id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3623 ISOLDE: cannot import name 'save' from 'chimerax.core.commands' td373@… Tristan Croll "{{{ The following bug report has been submitted: Platform: Linux-4.15.0-91-generic-x86_64-with-debian-stretch-sid ChimeraX Version: 1.0 (2020-06-04 23:15:07 UTC) Description I'm trying to save my model after fixing the geometry with isolde. When I click 'save current model as' and fill in a name, then hit save, I get the following error: ImportError: cannot import name 'save' from 'chimerax.core.commands' (/opt/em/chimerax-1.0/lib/python3.7/site-packages/chimerax/core/commands/__init__.py) File ""/home/td373/.local/share/ChimeraX/1.0/site-packages/chimerax/isolde/isolde.py"", line 1177, in save_cif_file from chimerax.core.commands import save See log for complete Python traceback. Any feedback would be much appreciated Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.0 (2020-06-04) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX Some installed bundles are out of date. Please update the following bundles: * UI to version 1.2.1 (currently 1.0) * UI to version 1.2 (currently 1.0) > open > /mnt/raid0/td373/PNPase_model_refinements/PNP_ETS_Hfq/manual_Corr_refmac5_1.pdb manual_Corr_refmac5_1.pdb title: \--- [more info...] Chain information for manual_Corr_refmac5_1.pdb #1 --- Chain | Description D | No description available E F | No description available I J | No description available K | No description available L | No description available N | No description available O | No description available P | No description available > hide atoms > show cartoons > ui tool show ISOLDE > set selectionWidth 4 manual_Corr_refmac5_1.pdb title: \--- [more info...] Chain information for manual_Corr_refmac5_1.pdb --- Chain | Description 1.2/D | No description available 1.2/E 1.2/F | No description available 1.2/I 1.2/J | No description available 1.2/K | No description available 1.2/L | No description available 1.2/N | No description available 1.2/O | No description available 1.2/P | No description available Done loading forcefield > open /mnt/raid0/td373/PNPase_model_refinements/PNP_ETS_Hfq/State1.mrc Opened State1.mrc, grid size 300,300,300, pixel 1.07, shown at level 0.224, step 2, values float32 > volume #2 level 0.4342 > volume #2 step 1 > volume #2 level 0.4779 > volume #2 style mesh > volume #2 style surface > lighting simple > addh hbond true Summary of feedback from adding hydrogens to manual_Corr_refmac5_1.pdb #1.2 --- warnings | Not adding hydrogens to /I ARG 66 CB because it is missing heavy- atom bond partners Not adding hydrogens to /D LYS 47 CB because it is missing heavy-atom bond partners Not adding hydrogens to /D ARG 66 CB because it is missing heavy-atom bond partners Not adding hydrogens to /E ARG 19 CB because it is missing heavy-atom bond partners Not adding hydrogens to /E VAL 68 CB because it is missing heavy-atom bond partners 2 messages similar to the above omitted notes | No usable SEQRES records for manual_Corr_refmac5_1.pdb (#1.2) chain D; guessing termini instead No usable SEQRES records for manual_Corr_refmac5_1.pdb (#1.2) chain E; guessing termini instead No usable SEQRES records for manual_Corr_refmac5_1.pdb (#1.2) chain F; guessing termini instead No usable SEQRES records for manual_Corr_refmac5_1.pdb (#1.2) chain I; guessing termini instead No usable SEQRES records for manual_Corr_refmac5_1.pdb (#1.2) chain J; guessing termini instead 5 messages similar to the above omitted Chain-initial residues that are actual N termini: /D ASP 9, /E GLN 8, /F GLN 8, /I SER 6, /J SER 6, /K LEU 7, /L MET 1, /N MET 1, /O MET 1, /P A 1 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: /N ILE 689, /O GLN 695, /P U 50 Chain-final residues that are not actual C termini: /D ALA 75, /E VAL 68, /F VAL 68, /I VAL 68, /J VAL 68, /K VAL 68, /L THR 693 1968 hydrogen bonds /D ALA 75 is not terminus, removing H atom from 'C' /E VAL 68 is not terminus, removing H atom from 'C' /F VAL 68 is not terminus, removing H atom from 'C' /I VAL 68 is not