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Opened 6 years ago
Closed 6 years ago
#2199 closed defect (duplicate)
map-open func sometimes returns None
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Volume Data | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: Windows-10-10.0.17763 ChimeraX Version: 0.91 (2019-07-07) Description take 2 with info: cannot open .map from chimera tutorial at SLAC, but .cif open fine Log: UCSF ChimeraX version: 0.91 (2019-07-07) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX Downloading bundle ChimeraX_ISOLDE-1.0b3.dev1-cp37-cp37m-win_amd64.whl Successfully installed ChimeraX-Clipper-0.9.6 ChimeraX-ISOLDE-1.0b3.dev1 Installed ChimeraX-Clipper (0.9.6) Installed ChimeraX-ISOLDE (1.0b3.dev1) > open C:/Users/msachs/Dropbox/2019_SLAC_Cryo/chimerax_tutorial/chimerax_tutorial/emd_9333.map Traceback (most recent call last): File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py", line 582, in _qt_safe run(session, "open " + " ".join([quote_if_necessary(p) for p in paths])) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\run.py", line 31, in run results = command.run(text, log=log) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py", line 2646, in run result = ci.function(session, **kw_args) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\open.py", line 73, in open _handle_unexpected_keyword_error(e, 4) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\open.py", line 68, in open path_models = session.models.open(paths, format=format, name=name, **kw) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\models.py", line 613, in open session, filenames, format=format, name=name, **kw) File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\io.py", line 479, in open_multiple_data models, status = open_data(session, fspec, format=format, name=name, **kw) File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\io.py", line 435, in open_data models, status = open_func(*args, **kw) TypeError: cannot unpack non-iterable NoneType object TypeError: cannot unpack non-iterable NoneType object File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\io.py", line 435, in open_data models, status = open_func(*args, **kw) See log for complete Python traceback. > open C:/Users/msachs/Dropbox/2019_SLAC_Cryo/chimerax_tutorial/chimerax_tutorial/6n2d.cif 6n2d.cif title: Bacillus PS3 ATP synthase membrane region [more info...] Chain information for 6n2d.cif #1 --- Chain | Description a | ATP synthase subunit a b1 b2 | ATP synthase subunit b c0 c1 c2 c3 c4 c5 c6 c7 c8 c9 | ATP synthase subunit c > close > open C:/Users/msachs/Dropbox/2019_SLAC_Cryo/chimerax_tutorial/chimerax_tutorial/6n2y.cif 6n2y.cif title: Bacillus PS3 ATP synthase class 1 [more info...] Chain information for 6n2y.cif #1 --- Chain | Description A B C | ATP synthase subunit α D E F | ATP synthase subunit β G | ATP synthase γ chain H | ATP synthase ε chain I | ATP synthase subunit δ a | ATP synthase subunit a b1 | ATP synthase subunit b b2 | ATP synthase subunit b c0 c1 c2 c3 c4 c5 c6 c7 c8 c9 | ATP synthase subunit c Non-standard residues in 6n2y.cif #1 --- ADP — adenosine-5'-diphosphate ATP — adenosine-5'-triphosphate MG — magnesium ion PO4 — phosphate ion > open C:/Users/msachs/Dropbox/2019_SLAC_Cryo/chimerax_tutorial/chimerax_tutorial/emd_9333.map Traceback (most recent call last): File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py", line 582, in _qt_safe run(session, "open " + " ".join([quote_if_necessary(p) for p in paths])) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\run.py", line 31, in run results = command.run(text, log=log) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py", line 2646, in run result = ci.function(session, **kw_args) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\open.py", line 73, in open _handle_unexpected_keyword_error(e, 4) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\open.py", line 68, in open path_models = session.models.open(paths, format=format, name=name, **kw) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\models.py", line 613, in open session, filenames, format=format, name=name, **kw) File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\io.py", line 479, in open_multiple_data models, status = open_data(session, fspec, format=format, name=name, **kw) File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\io.py", line 435, in open_data models, status = open_func(*args, **kw) TypeError: cannot unpack non-iterable NoneType object TypeError: cannot unpack non-iterable NoneType object File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\io.py", line 435, in open_data models, status = open_func(*args, **kw) See log for complete Python traceback. > open C:/Users/msachs/Dropbox/2019_SLAC_Cryo/chimerax_tutorial/chimerax_tutorial/emd_9334.map Traceback (most recent call last): File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py", line 582, in _qt_safe run(session, "open " + " ".join([quote_if_necessary(p) for p in paths])) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\run.py", line 31, in run results = command.run(text, log=log) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py", line 2646, in run result = ci.function(session, **kw_args) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\open.py", line 73, in open _handle_unexpected_keyword_error(e, 4) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\open.py", line 68, in open path_models = session.models.open(paths, format=format, name=name, **kw) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\models.py", line 613, in open session, filenames, format=format, name=name, **kw) File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\io.py", line 479, in open_multiple_data models, status = open_data(session, fspec, format=format, name=name, **kw) File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\io.py", line 435, in open_data models, status = open_func(*args, **kw) TypeError: cannot unpack non-iterable NoneType object TypeError: cannot unpack non-iterable NoneType object File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\io.py", line 435, in open_data models, status = open_func(*args, **kw) See log for complete Python traceback. > open C:/Users/msachs/Dropbox/2019_SLAC_Cryo/chimerax_tutorial/chimerax_tutorial/emd_9333.map Traceback (most recent call last): File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py", line 582, in _qt_safe run(session, "open " + " ".join([quote_if_necessary(p) for p in paths])) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\run.py", line 31, in run results = command.run(text, log=log) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py", line 2646, in run result = ci.function(session, **kw_args) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\open.py", line 73, in open _handle_unexpected_keyword_error(e, 4) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\open.py", line 68, in open path_models = session.models.open(paths, format=format, name=name, **kw) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\models.py", line 613, in open session, filenames, format=format, name=name, **kw) File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\io.py", line 479, in open_multiple_data models, status = open_data(session, fspec, format=format, name=name, **kw) File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\io.py", line 435, in open_data models, status = open_func(*args, **kw) TypeError: cannot unpack non-iterable NoneType object TypeError: cannot unpack non-iterable NoneType object File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\io.py", line 435, in open_data models, status = open_func(*args, **kw) See log for complete Python traceback. > open C:/Users/msachs/Dropbox/2019_SLAC_Cryo/chimerax_tutorial/chimerax_tutorial/emd_9333.map Traceback (most recent call last): File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py", line 582, in _qt_safe run(session, "open " + " ".join([quote_if_necessary(p) for p in paths])) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\run.py", line 31, in run results = command.run(text, log=log) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py", line 2646, in run result = ci.function(session, **kw_args) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\open.py", line 73, in open _handle_unexpected_keyword_error(e, 4) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\open.py", line 68, in open path_models = session.models.open(paths, format=format, name=name, **kw) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\models.py", line 613, in open session, filenames, format=format, name=name, **kw) File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\io.py", line 479, in open_multiple_data models, status = open_data(session, fspec, format=format, name=name, **kw) File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\io.py", line 435, in open_data models, status = open_func(*args, **kw) TypeError: cannot unpack non-iterable NoneType object TypeError: cannot unpack non-iterable NoneType object File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\io.py", line 435, in open_data models, status = open_func(*args, **kw) See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 398.36 OpenGL renderer: GeForce 940MX/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation
Change History (3)
follow-up: 1 comment:1 by , 6 years ago
comment:2 by , 6 years ago
| Component: | Unassigned → Volume Data |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → map-open func sometimes returns None |
