![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Trac Ticket Queries
Table of Contents
In addition to reports, Trac provides support for custom ticket queries, which can be used to display tickets that meet specified criteria.
To configure and execute a custom query, switch to the View Tickets module from the navigation bar, and select the Custom Query link.
Filters
When you first go to the query page, the default filter will display tickets relevant to you:
- If logged in then all open tickets, it will display open tickets assigned to you.
- If not logged in but you have specified a name or email address in the preferences, then it will display all open tickets where your email (or name if email not defined) is in the CC list.
- If not logged in and no name/email is defined in the preferences, then all open issues are displayed.
Current filters can be removed by clicking the button to the left with the minus sign on the label. New filters are added from the pulldown lists at the bottom corners of the filters box; 'And' conditions on the left, 'Or' conditions on the right. Filters with either a text box or a pulldown menu of options can be added multiple times to perform an Or on the criteria.
You can use the fields just below the filters box to group the results based on a field, or display the full description for each ticket.
After you have edited your filters, click the Update button to refresh your results.
Some shortcuts can be used to manipulate checkbox filters.
- Clicking on a filter row label toggles all checkboxes.
- Pressing the modifier key while clicking on a filter row label inverts the state of all checkboxes.
- Pressing the modifier key while clicking on a checkbox selects the checkbox and deselects all other checkboxes in the filter.
The modifier key is platform and browser dependent. On Mac the modified key is Option/Alt or Command. On Linux the modifier key is Ctrl + Alt. Opera on Windows seems to use Ctrl + Alt, while Alt is effective for other Windows browsers.
Navigating Tickets
Clicking on one of the query results will take you to that ticket. You can navigate through the results by clicking the Next Ticket or Previous Ticket links just below the main menu bar, or click the Back to Query link to return to the query page.
You can safely edit any of the tickets and continue to navigate through the results using the Next/Previous/Back to Query links after saving your results. When you return to the query any tickets which were edited will be displayed with italicized text. If one of the tickets was edited such that it no longer matches the query criteria , the text will also be greyed. Lastly, if a new ticket matching the query criteria has been created, it will be shown in bold.
The query results can be refreshed and cleared of these status indicators by clicking the Update button again.
Saving Queries
Trac allows you to save the query as a named query accessible from the reports module. To save a query ensure that you have Updated the view and then click the Save query button displayed beneath the results. You can also save references to queries in Wiki content, as described below.
Note: one way to easily build queries like the ones below, you can build and test the queries in the Custom report module and when ready - click Save query. This will build the query string for you. All you need to do is remove the extra line breaks.
Note: you must have the REPORT_CREATE permission in order to save queries to the list of default reports. The Save query button will only appear if you are logged in as a user that has been granted this permission. If your account does not have permission to create reports, you can still use the methods below to save a query.
Using TracLinks
You may want to save some queries so that you can come back to them later. You can do this by making a link to the query from any Wiki page.
[query:status=new|assigned|reopened&version=1.0 Active tickets against 1.0]
Which is displayed as:
This uses a very simple query language to specify the criteria, see Query Language.
Alternatively, you can copy the query string of a query and paste that into the Wiki link, including the leading ? character:
[query:?status=new&status=assigned&status=reopened&group=owner Assigned tickets by owner]
Which is displayed as:
Customizing the table format
You can also customize the columns displayed in the table format (format=table) by using col=<field>. You can specify multiple fields and what order they are displayed in by placing pipes (|) between the columns:
[[TicketQuery(max=3,status=closed,order=id,desc=1,format=table,col=resolution|summary|owner|reporter)]]
This is displayed as:
Results (1 - 3 of 14162)
Full rows
In table format you can also have full rows by using rows=<field>:
[[TicketQuery(max=3,status=closed,order=id,desc=1,format=table,col=resolution|summary|owner|reporter,rows=description)]]
This is displayed as:
Results (1 - 3 of 14162)
| Ticket | Resolution | Summary | Owner | Reporter |
|---|---|---|---|---|
| #20831 | duplicate | Boltz: Failed to import Triton-based component: triangle_multiplicative_update | ||
| Description |
The following bug report has been submitted:
Platform: Linux-6.17.0-1030-oem-x86_64-with-glibc2.39
ChimeraX Version: 1.12rc202605142114 (2026-05-14 21:14:16 UTC)
Description
I'm trying to run Boltz2 in Chimera and the installation went fine. However, I'm getting the error in the attached file. I have triton 3.3.0 installed as shown below.
(base) swlovell@crystal15:~$ python -c "import triton; print(triton.__version__)"
3.3.0
Log:
Startup Messages
---
warning | GBM is not supported with the current configuration. Fallback to Vulkan rendering in Chromium.
