id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3057 pseudobond's atoms pb_scene_coord is None(?) 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 Running 'hbonds' on a model initialised in ISOLDE. 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 6yla_refine_12.pdb Summary of feedback from opening 6yla_refine_12.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK Date 2020-04-16 Time 14:03:37 BST +0100 (1587042217.07 s) Ignored bad PDB record found on line 2 REMARK PHENIX refinement Ignored bad PDB record found on line 4 REMARK ****************** INPUT FILES AND LABELS ****************************** Ignored bad PDB record found on line 5 REMARK Reflections: Ignored bad PDB record found on line 6 REMARK file name : /run/media/tic20/storage/structure_dump/covid-19/6yla/6yla.mtz 49 messages similar to the above omitted Chain information for 6yla_refine_12.pdb #1 --- Chain | Description A | No description available B | No description available C L | No description available E | No description available H | No description available > isolde start > set selectionWidth 4 Chain information for 6yla_refine_12.pdb --- Chain | Description 1.2/A | No description available 1.2/B | No description available 1.2/C 1.2/L | No description available 1.2/E | No description available 1.2/H | No description available Done loading forcefield QWidget::repaint: Recursive repaint detected WARNING: found multiple possible R-free arrays: (dataset) R-free-flags, (dataset) R-free-flags-1 Automatically choosing ""(dataset) R-free-flags"". If this is incorrect, please either provide a file with a single flag array, or load the file again using the free_flag_label argument. Reflection data provided as intensities. Performing French & Wilson scaling to convert to amplitudes... > view /A:454 > set bgColor white > open2 > /run/media/tic20/storage/structure_dump/covid-19/6yla/Refine_13/6yla_refine_13.pdb Summary of feedback from opening <_io.textiowrapper name=""/run/media/tic20/storage/structure_dump/covid-19/6yla/Refine_13/6yla_refine_13.pdb"" mode=""rt"" encoding=""utf-8""> --- warnings | Ignored bad PDB record found on line 1 REMARK Date 2020-04-16 Time 16:08:52 BST +0100 (1587049732.54 s) Ignored bad PDB record found on line 2 REMARK PHENIX refinement Ignored bad PDB record found on line 4 REMARK ****************** INPUT FILES AND LABELS ****************************** Ignored bad PDB record found on line 5 REMARK Reflections: Ignored bad PDB record found on line 6 REMARK file name : /run/media/tic20/storage/structure_dump/covid-19/6yla/6yla.mtz 54 messages similar to the above omitted Chain information for 6yla_refine_13.pdb #2 --- Chain | Description A | No description available B | No description available C L | No description available E | No description available H | No description available > select #2 10128 atoms, 10234 bonds, 6 pseudobonds, 2 models selected > style sel stick Changed 10128 atom styles > hide #!1 models > rama #2 Chain information for 6yla_refine_13.pdb --- Chain | Description 2.2/A | No description available 2.2/B | No description available 2.2/C 2.2/L | No description available 2.2/E | No description available 2.2/H | No description available > show #!1 models > hide #!2 models > show #!2 models > hide #!2.2 models > view /S:8 > addh Summary of feedback from adding hydrogens to multiple structures --- notes | No usable SEQRES records for 6yla_refine_12.pdb (#1.2) chain A; guessing termini instead No usable SEQRES records for 6yla_refine_12.pdb (#1.2) chain B; guessing termini instead No usable SEQRES records for 6yla_refine_12.pdb (#1.2) chain C; guessing termini instead No usable SEQRES records for 6yla_refine_12.pdb (#1.2) chain E; guessing termini instead No usable SEQRES records for 6yla_refine_12.pdb (#1.2) chain H; guessing termini instead 1 messages similar to the above omitted Chain-initial residues that are actual N termini: 6yla_refine_12.pdb #1.2/A ILE 332, 6yla_refine_12.pdb #1.2/B THR 0, 6yla_refine_12.pdb #1.2/C ASP 1, 6yla_refine_12.pdb #1.2/E GLU 327, 6yla_refine_12.pdb #1.2/H THR 0, 6yla_refine_12.pdb #1.2/L ASP 1 Chain-initial residues that are not actual N termini: 6yla_refine_12.pdb #1.2/A ASN 448, 6yla_refine_12.pdb #1.2/B GLY 137, 6yla_refine_12.pdb #1.2/H GLY 137 Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 6yla_refine_12.pdb #1.2/A ASN 532, 6yla_refine_12.pdb #1.2/A VAL 445, 6yla_refine_12.pdb #1.2/B CYS 220, 6yla_refine_12.pdb #1.2/B SER 132, 6yla_refine_12.pdb #1.2/C GLU 219, 6yla_refine_12.pdb #1.2/E LYS 529, 6yla_refine_12.pdb #1.2/H SER 219, 6yla_refine_12.pdb #1.2/H SER 132, 6yla_refine_12.pdb #1.2/L GLU 219 1594 hydrogen bonds Adding 'H' to 6yla_refine_12.pdb #1.2/A ASN 448 Adding 'H' to 6yla_refine_12.pdb #1.2/B GLY 137 Adding 'H' to 6yla_refine_12.pdb #1.2/H GLY 137 6yla_refine_12.pdb #1.2/A ASN 532 is not terminus, removing H atom from 'C' 6yla_refine_12.pdb #1.2/A VAL 445 is not terminus, removing H