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Greetings, For whatever reason, *.map files are loading with no problems in chimerax - as they always did with chimera - today - Thank you, Matt -----Original Message----- From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> Sent: Wednesday, July 10, 2019 1:01 PM To: Sachs, Matthew S <msachs@bio.tamu.edu> Subject: [ChimeraX] #2199: ChimeraX bug report submission #2199: ChimeraX bug report submission ------------------------+----------------------------- Reporter: msachs@… | Type: defect Status: new | Priority: normal Component: Unassigned | Blocked By: Blocking: | Notify when closed: ------------------------+----------------------------- {{{ The following bug report has been submitted: Platform: Windows-10-10.0.17763 ChimeraX Version: 0.91 (2019-07-07) Description take 2 with info: cannot open .map from chimera tutorial at SLAC, but .cif open fine Log: UCSF ChimeraX version: 0.91 (2019-07-07) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX Downloading bundle ChimeraX_ISOLDE-1.0b3.dev1-cp37-cp37m-win_amd64.whl Successfully installed ChimeraX-Clipper-0.9.6 ChimeraX-ISOLDE-1.0b3.dev1 Installed ChimeraX-Clipper (0.9.6) Installed ChimeraX-ISOLDE (1.0b3.dev1) > open C:/Users/msachs/Dropbox/2019_SLAC_Cryo/chimerax_tutorial/chimerax_tutorial/emd_9333.map Traceback (most recent call last): File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py", line 582, in _qt_safe run(session, "open " + " ".join([quote_if_necessary(p) for p in paths])) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\run.py", line 31, in run results = command.run(text, log=log) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py", line 2646, in run result = ci.function(session, **kw_args) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\open.py", line 73, in open _handle_unexpected_keyword_error(e, 4) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\open.py", line 68, in open path_models = session.models.open(paths, format=format, name=name, **kw) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\models.py", line 613, in open session, filenames, format=format, name=name, **kw) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\io.py", line 479, in open_multiple_data models, status = open_data(session, fspec, format=format, name=name, **kw) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\io.py", line 435, in open_data models, status = open_func(*args, **kw) TypeError: cannot unpack non-iterable NoneType object TypeError: cannot unpack non-iterable NoneType object File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\io.py", line 435, in open_data models, status = open_func(*args, **kw) See log for complete Python traceback. > open C:/Users/msachs/Dropbox/2019_SLAC_Cryo/chimerax_tutorial/chimerax_tutorial/6n2d.cif 6n2d.cif title: Bacillus PS3 ATP synthase membrane region [more info...] Chain information for 6n2d.cif #1 --- Chain | Description a | ATP synthase subunit a b1 b2 | ATP synthase subunit b c0 c1 c2 c3 c4 c5 c6 c7 c8 c9 | ATP synthase subunit c > close > open C:/Users/msachs/Dropbox/2019_SLAC_Cryo/chimerax_tutorial/chimerax_tutorial/6n2y.cif 6n2y.cif title: Bacillus PS3 ATP synthase class 1 [more info...] Chain information for 6n2y.cif #1 --- Chain | Description A B C | ATP synthase subunit α D E F | ATP synthase subunit β G | ATP synthase γ chain H | ATP synthase ε chain I | ATP synthase subunit δ a | ATP synthase subunit a b1 | ATP synthase subunit b b2 | ATP synthase subunit b c0 c1 c2 c3 c4 c5 c6 c7 c8 c9 | ATP synthase subunit c Non-standard residues in 6n2y.cif #1 --- ADP — adenosine-5'-diphosphate ATP — adenosine-5'-triphosphate MG — magnesium ion PO4 — phosphate ion > open C:/Users/msachs/Dropbox/2019_SLAC_Cryo/chimerax_tutorial/chimerax_tutorial/emd_9333.map Traceback (most recent call last): File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py", line 582, in _qt_safe run(session, "open " + " ".join([quote_if_necessary(p) for p in paths])) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\run.py", line 31, in run results = command.run(text, log=log) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py", line 2646, in run result = ci.function(session, **kw_args) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\open.py", line 73, in open _handle_unexpected_keyword_error(e, 4) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\open.py", line 68, in open path_models = session.models.open(paths, format=format, name=name, **kw) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\models.py", line 613, in open session, filenames, format=format, name=name, **kw) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\io.py", line 479, in open_multiple_data models, status = open_data(session, fspec, format=format, name=name, **kw) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\io.py", line 435, in open_data models, status = open_func(*args, **kw) TypeError: cannot unpack non-iterable NoneType object TypeError: cannot unpack non-iterable NoneType object File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\io.py", line 435, in open_data models, status = open_func(*args, **kw) See log for complete Python traceback. > open C:/Users/msachs/Dropbox/2019_SLAC_Cryo/chimerax_tutorial/chimerax_tutorial/emd_9334.map Traceback (most recent call last): File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py", line 