UCSF ChimeraX version: 1.12rc202605142114 (2026-05-14)
© 2016-2026 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
dbus reply error: [ "org.freedesktop.DBus.Error.UnknownMethod" ] "No such
interface “org.freedesktop.portal.Settings” on object at path
/org/freedesktop/portal/desktop"
[Repeated 1 time(s)]
> open
> /home/swlovell/structures/Gonzalez_Lina/TANGO2/PDBs/TANGO2_Protein_no_OCS.pdb
> format pdb
Chain information for TANGO2_Protein_no_OCS.pdb #1
---
Chain | Description
A | No description available
Computing secondary structure
> ui tool show Boltz
> boltz predict protein
> CIIFFKFDPRPVSKNAYRLILAANRDEFYSRPSKLADFWGNNNEILSGLDMEEGKEGGTWLGISTRGKLAALTNYLQPQLDWQARGRGELVTHFLTTDVDSLSYLKKVSMEGHLYNGFNLIAADLSTAKGDVICYYGNRGEPDPIVLTPGTYGLSNALLETPWRKLCFGKQLFLEAVERSQALPKDVLIASLLDVLNNEEAQLPDPAIEDQGGEYVQPMLSKYAAVCVRCPGYGTRTNTIILVDADGHVTFTERSMMDKDLSHWETRTYEFTLQS
> ligandSmiles
> C[C@H](CCC(O)=O)[C@H]1CC[C@H]2[C@@H]3CC[C@@H]4C[C@H](O)CC[C@]4(C)[C@H]3CC[C@]12C
> resultsDirectory
> /home/swlovell/structures/Gonzalez_Lina/TANGO2/Docking/boltz2/Lithocholic_acid/
> affinity
> C[C@H](CCC(O)=O)[C@H]1CC[C@H]2[C@@H]3CC[C@@H]4C[C@H](O)CC[C@]4(C)[C@H]3CC[C@]12C
> steering true
Boltz prediction directory
/home/swlovell/structures/Gonzalez_Lina/TANGO2/Docking/boltz2/Lithocholic_acid/
already exists. Files will be overwritten.
Running Boltz prediction of protein with 275 residues, 1 ligands
C[C@H](CCC(O)=O)[C@H]1CC[C@H]2[C@@H]3CC[C@@H]4C[C@H](O)CC[C@]4(C)[C@H]3CC[C@]12C
on gpu
Using cached multiple sequence alignment
/home/swlovell/Downloads/ChimeraX/BoltzMSA/TANGO2_lithocholic
Running boltz prediction failed with exit code 0:
command:
/home/swlovell/boltz22/bin/boltz predict
/home/swlovell/structures/Gonzalez_Lina/TANGO2/Docking/boltz2/Lithocholic_acid/.yaml
--use_potentials --accelerator gpu
stdout:
Boltz version 2.2.0
Checking input data.
Processing 1 inputs with 1 threads.
Failed to process
/home/swlovell/structures/Gonzalez_Lina/TANGO2/Docking/boltz2/Lithocholic_acid/.yaml.
Skipping. Error: Unable to parse filetype , please provide a .fasta or .yaml
file..
stderr:
0%| | 0/1 [00:00<?, ?it/s]Traceback (most recent call last):
File "/home/swlovell/boltz22/lib/python3.11/site-packages/boltz/main.py", line
553, in process_input
raise RuntimeError(msg) # noqa: TRY301
^^^^^^^^^^^^^^^^^^^^^^^
RuntimeError: Unable to parse filetype , please provide a .fasta or .yaml
file.
100%|██████████| 1/1 [00:00<00:00, 6765.01it/s]
Using bfloat16 Automatic Mixed Precision (AMP)
GPU available: True (cuda), used: True
TPU available: False, using: 0 TPU cores
HPU available: False, using: 0 HPUs
/home/swlovell/boltz22/lib/python3.11/site-
packages/pytorch_lightning/trainer/connectors/logger_connector/logger_connector.py:76:
Starting from v1.9.0, `tensorboardX` has been removed as a dependency of the
`pytorch_lightning` package, due to potential conflicts with other packages in
the ML ecosystem. For this reason, `logger=True` will use `CSVLogger` as the
default logger, unless the `tensorboard` or `tensorboardX` packages are found.
