id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3112 geometry.find_closest_points index problem(?) 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 Not sure if this is a bug or just me not understanding, but in chimerax.geometry.find_closest_points: i1, i2, near1 = find_closest_points(coords1, coords2) ... the documentation says: near1 : numpy int32 array A third array is returned that gives the index in set 2 of the closest for each point in set 1. This array has length equal to the number of points in set 1. If a set 1 point has no point from set 2 within the distance range then index returned is -1. Is this array supposed to be ordered such that the first value is the index of the point in coords2 closest to coords1[0], and so on? Because at the moment, that's not the case (it contains all the correct indices, but they're in random order). 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 6vsb_1_1_1.pdb Summary of feedback from opening 6vsb_1_1_1.pdb --- warnings | Duplicate atom serial number found: 69277 Duplicate atom serial number found: 69278 Duplicate atom serial number found: 69279 Duplicate atom serial number found: 69280 Duplicate atom serial number found: 69276 925 messages similar to the above omitted Chain information for 6vsb_1_1_1.pdb #1 --- Chain | Description A B C | No description available > open 6vsb 6vsb title: Prefusion 2019-nCoV spike glycoprotein with a single receptor-binding domain up [more info...] Chain information for 6vsb #2 --- Chain | Description A B C | Spike glycoprotein Non-standard residues in 6vsb #2 --- NAG — N-acetyl-D-glucosamine > open 21375 fromDatabase emdb Opened emd_21375.map, grid size 432,432,432, pixel 1.05, shown at level 0.0501, step 2, values float32 > sequence chain #2/A Alignment identifier is 2.A > 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"") ERROR:ipykernel.inprocess.ipkernel:Exception in message handler: Traceback (most recent call last): File ""/opt/UCSF/ChimeraX/lib/python3.7/site-packages/ipykernel/kernelbase.py"", line 268, in dispatch_shell yield gen.maybe_future(handler(stream, idents, msg)) File ""/opt/UCSF/ChimeraX/lib/python3.7/site-packages/tornado/gen.py"", line 735, in run value = future.result() File ""/opt/UCSF/ChimeraX/lib/python3.7/site-packages/tornado/gen.py"", line 209, in wrapper yielded = next(result) File ""/opt/UCSF/ChimeraX/lib/python3.7/site-packages/ipykernel/kernelbase.py"", line 579, in complete_request matches = yield gen.maybe_future(self.do_complete(code, cursor_pos)) File ""/opt/UCSF/ChimeraX/lib/python3.7/site-packages/ipykernel/ipkernel.py"", line 354, in do_complete return self._experimental_do_complete(code, cursor_pos) File ""/opt/UCSF/ChimeraX/lib/python3.7/site-packages/ipykernel/ipkernel.py"", line 379, in _experimental_do_complete completions = list(_rectify_completions(code, raw_completions)) File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/IPython/core/completer.py"", line 484, in rectify_completions completions = list(completions) File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/IPython/core/completer.py"", line 1815, in completions for c in self._completions(text, offset, _timeout=self.jedi_compute_type_timeout/1000): File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/IPython/core/completer.py"", line 1859, in _completions full_text=full_text, cursor_line=cursor_line, cursor_pos=cursor_column) File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/IPython/core/completer.py"", line 1983, in _complete text = self.splitter.split_line(line_buffer, cursor_pos) File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/IPython/core/completer.py"", line 562, in split_line l = line if cursor_pos is None else line[:cursor_pos] TypeError: 'NoneType' object is not subscriptable Traceback (most recent call last): File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/qtconsole/console_widget.py"", line 427, in eventFilter return self._event_filter_console_keypress(event) File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/qtconsole/frontend_widget.py"", line 349, in _event_filter_console_keypress