id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3613 ISOLDE: cannot import name 'save' from 'chimerax.core.commands' christl.gaubitz@… Tristan Croll "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.18362 ChimeraX Version: 1.0 (2020-06-04 23:15:07 UTC) Description Isolde's Save current model as... gives following error message: ImportError: cannot import name 'save' from 'chimerax.core.commands' (C:\Program Files\ChimeraX 1.0\bin\lib\site-packages\chimerax\core\commands\__init__.py) File ""C:\Users\Christl\AppData\Local\UCSF\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. Log: UCSF ChimeraX version: 1.0 (2020-06-04) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""C:/Users/Christl/Dropbox (UMass Medical School)/yRFC- > building/denmod_map.ccp4"" ""C:/Users/Christl/Dropbox (UMass Medical > School)/yRFC-building/DNA1_rigidbodyfitted-coot-1-loopFitted.pdb"" Chain information for DNA1_rigidbodyfitted-coot-1-loopFitted.pdb #2 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available J | No description available Opened denmod_map.ccp4, grid size 240,240,240, pixel 1.06, shown at level 1.2, step 1, values float32 > set bgColor white > hide atoms > show cartoons > ui tool show ISOLDE > set selectionWidth 4 Chain information for DNA1_rigidbodyfitted-coot-1-loopFitted.pdb --- Chain | Description 2.2/A | No description available 2.2/B | No description available 2.2/C | No description available 2.2/D | No description available 2.2/E | No description available 2.2/F | No description available 2.2/G | No description available 2.2/H | No description available 2.2/I | No description available 2.2/J | No description available Done loading forcefield > select #1/ A:412 Nothing selected > select #1/ A:410 Nothing selected > select #2/ A:412 9 atoms, 8 bonds, 1 model selected > view #2/ A:412 > addh Summary of feedback from adding hydrogens to DNA1_rigidbodyfitted- coot-1-loopFitted.pdb #2.2 --- notes | No usable SEQRES records for DNA1_rigidbodyfitted- coot-1-loopFitted.pdb (#2.2) chain A; guessing termini instead No usable SEQRES records for DNA1_rigidbodyfitted-coot-1-loopFitted.pdb (#2.2) chain B; guessing termini instead No usable SEQRES records for DNA1_rigidbodyfitted-coot-1-loopFitted.pdb (#2.2) chain C; guessing termini instead No usable SEQRES records for DNA1_rigidbodyfitted-coot-1-loopFitted.pdb (#2.2) chain D; guessing termini instead No usable SEQRES records for DNA1_rigidbodyfitted-coot-1-loopFitted.pdb (#2.2) chain E; guessing termini instead 5 messages similar to the above omitted Chain-initial residues that are actual N termini: /A VAL 291, /B THR 4, /C SER 9, /D SER 14, /E TRP 4, /F MET 1, /G MET 1, /H MET 1, /I DT 5, /J DA 3 Chain-initial residues that are not actual N termini: /E HIS 133, /G GLU 189, /H GLU 130 Chain-final residues that are actual C termini: /I DT 28, /J DA 20 Chain-final residues that are not actual C termini: /A MET 777, /B LYS 322, /C THR 335, /D LEU 353, /E LEU 353, /E GLU 120, /F ASN 255, /G ASN 255, /G ASP 187, /H LYS 253, /H ASP 120 2211 hydrogen bonds Adding 'H' to /E HIS 133 Adding 'H' to /G GLU 189 Adding 'H' to /H GLU 130 /A MET 777 is not terminus, removing H atom from 'C' /B LYS 322 is not terminus, removing H atom from 'C' /C THR 335 is not terminus, removing H atom from 'C' /D LEU 353 is not terminus, removing H atom from 'C' /E LEU 353 is not terminus, removing H atom from 'C' 5 messages similar to the above omitted 21175 hydrogens added Loading residue template for ADP from internal database Loading residue template for AGS from internal database > hide HC > close #2 Deleting atomic symmetry model... > open ""C:/Users/Christl/Dropbox (UMass Medical School)/yRFC- > building/DNA1_rigidbodyfitted-coot-1-loopFitted-NoATPDNA.pdb"" Chain information for DNA1_rigidbodyfitted-coot-1-loopFitted-NoATPDNA.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available Chain information for DNA1_rigidbodyfitted-coot-1-loopFitted-NoATPDNA.pdb --- Chain | Description 1.2/A | No description available 1.2/B | No description available 1.2/C | No description available 1.2/D | No description available 1.2/E | No description available 1.2/F | No description available 1.2/G | No description available 1.2/H | No description available > open ""C:/Users/Christl/Dropbox (UMass Medical School)/yRFC- > building/denmod_map.ccp4"" Opened denmod_map.ccp4, grid size 240,240,240, pixel 1.06, shown at level 1.2, step 1, values float32 > addh Summary of feedback from adding hydrogens to DNA1_rigidbodyfitted- coot-1-loopFitted-NoATPDNA.pdb #1.2 --- notes | No usable SEQRES records for DNA1_rigidbodyfitted-coot-1-loopFitted- NoATPDNA.pdb (#1.2) chain A; guessing termini instead No usable SEQRES records for DNA1_rigidbodyfitted-coot-1-loopFitted- NoATPDNA.pdb (#1.2) chain B; guessing termini instead No usable SEQRES records for DNA1_rigidbodyfitted-coot-1-loopFitted- NoATPDNA.pdb (#1.2) chain C; guessing termini instead No usable SEQRES records for DNA1_rigidbodyfitted-coot-1-loopFitted- NoATPDNA.pdb (#1.2) chain D; guessing termini instead No usable SEQRES records for DNA1_rigidbodyfitted-coot-1-loopFitted- NoATPDNA.pdb (#1.2) chain E; guessing termini instead 3 messages similar to the above omitted Chain-initial residues that are actual N termini: /A VAL 291, /B THR 4, /C SER 9, /D SER 14, /E TRP 4, /F MET 1, /G MET 1, /H MET 1 Chain-initial residues that are not actual N termini: /E HIS 133, /G GLU 189, /H GLU 130 Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A