Please `pip install lightning[extra]` or one of them to enable TensorBoard
support by default
> boltz predict protein
> CIIFFKFDPRPVSKNAYRLILAANRDEFYSRPSKLADFWGNNNEILSGLDMEEGKEGGTWLGISTRGKLAALTNYLQPQLDWQARGRGELVTHFLTTDVDSLSYLKKVSMEGHLYNGFNLIAADLSTAKGDVICYYGNRGEPDPIVLTPGTYGLSNALLETPWRKLCFGKQLFLEAVERSQALPKDVLIASLLDVLNNEEAQLPDPAIEDQGGEYVQPMLSKYAAVCVRCPGYGTRTNTIILVDADGHVTFTERSMMDKDLSHWETRTYEFTLQS
> ligandSmiles
> C[C@H](CCC(O)=O)[C@H]1CC[C@H]2[C@@H]3CC[C@@H]4C[C@H](O)CC[C@]4(C)[C@H]3CC[C@]12C
> name TANGO2_lithocholic_acid resultsDirectory
> /home/swlovell/structures/Gonzalez_Lina/TANGO2/Docking/boltz2/Lithocholic_acid/
> affinity
> C[C@H](CCC(O)=O)[C@H]1CC[C@H]2[C@@H]3CC[C@@H]4C[C@H](O)CC[C@]4(C)[C@H]3CC[C@]12C
> steering true
Boltz prediction directory
/home/swlovell/structures/Gonzalez_Lina/TANGO2/Docking/boltz2/Lithocholic_acid/
already exists. Files will be overwritten.
Running Boltz prediction of protein with 275 residues, 1 ligands
C[C@H](CCC(O)=O)[C@H]1CC[C@H]2[C@@H]3CC[C@@H]4C[C@H](O)CC[C@]4(C)[C@H]3CC[C@]12C
on gpu
Using cached multiple sequence alignment
/home/swlovell/Downloads/ChimeraX/BoltzMSA/TANGO2_lithocholic
Running boltz prediction failed with exit code 1:
command:
/home/swlovell/boltz22/bin/boltz predict
/home/swlovell/structures/Gonzalez_Lina/TANGO2/Docking/boltz2/Lithocholic_acid/TANGO2_lithocholic_acid.yaml
--use_potentials --accelerator gpu
stdout:
Boltz version 2.2.0
Checking input data.
All inputs are already processed.
Processing 0 inputs with 0 threads.
Running structure prediction for 1 input.
Predicting: | | 0/? [00:00<?, ?it/s] Predicting: 0%| | 0/1 [00:00<?, ?it/s] Predicting DataLoader 0: 0%| | 0/1 [00:00<?, ?it/s] Predicting DataLoader 0: 0%| | 0/1 [00:01<?, ?it/s]
stderr:
0it [00:00, ?it/s] 0it [00:00, ?it/s]
Using bfloat16 Automatic Mixed Precision (AMP)
GPU available: True (cuda), used: True
TPU available: False, using: 0 TPU cores
HPU available: False, using: 0 HPUs
/home/swlovell/boltz22/lib/python3.11/site-
packages/pytorch_lightning/trainer/connectors/logger_connector/logger_connector.py:76:
Starting from v1.9.0, `tensorboardX` has been removed as a dependency of the
`pytorch_lightning` package, due to potential conflicts with other packages in
the ML ecosystem. For this reason, `logger=True` will use `CSVLogger` as the
default logger, unless the `tensorboard` or `tensorboardX` packages are found.
Please `pip install lightning[extra]` or one of them to enable TensorBoard
support by default
Fri Aug 7 05:37:27 2026: Loading Boltz structure prediction weights
/home/swlovell/boltz22/lib/python3.11/site-
packages/pytorch_lightning/utilities/migration/utils.py:56: The loaded
checkpoint was produced with Lightning v2.5.0.post0, which is newer than your
current Lightning version: v2.5.0
Fri Aug 7 05:37:38 2026: Finished loading Boltz structure prediction weights
Fri Aug 7 05:37:38 2026: Starting structure inference
You are using a CUDA device ('NVIDIA RTX PRO 4500 Blackwell') that has Tensor Cores. To properly utilize them, you should set `torch.set_float32_matmul_precision('medium' | 'high')` which will trade-off precision for performance. For more details, read https://pytorch.org/docs/stable/generated/torch.set_float32_matmul_precision.html#torch.set_float32_matmul_precision
LOCAL_RANK: 0 - CUDA_VISIBLE_DEVICES: [0]
Fri Aug 7 05:37:39 2026: Begin structure inference TANGO2_lithocholic_acid (1
of 1)
Traceback (most recent call last):
File "/home/swlovell/boltz22/bin/boltz", line 8, in <module>
sys.exit(cli())
^^^^^
File "/home/swlovell/boltz22/lib/python3.11/site-packages/click/core.py", line
1157, in __call__
return self.main(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/swlovell/boltz22/lib/python3.11/site-packages/click/core.py", line
1078, in main
rv = self.invoke(ctx)
^^^^^^^^^^^^^^^^
File "/home/swlovell/boltz22/lib/python3.11/site-packages/click/core.py", line
1688, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/swlovell/boltz22/lib/python3.11/site-packages/click/core.py", line
1434, in invoke
return ctx.invoke(self.callback, **ctx.params)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/swlovell/boltz22/lib/python3.11/site-packages/click/core.py", line
783, in invoke
return __callback(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/swlovell/boltz22/lib/python3.11/site-packages/boltz/main.py", line
1355, in predict
trainer.predict(
File "/home/swlovell/boltz22/lib/python3.11/site-
