame self._update_selected_residue_info_live(None, None) File ""/home/tic20/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/isolde.py"", line 2217, in _update_selected_residue_info_live score = rot.score File ""/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/atomic/molc.py"", line 93, in get_prop cget(self._c_pointer_ref, 1, v_ref) IndexError: _Map_base::at Error processing trigger ""selection changed"": IndexError: _Map_base::at File ""/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/atomic/molc.py"", line 93, in get_prop cget(self._c_pointer_ref, 1, v_ref) See log for complete Python traceback. > select clear Traceback (most recent call last): File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/home/tic20/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/isolde.py"", line 1060, in _selection_changed self._enable_rebuild_residue_frame(r) File ""/home/tic20/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/isolde.py"", line 1664, in _enable_rebuild_residue_frame self._update_selected_residue_info_live(None, None) File ""/home/tic20/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/isolde.py"", line 2217, in _update_selected_residue_info_live score = rot.score File ""/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/atomic/molc.py"", line 93, in get_prop cget(self._c_pointer_ref, 1, v_ref) IndexError: _Map_base::at Error processing trigger ""selection changed"": IndexError: _Map_base::at File ""/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/atomic/molc.py"", line 93, in get_prop cget(self._c_pointer_ref, 1, v_ref) See log for complete Python traceback. > close #1.2.4 > select clear Traceback (most recent call last): File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/home/tic20/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/isolde.py"", line 1060, in _selection_changed self._enable_rebuild_residue_frame(r) File ""/home/tic20/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/isolde.py"", line 1664, in _enable_rebuild_residue_frame self._update_selected_residue_info_live(None, None) File ""/home/tic20/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/isolde.py"", line 2217, in _update_selected_residue_info_live score = rot.score File ""/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/atomic/molc.py"", line 93, in get_prop cget(self._c_pointer_ref, 1, v_ref) IndexError: _Map_base::at Error processing trigger ""selection changed"": IndexError: _Map_base::at File ""/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/atomic/molc.py"", line 93, in get_prop cget(self._c_pointer_ref, 1, v_ref) See log for complete Python traceback. Traceback (most recent call last): File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/home/tic20/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/isolde.py"", line 1060, in _selection_changed self._enable_rebuild_residue_frame(r) File ""/home/tic20/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/isolde.py"", line 1646, in _enable_rebuild_residue_frame rot_m = session_extensions.get_rotamer_mgr(self.session) File ""/home/tic20/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/molobject.py"", line 209, in get_rotamer_mgr if hasattr(session, 'rota_mgr') and not session.rota_mgr.deleted: AttributeError: 'NoneType' object has no attribute 'deleted' Error processing trigger ""selection changed"": AttributeError: 'NoneType' object has no attribute 'deleted' File ""/home/tic20/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/molobject.py"", line 209, in get_rotamer_mgr if hasattr(session, 'rota_mgr') and not session.rota_mgr.deleted: See log for complete Python traceback. Traceback (most recent call last): File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/home/tic20/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/isolde.py"", line 1060, in _selection_changed self._enable_rebuild_residue_frame(r) File ""/home/tic20/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/isolde.py"", line 1646, in _enable_rebuild_residue_frame rot_m = session_extensions.get_rotamer_mgr(self.session) File ""/home/tic20/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/molobject.py"", line 209, in get_rotamer_mgr if hasattr(session, 'rota_mgr') and not session.rota_mgr.deleted: AttributeError: 'NoneType' object has no attribute 'deleted' Error processing trigger ""selection changed"": AttributeError: 'NoneType' object has no attribute 