return super(FrontendWidget, self)._event_filter_console_keypress(event) File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/qtconsole/console_widget.py"", line 1405, in _event_filter_console_keypress if self._tab_pressed(): File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/qtconsole/frontend_widget.py"", line 293, in _tab_pressed self._complete() File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/qtconsole/frontend_widget.py"", line 735, in _complete msg_id = self.kernel_client.complete(code=code, cursor_pos=cursor_pos) File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/ipykernel/inprocess/client.py"", line 110, in complete self._dispatch_to_kernel(msg) File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/ipykernel/inprocess/client.py"", line 172, in _dispatch_to_kernel idents, reply_msg = self.session.recv(stream, copy=False) File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/jupyter_client/session.py"", line 803, in recv msg_list = socket.recv_multipart(mode, copy=copy) File ""/opt/UCSF/ChimeraX/lib/python3.7/site- packages/ipykernel/inprocess/socket.py"", line 57, in recv_multipart return self.queue.get_nowait() File ""/opt/UCSF/ChimeraX/lib/python3.7/queue.py"", line 198, in get_nowait return self.get(block=False) File ""/opt/UCSF/ChimeraX/lib/python3.7/queue.py"", line 167, in get raise Empty _queue.Empty _queue.Empty File ""/opt/UCSF/ChimeraX/lib/python3.7/queue.py"", line 167, in get raise Empty See log for complete Python traceback. > select #2/A:691-810@CA 120 atoms, 1 model selected > select #2/A:691-810@CA 120 atoms, 1 model selected > select #1/A:691-810@CA 120 atoms, 1 model selected > select #1 74033 atoms, 75355 bonds, 1 model selected > hide #!2 models > select clear > clipper associate #3 toModel #1 Chain information for 6vsb_1_1_1.pdb --- Chain | Description 1.2/A 1.2/B 1.2/C | No description available > isolde start > set selectionWidth 4 Done loading forcefield > select #1 74033 atoms, 75355 bonds, 12 models selected > select clear > select up 7491 atoms, 7637 bonds, 1 model selected > select up 7505 atoms, 7652 bonds, 1 model selected > select up 8397 atoms, 8547 bonds, 1 model selected > isolde ignore sel ISOLDE: currently ignoring 476 residues in model 1.2 > select clear > save 1_1_1_starting.cxs > select up 92 atoms, 92 bonds, 1 model selected > select up 185 atoms, 191 bonds, 1 model selected > select up 24677 atoms, 25118 bonds, 1 model selected > select down 185 atoms, 191 bonds, 1 model selected > select up 213 atoms, 220 bonds, 1 model selected > select up 239 atoms, 247 bonds, 1 model selected > select up 264 atoms, 273 bonds, 1 model selected > select up 24677 atoms, 25118 bonds, 1 model selected > select down 264 atoms, 273 bonds, 1 model selected > select :ILE@CD 228 atoms, 1 model selected > select clear > view sel > view /A:1098 > view /C:1098 > view /A:1098 > view /B:1098 > select up 13 atoms, 12 bonds, 1 model selected > set bgColor white 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 609, in __init__ raise e File ""/home/tic20/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 591, in __init__ isolde.forcefield_mgr) File ""/home/tic20/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1319, in __init__ template_dict = find_residue_templates(sim_construct.all_residues, ff, ligand_db=ligand_db, logger=session.logger) File ""/home/tic20/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 3044, in find_residue_templates tname, prot_res = find_glycan_template_name_and_link(sugar) File ""/home/tic20/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/openmm/amberff/glycam.py"", line 133, in find_glycan_template_name_and_link return ('GLYCAM_'+_glycam_prefix[bonded_atom_numbers]+core_name, link_res) KeyError: (3, 4, 5) KeyError: (3, 4, 5) File ""/home/tic20/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/openmm/amberff/glycam.py"", line 133, in find_glycan_template_name_and_link return ('GLYCAM_'+_glycam_prefix[bonded_atom_numbers]+core_name, link_res) See log for complete Python traceback. > select ~protein 16079 atoms, 16734 bonds, 19 models selected > select