packages/pytorch_lightning/trainer/trainer.py", line 859, in predict
return call._call_and_handle_interrupt(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/swlovell/boltz22/lib/python3.11/site-
packages/pytorch_lightning/trainer/call.py", line 47, in
_call_and_handle_interrupt
return trainer_fn(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/swlovell/boltz22/lib/python3.11/site-
packages/pytorch_lightning/trainer/trainer.py", line 898, in _predict_impl
results = self._run(model, ckpt_path=ckpt_path)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/swlovell/boltz22/lib/python3.11/site-
packages/pytorch_lightning/trainer/trainer.py", line 982, in _run
results = self._run_stage()
^^^^^^^^^^^^^^^^^
File "/home/swlovell/boltz22/lib/python3.11/site-
packages/pytorch_lightning/trainer/trainer.py", line 1021, in _run_stage
return self.predict_loop.run()
^^^^^^^^^^^^^^^^^^^^^^^
File "/home/swlovell/boltz22/lib/python3.11/site-
packages/pytorch_lightning/loops/utilities.py", line 179, in _decorator
return loop_run(self, *args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/swlovell/boltz22/lib/python3.11/site-
packages/pytorch_lightning/loops/prediction_loop.py", line 125, in run
self._predict_step(batch, batch_idx, dataloader_idx, dataloader_iter)
File "/home/swlovell/boltz22/lib/python3.11/site-
packages/pytorch_lightning/loops/prediction_loop.py", line 255, in
_predict_step
predictions = call._call_strategy_hook(trainer, "predict_step", *step_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/swlovell/boltz22/lib/python3.11/site-
packages/pytorch_lightning/trainer/call.py", line 323, in _call_strategy_hook
output = fn(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^
File "/home/swlovell/boltz22/lib/python3.11/site-
packages/pytorch_lightning/strategies/strategy.py", line 438, in predict_step
return self.lightning_module.predict_step(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/swlovell/boltz22/lib/python3.11/site-
packages/boltz/model/models/boltz2.py", line 1059, in predict_step
out = self(
^^^^^
File "/home/swlovell/boltz22/lib/python3.11/site-
packages/torch/nn/modules/module.py", line 1751, in _wrapped_call_impl
return self._call_impl(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/swlovell/boltz22/lib/python3.11/site-
packages/torch/nn/modules/module.py", line 1762, in _call_impl
return forward_call(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/swlovell/boltz22/lib/python3.11/site-
packages/boltz/model/models/boltz2.py", line 464, in forward
z = z + template_module(
^^^^^^^^^^^^^^^^
File "/home/swlovell/boltz22/lib/python3.11/site-
packages/torch/nn/modules/module.py", line 1751, in _wrapped_call_impl
return self._call_impl(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/swlovell/boltz22/lib/python3.11/site-
packages/torch/nn/modules/module.py", line 1762, in _call_impl
return forward_call(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/swlovell/boltz22/lib/python3.11/site-
packages/boltz/model/modules/trunkv2.py", line 498, in forward
v = v + self.pairformer(v, pair_mask, use_kernels=use_kernels)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/swlovell/boltz22/lib/python3.11/site-
packages/torch/nn/modules/module.py", line 1751, in _wrapped_call_impl
return self._call_impl(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/swlovell/boltz22/lib/python3.11/site-
packages/torch/nn/modules/module.py", line 1762, in _call_impl
return forward_call(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/swlovell/boltz22/lib/python3.11/site-
packages/boltz/model/layers/pairformer.py", line 329, in forward
z = layer(
^^^^^^
File "/home/swlovell/boltz22/lib/python3.11/site-
packages/torch/nn/modules/module.py", line 1751, in _wrapped_call_impl
return self._call_impl(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/swlovell/boltz22/lib/python3.11/site-
packages/torch/nn/modules/module.py", line 1762, in _call_impl
return forward_call(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/swlovell/boltz22/lib/python3.11/site-
packages/boltz/model/layers/pairformer.py", line 243, in forward
z = z + dropout * self.tri_mul_out(
^^^^^^^^^^^^^^^^^
File "/home/swlovell/boltz22/lib/python3.11/site-
packages/torch/nn/modules/module.py", line 1751, in _wrapped_call_impl
return self._call_impl(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/swlovell/boltz22/lib/python3.11/site-
packages/torch/nn/modules/module.py", line 1762, in _call_impl