atom from 'C' 6yla_refine_12.pdb #1.2/B CYS 220 is not terminus, removing H atom from 'C' 6yla_refine_12.pdb #1.2/B SER 132 is not terminus, removing H atom from 'C' 6yla_refine_12.pdb #1.2/C GLU 219 is not terminus, removing H atom from 'C' 4 messages similar to the above omitted No usable SEQRES records for 6yla_refine_13.pdb (#2.2) chain A; guessing termini instead No usable SEQRES records for 6yla_refine_13.pdb (#2.2) chain B; guessing termini instead No usable SEQRES records for 6yla_refine_13.pdb (#2.2) chain C; guessing termini instead No usable SEQRES records for 6yla_refine_13.pdb (#2.2) chain E; guessing termini instead No usable SEQRES records for 6yla_refine_13.pdb (#2.2) chain H; guessing termini instead 1 messages similar to the above omitted Chain-initial residues that are actual N termini: 6yla_refine_13.pdb #2.2/A ILE 332, 6yla_refine_13.pdb #2.2/B THR 0, 6yla_refine_13.pdb #2.2/C ASP 1, 6yla_refine_13.pdb #2.2/E GLU 327, 6yla_refine_13.pdb #2.2/H THR 0, 6yla_refine_13.pdb #2.2/L ASP 1 Chain-initial residues that are not actual N termini: 6yla_refine_13.pdb #2.2/A ASN 448, 6yla_refine_13.pdb #2.2/B GLY 137, 6yla_refine_13.pdb #2.2/H GLY 137 Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 6yla_refine_13.pdb #2.2/A ASN 532, 6yla_refine_13.pdb #2.2/A VAL 445, 6yla_refine_13.pdb #2.2/B CYS 220, 6yla_refine_13.pdb #2.2/B SER 132, 6yla_refine_13.pdb #2.2/C GLU 219, 6yla_refine_13.pdb #2.2/E LYS 529, 6yla_refine_13.pdb #2.2/H SER 219, 6yla_refine_13.pdb #2.2/H SER 132, 6yla_refine_13.pdb #2.2/L GLU 219 1560 hydrogen bonds Adding 'H' to 6yla_refine_13.pdb #2.2/A ASN 448 Adding 'H' to 6yla_refine_13.pdb #2.2/B GLY 137 Adding 'H' to 6yla_refine_13.pdb #2.2/H GLY 137 6yla_refine_13.pdb #2.2/A ASN 532 is not terminus, removing H atom from 'C' 6yla_refine_13.pdb #2.2/A VAL 445 is not terminus, removing H atom from 'C' 6yla_refine_13.pdb #2.2/B CYS 220 is not terminus, removing H atom from 'C' 6yla_refine_13.pdb #2.2/B SER 132 is not terminus, removing H atom from 'C' 6yla_refine_13.pdb #2.2/C GLU 219 is not terminus, removing H atom from 'C' 4 messages similar to the above omitted 19986 hydrogens added Loading residue template for DMS from internal database Loading residue template for PG0 from internal database > select clear Updating bulk solvent parameters... > hide HC > hbonds #1 4021 hydrogen bonds found 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 ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/atomic/pbgroup.py"", line 63, in pbg_update self._update_graphics() File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/atomic/pbgroup.py"", line 218, in _update_graphics d.positions = self._update_positions(pbonds, bond_atoms) File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/atomic/pbgroup.py"", line 231, in _update_positions axyz0, axyz1 = to_pbg*ba1.pb_scene_coords, to_pbg*ba2.pb_scene_coords File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/atomic/molarray.py"", line 749, in pb_scene_coords v[i] = a.pb_scene_coord File ""cymol.pyx"", line 242, in chimerax.atomic.cymol.CyAtom.pb_scene_coord.__get__ File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/geometry/place.py"", line 122, in __mul__ raise TypeError('Cannot multiply Place times ""%s""' % str(p)) TypeError: Cannot multiply Place times ""None"" Error processing trigger ""changes"": TypeError: Cannot multiply Place times ""None"" File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/geometry/place.py"", line 122, in __mul__ raise TypeError('Cannot multiply Place times ""%s""' % str(p)) 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 ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/atomic/pbgroup.py"", line 185, in _update_graphics_if_needed self._update_graphics(gc) File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/atomic/pbgroup.py"", line 218, in _update_graphics d.positions = self._update_positions(pbonds, bond_atoms) File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/atomic/pbgroup.py"", line 231, in _update_positions axyz0, axyz1 = to_pbg*ba1.pb_scene_coords, to_pbg*ba2.pb_scene_coords File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/atomic/molarray.py"", line 749, in pb_scene_coords v[i] = a.pb_scene_coord File ""cymol.pyx"", line 242, in chimerax.atomic.cymol.CyAtom.pb_scene_coord.__get__ File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/geometry/place.py"", line 122, in __mul__ raise TypeError('Cannot multiply Place times ""%s""' % str(p)) TypeError: Cannot multiply Place times ""None"" Error processing trigger ""graphics update"": TypeError: Cannot multiply Place times ""None"" File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/geometry/place.py"", line 122, in __mul__ raise TypeError('Cannot multiply Place times ""%s""' % str(p)) See log for complete Python traceback. 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 }}} " defect closed normal Depiction fixed Eric Pettersen all ChimeraX