clear > view /A:1 > select /A:1 45 atoms, 44 bonds, 1 model selected > select ~protein 16079 atoms, 16734 bonds, 19 models selected > select clear > select @C5 658 atoms, 2 models selected > select @O5 640 atoms, 2 models selected > select ~protein 16079 atoms, 16734 bonds, 19 models selected > select clear > select up 51 atoms, 52 bonds, 1 model selected > show sel > select clear > select @C5 658 atoms, 2 models selected > hide HC > select :AFU@C6,O6 114 atoms, 36 bonds, 1 model selected > select up 25 atoms, 25 bonds, 1 model selected > select up 24664 atoms, 25106 bonds, 1 model selected > select down 12 atoms, 12 bonds, 1 model selected > show sel > select up 12 atoms, 13 bonds, 1 model selected > show sel > select up 12 atoms, 13 bonds, 1 model selected Expected an objects specifier or a keyword > select sel&@C6,O6 3 atoms, 1 bond, 1 model selected > delete sel > preset custom ""make bond"" executed make_bond.py Preset implemented in Python; no expansion to individual ChimeraX commands available. > select up 10 atoms, 10 bonds, 1 model selected > style sel stick Changed 10 atom styles > select up 23 atoms, 23 bonds, 1 model selected > style sel stick Changed 23 atom styles > delete sel > select :AFU@C6,O6 112 atoms, 35 bonds, 1 model selected > select clear > select clear > select ~protein 16040 atoms, 16660 bonds, 1 pseudobond, 20 models selected Expected an objects specifier or a keyword > select /A&~protein 5326 atoms, 5532 bonds, 1 pseudobond, 3 models selected > select /B&~protein 5357 atoms, 5564 bonds, 2 models selected > select /C&~protein 5357 atoms, 5564 bonds, 2 models selected > select clear > view /B:1098 No objects specified. > select clear > select /C&~protein 5357 atoms, 5564 bonds, 2 models selected > select clear > select /B:3098 Nothing selected > view /A:1098 No objects specified. > view sel > select clear > select :ASN 5303 atoms, 4864 bonds, 2 models selected > view /A:99 > select up 14 atoms, 13 bonds, 1 model selected > view /B:1098 > select clear 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 609, in __init__ raise e File ""/home/tic20/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 591, in __init__ isolde.forcefield_mgr) File ""/home/tic20/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1319, in __init__ template_dict = find_residue_templates(sim_construct.all_residues, ff, ligand_db=ligand_db, logger=session.logger) File ""/home/tic20/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 3044, in find_residue_templates tname, prot_res = find_glycan_template_name_and_link(sugar) File ""/home/tic20/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/openmm/amberff/glycam.py"", line 133, in find_glycan_template_name_and_link return ('GLYCAM_'+_glycam_prefix[bonded_atom_numbers]+core_name, link_res) KeyError: (3, 4, 5) KeyError: (3, 4, 5) File ""/home/tic20/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/openmm/amberff/glycam.py"", line 133, in find_glycan_template_name_and_link return ('GLYCAM_'+_glycam_prefix[bonded_atom_numbers]+core_name, link_res) See log for complete Python traceback. > select ~protein 16040 atoms, 16660 bonds, 1 pseudobond, 20 models selected > select clear > view /A:2022 > select /A:2022@C5,O6 2 atoms, 1 model selected > select /A:2022@C6,O6 2 atoms, 1 bond, 1 model selected > select /A:2027@C6,O6 4 atoms, 2 bonds, 1 model selected > select :AMA 4596 atoms, 4659 bonds, 1 model selected > select :AMA@C6,O6 576 atoms, 288 bonds, 1 model selected > preset custom ""make bond"" executed make_bond.py Preset implemented in Python; no expansion to individual ChimeraX commands available. > select :AMA@C1 195 atoms, 1 model selected > select :BMA@O6 66 atoms, 1 model selected > select :AMA@C1 195 atoms, 1 model selected > select :AMA@C1|:BMA@O6 261 atoms, 70 bonds, 1 model selected > select :AMA@C1 195 atoms, 1 model selected > select :BMA@O6 66 atoms, 1 model selected > select :AMA@C1|:BMA@O6 261 atoms, 66 bonds, 1 model selected > select clear > select :AMA@C1|:BMA@O6 261 atoms, 66 bonds, 1 model selected 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 Core fixed all ChimeraX