return forward_call(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/swlovell/boltz22/lib/python3.11/site-
packages/boltz/model/layers/triangular_mult.py", line 92, in forward
return kernel_triangular_mult(
^^^^^^^^^^^^^^^^^^^^^^^
File "/home/swlovell/boltz22/lib/python3.11/site-
packages/torch/_dynamo/eval_frame.py", line 838, in _fn
return fn(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^
File "/home/swlovell/boltz22/lib/python3.11/site-
packages/boltz/model/layers/triangular_mult.py", line 23, in
kernel_triangular_mult
return triangle_multiplicative_update(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/swlovell/boltz22/lib/python3.11/site-
packages/cuequivariance_torch/primitives/triangle.py", line 314, in
triangle_multiplicative_update
return f(
^^
File "/home/swlovell/boltz22/lib/python3.11/site-
packages/cuequivariance_ops_torch/__init__.py", line 97, in
triangle_multiplicative_update
_raise_triton_import_error("triangle_multiplicative_update")
File "/home/swlovell/boltz22/lib/python3.11/site-
packages/cuequivariance_ops_torch/__init__.py", line 91, in
_raise_triton_import_error
raise Exception(
Exception: Failed to import Triton-based component:
triangle_multiplicative_update:
Traceback (most recent call last):
File "/home/swlovell/boltz22/lib/python3.11/site-
packages/cuequivariance_ops_torch/attention_pair_bias.py", line 27, in
<module>
from torch.fx._symbolic_trace import is_fx_symbolic_tracing
ImportError: cannot import name 'is_fx_symbolic_tracing' from
'torch.fx._symbolic_trace' (/home/swlovell/boltz22/lib/python3.11/site-
packages/torch/fx/_symbolic_trace.py)
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/swlovell/boltz22/lib/python3.11/site-
packages/cuequivariance_ops_torch/__init__.py", line 64, in <module>
from cuequivariance_ops_torch.attention_pair_bias import (
File "/home/swlovell/boltz22/lib/python3.11/site-
packages/cuequivariance_ops_torch/attention_pair_bias.py", line 29, in
<module>
from torch.fx._symbolic_trace import (
ImportError: cannot import name 'is_fx_tracing_symbolic_tracing' from
'torch.fx._symbolic_trace' (/home/swlovell/boltz22/lib/python3.11/site-
packages/torch/fx/_symbolic_trace.py)
Please make sure to install triton==3.3.0. Other versions may not work!
sys:1: DeprecationWarning: builtin type swigvarlink has no __module__
attribute
OpenGL version: 3.3.0 NVIDIA 580.173.02
OpenGL renderer: NVIDIA RTX PRO 4500 Blackwell/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.11.13
Locale: en_US.UTF-8
Qt version: PyQt6 6.10.2, Qt 6.10.0
Qt runtime version: 6.10.1
Qt platform: xcb
XDG_SESSION_TYPE=x11
DESKTOP_SESSION=xfce
XDG_SESSION_DESKTOP=xfce
XDG_CURRENT_DESKTOP=XFCE
DISPLAY=:0.0
Manufacturer: Dell Inc.
Model: Dell Pro Max Tower T2 FCT2250
OS: Ubuntu 24.04
Architecture: 64bit ELF
Virtual Machine: none
CPU: 24 Intel(R) Core(TM) Ultra 9 285K
Cache Size: 36864 KB
Memory:
total used free shared buff/cache available
Mem: 125Gi 7.2Gi 98Gi 373Mi 21Gi 118Gi
Swap: 8.0Gi 0B 8.0Gi
Graphics:
00:02.0 VGA compatible controller [0300]: Intel Corporation Arrow Lake-U [Intel Graphics] [8086:7d67] (rev 06)
Subsystem: Dell Device [1028:0ce1]
Kernel driver in use: i915
Installed Packages:
accessible-pygments: 0.0.5
aiohappyeyeballs: 2.6.1
aiohttp: 3.13.1
aiosignal: 1.4.0
alabaster: 1.0.0
annotated-types: 0.7.0
anyio: 4.13.0
appdirs: 1.4.4
asttokens: 3.0.1
attrs: 26.1.0
babel: 2.18.0
beautifulsoup4: 4.13.5
biopython: 1.83
blockdiag: 3.0.0
blosc2: 4.2.0
bs4: 0.0.2
build: 1.3.0
certifi: 2026.4.22
cftime: 1.6.5
charset-normalizer: 3.4.7
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.2.8
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.2
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Animations: 1.0
ChimeraX-Aniso: 1.3.2
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.67.1
ChimeraX-AtomicLibrary: 14.4
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.1
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.6.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4.1
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.4
ChimeraX-Cluster: 1.0
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3.1
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.12rc202605142114
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.2.1
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5.3
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.4
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.8.2