'deleted' File ""/home/tic20/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/molobject.py"", line 209, in get_rotamer_mgr if hasattr(session, 'rota_mgr') and not session.rota_mgr.deleted: See log for complete Python traceback. > select clear > view sel > color sel bychain > color sel byhetero > view sel > color sel bychain > color sel byhetero > view sel > view /F:1000 > select up 19 atoms, 18 bonds, 1 model selected > color sel bychain > color sel byhetero > select up 19 atoms, 18 bonds, 1 model selected > color sel bychain > color sel byhetero > select up 19 atoms, 18 bonds, 1 model selected > color sel bychain > color sel byhetero > view sel > color sel bychain > color sel byhetero Unknown command: v.atview sel > view sel > color sel bychain > color sel byhetero > view sel > color sel bychain > color sel byhetero > view sel > color sel bychain > color sel byhetero > view sel > color sel bychain > color sel byhetero > select :1000 152 atoms, 144 bonds, 1 model selected > select clear > view sel > select clear > view sel > select clear > view sel > select clear > select clear > view sel No template found for residue B732 (FAD) Doing nothing > delete :FAD@H1 > select clear > view sel > select clear > select clear > view sel > select clear > view sel > select clear > select clear > view sel > select clear > select clear > view sel > view sel > select clear > select clear > view sel > select clear > view sel > select clear > view sel > select clear > view sel > select clear > view sel > select clear > pwd Current working directory is: /run/media/tic20/storage/structure_dump/aus/brisbane/guddat/ahas > view sel > select up 19 atoms, 18 bonds, 1 model selected > select up 35 atoms, 33 bonds, 1 model selected > select up 55 atoms, 53 bonds, 1 model selected > select up 74 atoms, 71 bonds, 1 model selected > select up 91 atoms, 88 bonds, 1 model selected > select up 107 atoms, 103 bonds, 1 model selected > select up 126 atoms, 121 bonds, 1 model selected > select up 136 atoms, 130 bonds, 1 model selected > select sel&sidechain 104 atoms, 97 bonds, 1 model selected > show sel surfaces > mlp sel Map values for surface ""working_noh_ligand_atoms_renamed_real_space_refined.pdb_N SES surface"": minimum -25.26, mean -2.375, maximum 24.48 Map values for surface ""working_noh_ligand_atoms_renamed_real_space_refined.pdb_O SES surface"": minimum -27.95, mean -2.516, maximum 25.46 > select clear > hide #1.3 models > hide HC > hbonds 5287 hydrogen bonds found > set bgColor white > lighting soft > lighting full > hide #!1.1 models > lighting soft > show #!1.1 models > hide #!1.1 models > show #!1.1 models > hide #!1.1 models > select up 19 atoms, 18 bonds, 1 model selected > style sel ball Changed 19 atom styles > select clear > select up 19 atoms, 18 bonds, 1 model selected > color sel tan > color sel byhetero > hide sel > select up 26 atoms, 25 bonds, 2 models selected > select down 16 atoms, 2 models selected > select up 11 atoms, 10 bonds, 2 models selected > select up 11 atoms, 10 bonds, 2 models selected > hide sel > ui mousemode rightMode label > label #1.2/N:95 > select clear > label #1.2/O:346 > label #1.2/O:347 > label #1.2/N:98 > label #1.2/N:100 > lighting full > lighting soft > graphics silhouettes true > label #1.2/N:100 > cofr showPivot false > save val_N_chain_binding_pocket.jpg > close #1.2.14 > show #1.3 models > show #!1.1 models Missing command > hide surfaces > select clear > graphics silhouettes false > lighting simple > save working.cxs > select up 19 atoms, 18 bonds, 1 model selected > style sel stick Changed 19 atom styles > select clear > close #1.2.15 > save working.cxs > show ~H > save working.cxs > save working.pdb #1 > lighting simple > close #1.2.12-13 > select up 21 atoms, 21 bonds, 1 model selected > surface sel > ~surface > select clear > select clear > select up 21 atoms, 21 bonds, 2 models selected > surface sel > ~surface OpenGL version: 3.3.0 NVIDIA 440.33.01 OpenGL renderer: TITAN Xp/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: Dell Inc. Model: Precision T5600 OS: CentOS Linux 7 Core Architecture: 64bit ELF CPU: 32 Intel(R) Xeon(R) CPU E5-2687W 0 @ 3.10GHz Cache Size: 20480 KB Graphics: 03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP102 [TITAN Xp] [10de:1b02] (rev a1) Subsystem: NVIDIA Corporation Device [10de:11df] Kernel driver in use: nvidia }}} " enhancement closed normal Surface not a bug all ChimeraX