terminus, removing H atom from 'C' /J VAL 68 is not terminus, removing H atom from 'C' 2 messages similar to the above omitted 19752 hydrogens added > volume #1.1.1.1 level 0.3167 > volume #1.1.1.1 level 0.8695 > volume #1.1.1.1 level 0.7736 > volume #1.1.1.1 level 0.4541 > set bgColor white > show H > hide H > clipper spotlight radius 13.00 > clipper spotlight radius 14.00 > clipper spotlight radius 15.00 > volume #1.1.1.1 level 0.4204 > ui mousemode right ""contour level"" > volume #1.1.1.1 level 0.3615 > volume #1.1.1.1 level 0.3471 > volume #1.1.1.1 level 0.3141 > volume #1.1.1.1 level 0.5264 > volume #1.1.1.1 level 0.4653 > volume #1.1.1.1 level 0.4676 > volume #1.1.1.1 level 0.4387 > volume #1.1.1.1 level 0.5172 > volume #1.1.1.1 level 0.4826 > volume #1.1.1.1 level 0.4295 > volume #1.1.1.1 level 0.7441 > select up 42 atoms, 42 bonds, 1 model selected Traceback (most recent call last): File ""/home/td373/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/isolde.py"", line 2597, in _xtal_step_backward self._xtal_mask_to_atoms(sel, focus=False) File ""/home/td373/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/isolde.py"", line 2617, in _xtal_mask_to_atoms atoms, 0, context, cutoff, focus=focus) File ""/home/td373/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/symmetry.py"", line 973, in isolate_and_cover_selection extra_padding=extra_padding) File ""/home/td373/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/map_mgr.py"", line 358, in cover_atoms zm.set_symmetry_map(atoms, transforms, transform_indices) File ""/home/td373/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py"", line 111, in set_symmetry_map self.structure = self._unique_structure(atoms) File ""/home/td373/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py"", line 177, in _unique_structure raise TypeError('All atoms for zone mask must be from a single model!') TypeError: All atoms for zone mask must be from a single model! TypeError: All atoms for zone mask must be from a single model! File ""/home/td373/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py"", line 177, in _unique_structure raise TypeError('All atoms for zone mask must be from a single model!') See log for complete Python traceback. > volume #1.1.1.1 level 0.8303 > volume #1.1.1.1 level 0.6616 > volume #1.1.1.1 level 1.023 > volume #1.1.1.1 level 0.6413 > volume #1.1.1.1 level 0.6495 > volume #1.1.1.1 level 0.8458 Traceback (most recent call last): File ""/home/td373/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/isolde.py"", line 2608, in _xtal_mask_to_selection self._xtal_mask_to_atoms(sel, focus) File ""/home/td373/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/isolde.py"", line 2617, in _xtal_mask_to_atoms atoms, 0, context, cutoff, focus=focus) File ""/home/td373/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/symmetry.py"", line 973, in isolate_and_cover_selection extra_padding=extra_padding) File ""/home/td373/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/map_mgr.py"", line 358, in cover_atoms zm.set_symmetry_map(atoms, transforms, transform_indices) File ""/home/td373/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py"", line 111, in set_symmetry_map self.structure = self._unique_structure(atoms) File ""/home/td373/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py"", line 177, in _unique_structure raise TypeError('All atoms for zone mask must be from a single model!') TypeError: All atoms for zone mask must be from a single model! TypeError: All atoms for zone mask must be from a single model! File ""/home/td373/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py"", line 177, in _unique_structure raise TypeError('All atoms for zone mask must be from a single model!') See log for complete Python traceback. > select up 42 atoms, 42 bonds, 1 model selected > select up 104 atoms, 104 bonds, 1 model selected Traceback (most recent call last): File ""/home/td373/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/isolde.py"", line 2596, in _xtal_step_backward sel = sh.stepper.step_backward() File ""/home/td373/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/structurestepper.py"", line 74, in step_backward return self._step(direction=self.BACKWARD) File ""/home/td373/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/structurestepper.py"", line 81, in _step return self._step_generic(direction) File ""/home/td373/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/structurestepper.py"", line 104, in _step_generic first_index = indices[-overlap] IndexError: index -5 is out of bounds for axis 0 with size 0 IndexError: index -5 is out of bounds for axis 0 with size 0 File ""/home/td373/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/structurestepper.py"", line 104, in _step_generic first_index = indices[-overlap] See log for complete Python traceback. > select clear > select up 12 atoms, 11 bonds, 1 model selected > select up 19 atoms, 18 bonds, 1 model selected > select up 10656 atoms, 10730 bonds, 1 model selected > select down 19 atoms, 18 bonds, 1 model selected Traceback (most recent call last): File ""/home/td373/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/isolde.py"", line 2580, in _xtal_step_forward sel = sh.stepper.step_forward() File ""/home/td373/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/structurestepper.py"", line 71, in step_forward return self._step(direction=self.FORWARD) File ""/home/td373/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/structurestepper.py"", line 81, in _step return self._step_generic(direction) File ""/home/td373/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/structurestepper.py"", line 104, in _step_generic first_index = indices[-overlap] IndexError: index -5 is out of bounds for axis 0 with size 0 IndexError: index -5 is out of bounds for axis 0 with size 0 File ""/home/td373/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/structurestepper.py"", line 104, in _step_generic first_index = indices[-overlap] See log for complete Python traceback. > volume #1.1.1.1 level 0.8327 > volume #1.1.1.1 level 0.8897 > clipper spotlight radius 14.00 > clipper spotlight radius 13.00 > clipper spotlight radius 12.00 > clipper spotlight radius 11.00 > select clear > select up 24 atoms, 23 bonds, 1 model selected > select up 116 atoms, 115 bonds, 1 model selected > select up 10594 atoms, 10668 bonds, 1 model selected > select up 39670 atoms, 40082 bonds, 1 model selected Fetching CCD ILE_LL from http://ligand- expo.rcsb.org/reports/I/ILE_LL/ILE_LL.cif Fetching CCD ILE_LSN3 from http://ligand- expo.rcsb.org/reports/I/ILE_LSN3/ILE_LSN3.cif Fetching CCD ILE_LEO2 from http://ligand- expo.rcsb.org/reports/I/ILE_LEO2/ILE_LEO2.cif Fetching CCD ILE_LFZW from http://ligand- expo.rcsb.org/reports/I/ILE_LFZW/ILE_LFZW.cif Fetching CCD GLN_LL from http://ligand- expo.rcsb.org/reports/G/GLN_LL/GLN_LL.cif Fetching CCD GLN_LSN3 from http://ligand- expo.rcsb.org/reports/G/GLN_LSN3/GLN_LSN3.cif Fetching CCD GLN_LEO2 from http://ligand- expo.rcsb.org/reports/G/GLN_LEO2/GLN_LEO2.cif Fetching CCD GLN_LFZW from http://ligand- expo.rcsb.org/reports/G/GLN_LFZW/GLN_LFZW.cif Fetching CCD ORN from http://ligand-expo.rcsb.org/reports/O/ORN/ORN.cif Deleted the following atoms from residue A P1: H, OP1 > select up 34 atoms, 36 bonds, 1 model selected > select up 1610 atoms, 1744 bonds, 1 model selected > select up 39674 atoms, 40086 bonds, 1 model selected > volume #1.1.1.1 level 0.8897 > volume #1.1.1.1 level 0.6329 > select up 17 atoms, 16 bonds, 1 model selected > volume #1.1.1.1 level 0.4977 Traceback (most recent call last): File ""/home/td373/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/isolde.py"", line 1165, in _save_cif_file self.save_cif_file(self._selected_model, filename) File ""/home/td373/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/isolde.py"", line 1177, in save_cif_file from chimerax.core.commands import save ImportError: cannot import name 'save' from 'chimerax.core.commands' (/opt/em/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/commands/__init__.py) ImportError: cannot import name 