ChimeraX-Label: 1.5
ChimeraX-LightingGUI: 1.0
ChimeraX-LinuxSupport: 1.0.1
ChimeraX-ListInfo: 1.3.1
ChimeraX-Log: 1.2.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.3
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchAlign: 1.1
ChimeraX-MatchMaker: 2.4
ChimeraX-MCopy: 1.0
ChimeraX-MCPServer: 0.2.0
ChimeraX-MDcrds: 2.19
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.3.8
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.23
ChimeraX-ModelPanel: 1.6.1
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0.1
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.15.4
ChimeraX-OpenFold: 1.0
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.13
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.5
ChimeraX-PDBMatrices: 1.0
ChimeraX-PhenixUI: 1.6.4
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.4
ChimeraX-ProfileGrids: 1.6
ChimeraX-PubChem: 2.2
ChimeraX-QScore: 1.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.8.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.3
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.2
ChimeraX-Scenes: 0.3.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.12
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.18
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SNFG: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5.3
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.4
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.50.6
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.6.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.5
ChimeraX-Zone: 1.0.1
click: 8.4.0
colorama: 0.4.6
comm: 0.2.3
contourpy: 1.3.3
coverage: 7.14.0
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.2.4
debugpy: 1.8.20
decorator: 5.3.1
DiffFit: 0.7.0
distro: 1.9.0
docutils: 0.21.2
executing: 2.2.1
filelock: 3.19.1
fonttools: 4.63.0
frozenlist: 1.8.0
fsspec: 2026.4.0
funcparserlib: 2.0.0a0
glfw: 2.10.0
grako: 3.16.5
h11: 0.16.0
h5py: 3.16.0
html2text: 2025.4.15
httpcore: 1.0.9
httpx: 0.28.1
httpx-sse: 0.4.3
idna: 3.15
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 2.0.0
iniconfig: 2.3.0
ipykernel: 7.1.0
ipython: 9.9.0
ipython_pygments_lexers: 1.1.1
jedi: 0.19.2
Jinja2: 3.1.6
jsonschema: 4.26.0
jsonschema-specifications: 2025.9.1
jupyter_client: 8.8.0
jupyter_core: 5.9.1
kiwisolver: 1.5.0
line_profiler: 5.0.0
lxml: 6.0.2
lz4: 4.3.2
Markdown: 3.8.2
MarkupSafe: 3.0.3
matplotlib: 3.10.7
matplotlib-inline: 0.2.2
mcp: 1.18.0
MolecularDynamicsViewer: 1.6
mpmath: 1.3.0
mrcfile: 1.5.0
msgpack: 1.1.1
multidict: 6.7.1
narwhals: 2.21.2
ndindex: 1.10.1
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.14.1
numpy: 2.4.6
numpy: 1.26.4
nvidia-cublas-cu12: 12.1.3.1
nvidia-cuda-cupti-cu12: 12.1.105
nvidia-cuda-nvrtc-cu12: 12.1.105
nvidia-cuda-runtime-cu12: 12.1.105
nvidia-cudnn-cu12: 8.9.2.26
nvidia-cufft-cu12: 11.0.2.54
nvidia-curand-cu12: 10.3.2.106
nvidia-cusolver-cu12: 11.4.5.107
nvidia-cusparse-cu12: 12.1.0.106
nvidia-nccl-cu12: 2.19.3
nvidia-nvjitlink-cu12: 12.9.86
nvidia-nvtx-cu12: 12.1.105
OpenMM: 8.4.0
OpenMM-CUDA-12: 8.4.0
openvr: 1.26.701
packaging: 25.0
ParmEd: 4.2.2
parso: 0.8.7
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 11.3.0
pip: 25.2
pkginfo: 1.12.1.2
platformdirs: 4.9.6
plotly: 6.7.0
pluggy: 1.6.0
prompt_toolkit: 3.0.52
propcache: 0.5.2
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pybind11: 3.0.1
pycollada: 0.8
pydantic: 2.13.4
pydantic-settings: 2.14.1
pydantic_core: 2.46.4
pydata-sphinx-theme: 0.17.1
pydicom: 2.4.4
Pygments: 2.18.0
pyKVFinder: 0.9.3
pynmrstar: 3.5.1
pynrrd: 1.0.0
PyOpenGL: 3.1.10
PyOpenGL-accelerate: 3.1.10
pyopenxr: 1.1.4501
pyparsing: 3.3.2
pyproject_hooks: 1.2.0
PyQt6: 6.10.2
PyQt6-Qt6: 6.10.1
PyQt6-WebEngine: 6.10.0
PyQt6-WebEngine-Qt6: 6.10.1
PyQt6_sip: 13.10.3
pytest: 9.0.3
pytest-cov: 7.1.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.2.2
python-multipart: 0.0.29
pyzmq: 27.1.0
qtconsole: 5.7.0
QtPy: 2.4.3
qtshim: 1.2.2
RandomWords: 0.4.0
referencing: 0.37.0
requests: 2.32.5
roman-numerals: 4.1.0
rpds-py: 0.30.0
scipy: 1.14.0
setuptools: 80.9.0
sfftk-rw: 0.8.1
six: 1.17.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.8.3
Sphinx: 9.0.4
sphinx-autodoc-typehints: 3.6.1
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
sse-starlette: 3.4.4
stack-data: 0.6.3
starlette: 1.0.0
superqt: 0.7.6
sympy: 1.14.0
tables: 3.10.2
tcia_utils: 3.2.1
threadpoolctl: 3.6.0
tifffile: 2025.3.13
tinyarray: 1.2.5
tomlkit: 0.15.1
torch: 2.2.1