582, in _qt_safe run(session, "open " + " ".join([quote_if_necessary(p) for p in paths])) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\run.py", line 31, in run results = command.run(text, log=log) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py", line 2646, in run result = ci.function(session, **kw_args) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\open.py", line 73, in open _handle_unexpected_keyword_error(e, 4) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\open.py", line 68, in open path_models = session.models.open(paths, format=format, name=name, **kw) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\models.py", line 613, in open session, filenames, format=format, name=name, **kw) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\io.py", line 479, in open_multiple_data models, status = open_data(session, fspec, format=format, name=name, **kw) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\io.py", line 435, in open_data models, status = open_func(*args, **kw) TypeError: cannot unpack non-iterable NoneType object TypeError: cannot unpack non-iterable NoneType object File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\io.py", line 435, in open_data models, status = open_func(*args, **kw) See log for complete Python traceback. > open C:/Users/msachs/Dropbox/2019_SLAC_Cryo/chimerax_tutorial/chimerax_tutorial/emd_9333.map Traceback (most recent call last): File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py", line 582, in _qt_safe run(session, "open " + " ".join([quote_if_necessary(p) for p in paths])) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\run.py", line 31, in run results = command.run(text, log=log) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py", line 2646, in run result = ci.function(session, **kw_args) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\open.py", line 73, in open _handle_unexpected_keyword_error(e, 4) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\open.py", line 68, in open path_models = session.models.open(paths, format=format, name=name, **kw) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\models.py", line 613, in open session, filenames, format=format, name=name, **kw) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\io.py", line 479, in open_multiple_data models, status = open_data(session, fspec, format=format, name=name, **kw) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\io.py", line 435, in open_data models, status = open_func(*args, **kw) TypeError: cannot unpack non-iterable NoneType object TypeError: cannot unpack non-iterable NoneType object File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\io.py", line 435, in open_data models, status = open_func(*args, **kw) See log for complete Python traceback. > open C:/Users/msachs/Dropbox/2019_SLAC_Cryo/chimerax_tutorial/chimerax_tutorial/emd_9333.map Traceback (most recent call last): File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py", line 582, in _qt_safe run(session, "open " + " ".join([quote_if_necessary(p) for p in paths])) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\run.py", line 31, in run results = command.run(text, log=log) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py", line 2646, in run result = ci.function(session, **kw_args) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\open.py", line 73, in open _handle_unexpected_keyword_error(e, 4) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\commands\open.py", line 68, in open path_models = session.models.open(paths, format=format, name=name, **kw) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\models.py", line 613, in open session, filenames, format=format, name=name, **kw) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\io.py", line 479, in open_multiple_data models, status = open_data(session, fspec, format=format, name=name, **kw) File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\io.py", line 435, in open_data models, status = open_func(*args, **kw) TypeError: cannot unpack non-iterable NoneType object TypeError: cannot unpack non-iterable NoneType object File "C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\io.py", line 435, in open_data models, status = open_func(*args, **kw) See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 398.36 OpenGL renderer: GeForce 940MX/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation }}} -- Ticket URL: <https://urldefense.proofpoint.com/v2/url?u=https-3A__plato.cgl.ucsf.edu_trac_ChimeraX_ticket_2199&d=DwIGaQ&c=u6LDEWzohnDQ01ySGnxMzg&r=4qBP-PkJAFU7LaiIYIv3mPYaE4MoDiWqg8WgKvq_Cs4&m=NtEPvTs1NETiOTgIucMiViVGlSgB8id5N8T8bqJBEf4&s=Le1DZ1pOM31QRyVldKLgD7Vh9MXIQfWF9otAz6yk750&e= > ChimeraX <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chimerax_&d=DwIGaQ&c=u6LDEWzohnDQ01ySGnxMzg&r=4qBP-PkJAFU7LaiIYIv3mPYaE4MoDiWqg8WgKvq_Cs4&m=NtEPvTs1NETiOTgIucMiViVGlSgB8id5N8T8bqJBEf4&s=vQ74alEHPXDTUhHqHlMogTxIqlNurDZRFb8g3JFjbQg&e= > ChimeraX Issue Tracker