MET 777, /B LYS 322, /C THR 335, /D LEU 353, /E LEU 353, /E GLU 120, /F ASN 255, /G ASN 255, /G ASP 187, /H LYS 253, /H ASP 120 2102 hydrogen bonds Adding 'H' to /E HIS 133 Adding 'H' to /G GLU 189 Adding 'H' to /H GLU 130 /A MET 777 is not terminus, removing H atom from 'C' /B LYS 322 is not terminus, removing H atom from 'C' /C THR 335 is not terminus, removing H atom from 'C' /D LEU 353 is not terminus, removing H atom from 'C' /E LEU 353 is not terminus, removing H atom from 'C' 5 messages similar to the above omitted 20633 hydrogens added > hide HC > select clear > select clear > select clear > select clear > select clear > select clear > select clear Unable to flip peptide bond after 50 rounds. Giving up. > select clear Traceback (most recent call last): File ""C:\Users\Christl\AppData\Local\UCSF\ChimeraX\1.0\site- packages\chimerax\isolde\isolde.py"", line 1165, in _save_cif_file self.save_cif_file(self._selected_model, filename) File ""C:\Users\Christl\AppData\Local\UCSF\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' (C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\core\commands\\__init__.py) ImportError: cannot import name 'save' from 'chimerax.core.commands' (C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\core\commands\\__init__.py) File ""C:\Users\Christl\AppData\Local\UCSF\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 ""C:\Users\Christl\AppData\Local\UCSF\ChimeraX\1.0\site- packages\chimerax\isolde\isolde.py"", line 1165, in _save_cif_file self.save_cif_file(self._selected_model, filename) File ""C:\Users\Christl\AppData\Local\UCSF\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' (C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\core\commands\\__init__.py) ImportError: cannot import name 'save' from 'chimerax.core.commands' (C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\core\commands\\__init__.py) File ""C:\Users\Christl\AppData\Local\UCSF\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 ""C:\Users\Christl\AppData\Local\UCSF\ChimeraX\1.0\site- packages\chimerax\isolde\isolde.py"", line 1165, in _save_cif_file self.save_cif_file(self._selected_model, filename) File ""C:\Users\Christl\AppData\Local\UCSF\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' (C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\core\commands\\__init__.py) ImportError: cannot import name 'save' from 'chimerax.core.commands' (C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\core\commands\\__init__.py) File ""C:\Users\Christl\AppData\Local\UCSF\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 ""C:\Users\Christl\AppData\Local\UCSF\ChimeraX\1.0\site- packages\chimerax\isolde\isolde.py"", line 1165, in _save_cif_file self.save_cif_file(self._selected_model, filename) File ""C:\Users\Christl\AppData\Local\UCSF\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' (C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\core\commands\\__init__.py) ImportError: cannot import name 'save' from 'chimerax.core.commands' (C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\core\commands\\__init__.py) File ""C:\Users\Christl\AppData\Local\UCSF\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 clear Traceback (most recent call last): File ""C:\Users\Christl\AppData\Local\UCSF\ChimeraX\1.0\site- packages\chimerax\isolde\isolde.py"", line 1165, in _save_cif_file self.save_cif_file(self._selected_model, filename) File ""C:\Users\Christl\AppData\Local\UCSF\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' (C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\core\commands\\__init__.py) ImportError: cannot import name 'save' from 'chimerax.core.commands' (C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\core\commands\\__init__.py) File ""C:\Users\Christl\AppData\Local\UCSF\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. > save ""C:/Users/Christl/Dropbox (UMass Medical School)/yRFC- > building/fuck.cxs"" > hide #!1 models > show #!1 models > save_cif_file #1, test Unknown command: save_cif_file #1, test > save_cif_file Unknown command: save_cif_file Cannot determine format for '#1' > save test format pdb models #1 > hide #!1.1 models > show #!1.1 models > hide #!1 models > show #!1 models > hide #!1.2 models > show #!1.2 models > hide #1.3 models > show #1.3 models > hide #1.3 models > show #1.3 models > hide #1.3 models > save test format pdb models #1.2 Traceback (most recent call last): File ""C:\Users\Christl\AppData\Local\UCSF\ChimeraX\1.0\site- packages\chimerax\isolde\isolde.py"", line 1165, in _save_cif_file self.save_cif_file(self._selected_model, filename) File ""C:\Users\Christl\AppData\Local\UCSF\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' (C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\core\commands\\__init__.py) ImportError: cannot import name 'save' from 'chimerax.core.commands' (C:\Program Files\ChimeraX 1.0\bin\lib\site- packages\chimerax\core\commands\\__init__.py) File ""C:\Users\Christl\AppData\Local\UCSF\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 376.54 OpenGL renderer: GeForce GT 730M/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: LENOVO Model: 20270 OS: Microsoft Windows 10 Home (Build 18362) Memory: 8,509,480,960 MaxProcessMemory: 137,438,953,344 CPU: 4 Intel(R) Core(TM) i5-4210U CPU @ 1.70GHz"" PyQt version: 5.12.3 Compiled Qt version: 5.12.4 Runtime Qt version: 5.12.8 }}} " defect closed normal Third Party fixed Eric Pettersen all ChimeraX