tornado: 6.5.5
tqdm: 4.67.3
traitlets: 5.14.3
triton: 2.2.0
typing-inspection: 0.4.2
typing_extensions: 4.15.0
Unidecode: 1.4.0
urllib3: 2.7.0
uvicorn: 0.47.0
wcwidth: 0.7.0
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
yarl: 1.23.0
File attachment: Boltz_error
|
|||
| #20830 | can't reproduce | Crash while exiting in _enter_buffered_busy | ||
| Description |
The following bug report has been submitted:
Platform: macOS-26.5.1-arm64-arm-64bit
ChimeraX Version: 1.12 (2026-06-12 03:42:34 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
{"app_name":"ChimeraX","timestamp":"2026-08-06 11:34:35.00 -0700","app_version":"1.12.0","slice_uuid":"544eb719-b770-3601-b425-1ceb237637ac","build_version":"1.12.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 26.5.1 (25F80)","roots_installed":0,"name":"ChimeraX","incident_id":"6DBBFF7A-A446-4453-A794-2A5FCE56DC3A"}
{
"uptime" : 1300000,
"procRole" : "Unspecified",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "MacBookPro17,1",
"coalitionID" : 413467,
"osVersion" : {
"train" : "macOS 26.5.1",
"build" : "25F80",
"releaseType" : "User"
},
"captureTime" : "2026-08-06 11:34:31.6240 -0700",
"codeSigningMonitor" : 1,
"incident" : "6DBBFF7A-A446-4453-A794-2A5FCE56DC3A",
"pid" : 5162,
"translated" : false,
"cpuType" : "ARM-64",
"procLaunch" : "2026-08-06 11:32:34.8495 -0700",
"procStartAbsTime" : 32196761619462,
"procExitAbsTime" : 32199562878944,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.12.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.12.0","CFBundleVersion":"1.12.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"02620107-3C3C-53AD-84AD-4548958737BD","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "com.anthropic.claudefordesktop",
"crashReporterKey" : "AC9759F8-4628-DB3C-6D97-3038A20E5E71",
"lowPowerMode" : 1,
"appleIntelligenceStatus" : {"state":"unavailable","reasons":["assetIsNotReady","notOptedIn"]},
"developerMode" : 1,
"bootProgressRegister" : "0x2f000000",
"responsiblePid" : 5017,
"responsibleProc" : "claude",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRCuD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkf\/f\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"bootSessionUUID" : "82724E22-0F0A-4299-8931-E135F1724492",
"wakeTime" : 8338,
"sleepWakeUUID" : "52F87349-BD76-4B29-B350-6FD119DEF107",
"sip" : "enabled",
"exception" : {"codes":"0x0000000000000000, 0x0000000000000000","rawCodes":[0,0],"type":"EXC_CRASH","signal":"SIGABRT"},
"termination" : {"flags":0,"code":6,"namespace":"SIGNAL","indicator":"Abort trap: 6","byProc":"ChimeraX","byPid":5162},
"asi" : {"libsystem_c.dylib":["abort() called"]},
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 0,
"threads" : [{"triggered":true,"id":28123171,
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"uuid" : "f0b958ae-cf48-3682-8bf2-e30217be027d",
"path" : "\/Applications\/ChimeraX-1.12.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/mmcif\/_mmcif.cpython-311-darwin.so",
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"path" : "\/Applications\/ChimeraX-1.12.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/atomic\/_ribbons.cpython-311-darwin.so",
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"path" : "\/Applications\/ChimeraX-1.12.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/pdb\/_pdbio.cpython-311-darwin.so",
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"name" : "pyexpat.cpython-311-darwin.so"
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{
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"path" : "\/Applications\/ChimeraX-1.12.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/alignment_algs\/_sw.cpython-311-darwin.so",
"name" : "_sw.cpython-311-darwin.so"
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"path" : "\/Applications\/ChimeraX-1.12.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/alignment_algs\/libalign_algs.dylib",
"name" : "libalign_algs.dylib"
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"path" : "\/Applications\/ChimeraX-1.12.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/dssp\/_dssp.cpython-311-darwin.so",
"name" : "_dssp.cpython-311-darwin.so"
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"name" : "_nw.cpython-311-darwin.so"
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"path" : "\/Applications\/ChimeraX-1.12.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/lz4\/_version.cpython-311-darwin.so",