'save' from 'chimerax.core.commands' (/opt/em/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/commands/__init__.py) File ""/home/td373/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/isolde.py"", line 1177, in save_cif_file from chimerax.core.commands import save See log for complete Python traceback. Traceback (most recent call last): File ""/home/td373/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/isolde.py"", line 1165, in _save_cif_file self.save_cif_file(self._selected_model, filename) File ""/home/td373/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/isolde.py"", line 1177, in save_cif_file from chimerax.core.commands import save ImportError: cannot import name 'save' from 'chimerax.core.commands' (/opt/em/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/commands/__init__.py) ImportError: cannot import name 'save' from 'chimerax.core.commands' (/opt/em/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/commands/__init__.py) File ""/home/td373/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/isolde.py"", line 1177, in save_cif_file from chimerax.core.commands import save See log for complete Python traceback. Traceback (most recent call last): File ""/home/td373/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/isolde.py"", line 1165, in _save_cif_file self.save_cif_file(self._selected_model, filename) File ""/home/td373/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/isolde.py"", line 1177, in save_cif_file from chimerax.core.commands import save ImportError: cannot import name 'save' from 'chimerax.core.commands' (/opt/em/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/commands/__init__.py) ImportError: cannot import name 'save' from 'chimerax.core.commands' (/opt/em/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/commands/__init__.py) File ""/home/td373/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/isolde.py"", line 1177, in save_cif_file from chimerax.core.commands import save See log for complete Python traceback. > select #1 39674 atoms, 40086 bonds, 18 models selected > ~select #1.1 39674 atoms, 40086 bonds, 13 models selected > ~select #1.3 39674 atoms, 40086 bonds, 12 models selected > select #1 39674 atoms, 40086 bonds, 18 models selected > ~select #1.1 39674 atoms, 40086 bonds, 13 models selected > ~select #1.3 39674 atoms, 40086 bonds, 12 models selected > select #1.2 39674 atoms, 40086 bonds, 11 models selected > select #1.2 39674 atoms, 40086 bonds, 11 models selected Traceback (most recent call last): File ""/home/td373/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/isolde.py"", line 1165, in _save_cif_file self.save_cif_file(self._selected_model, filename) File ""/home/td373/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/isolde.py"", line 1177, in save_cif_file from chimerax.core.commands import save ImportError: cannot import name 'save' from 'chimerax.core.commands' (/opt/em/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/commands/__init__.py) ImportError: cannot import name 'save' from 'chimerax.core.commands' (/opt/em/chimerax-1.0/lib/python3.7/site- packages/chimerax/core/commands/__init__.py) File ""/home/td373/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/isolde.py"", line 1177, in save_cif_file from chimerax.core.commands import save See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 440.33.01 OpenGL renderer: GeForce GTX 1080 Ti/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: System manufacturer Model: System Product Name OS: Ubuntu 16.04 xenial Architecture: 64bit ELF CPU: 12 Intel(R) Core(TM) i7-8700K CPU @ 3.70GHz Cache Size: 12288 KB Memory: total used free shared buff/cache available Mem: 62G 8.5G 2.7G 411M 51G 53G Swap: 63G 6.2G 57G Graphics: 01:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP102 [GeForce GTX 1080 Ti] [10de:1b06] (rev a1) Subsystem: eVga.com. Corp. Device [3842:6393] Kernel driver in use: nvidia PyQt version: 5.12.3 Compiled Qt version: 5.12.4 Runtime Qt version: 5.12.8 }}} " defect closed normal Third Party duplicate all ChimeraX