"name" : "_version.cpython-311-darwin.so"
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{
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"name" : "_frame.cpython-311-darwin.so"
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"path" : "\/Applications\/ChimeraX-1.12.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/core\/_serialize.cpython-311-darwin.so",
"name" : "_serialize.cpython-311-darwin.so"
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"path" : "\/Applications\/ChimeraX-1.12.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/msgpack\/_cmsgpack.cpython-311-darwin.so",
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"name" : "_imaging.cpython-311-darwin.so"
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"path" : "\/Applications\/ChimeraX-1.12.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PIL\/.dylibs\/libtiff.6.dylib",
"name" : "libtiff.6.dylib"
},
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"uuid" : "688c6473-716c-32eb-8cfe-f11203c4574d",
"path" : "\/Applications\/ChimeraX-1.12.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PIL\/.dylibs\/libjpeg.62.4.0.dylib",
"name" : "libjpeg.62.4.0.dylib"
},
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"uuid" : "6994e1d8-b3e5-38d6-aef0-721586b2d5ce",
"path" : "\/Applications\/ChimeraX-1.12.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PIL\/.dylibs\/libopenjp2.2.5.3.dylib",
"name" : "libopenjp2.2.5.3.dylib"
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"path" : "\/Applications\/ChimeraX-1.12.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PIL\/.dylibs\/libz.1.3.1.zlib-ng.dylib",
"name" : "libz.1.3.1.zlib-ng.dylib"
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===== Log before crash start =====
UCSF ChimeraX version: 1.12 (2026-06-12)
© 2016-2026 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/hwu/Desktop/HeightDB/result-0nvi6/3GJF and 0nvi6.cxs" format
> session
> view name session-start
opened ChimeraX session
> hide #1 models
> show #1 models
> hide #!2 models
> show #!2 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> open
> /Users/hwu/Downloads/test_77ace/test_77ace_relaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb
> format pdb
No such file/path:
/Users/hwu/Downloads/test_77ace/test_77ace_relaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb
> open "/Users/hwu/Desktop/HeightDB/result-0nvi6/3GJF and 0nvi6.cxs" format
> session
> view name session-start
opened ChimeraX session
> open
> /Users/hwu/Desktop/HeightDB/test_77ace/test_77ace_scores_rank_001_alphafold2_ptm_model_2_seed_000.json
Opening an AlphaFold PAE file requires first opening the predicted atomic
model. Did not find an open atomic model from the same directory. If the
atomic model is already open choose it using menu
Tools / Structure Prediction / AlphaFold Error Plot
or use the open command structure option, for example
open
/Users/hwu/Desktop/HeightDB/test_77ace/test_77ace_scores_rank_001_alphafold2_ptm_model_2_seed_000.json
structure #1
If you are trying to open a JSON file that is not AlphaFold PAE data then you
need to specify the specific JSON format such as
open mole_channels.json format mole
> open
> /Users/hwu/Desktop/HeightDB/test_77ace/test_77ace_relaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb
Chain information for
test_77ace_relaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb #3
---
Chain | Description
A | No description available
Computing secondary structure
> matchmaker #3 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3gjf, chain M (#2) with
test_77ace_relaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb, chain A (#3),
sequence alignment score = 622.8
RMSD between 102 pruned atom pairs is 0.290 angstroms; (across all 218 pairs:
25.827)
> hide #1 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #!2 models
> show #!2 models
> hide #3 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #3 models
> select #2/D:245
5 atoms, 4 bonds, 1 residue, 1 model selected
> open /Users/hwu/Downloads/linker.fasta
Failed opening file /Users/hwu/Downloads/linker.fasta:
Sequence 'DP03824' differs in length from preceding sequences, and it is
therefore impossible to open these sequences as an alignment. If you want to
open the sequences individually, specify 'false' as the value of the
'alignment' keyword in the 'open' command.
> open /Users/hwu/Downloads/linker.fasta
Failed opening file /Users/hwu/Downloads/linker.fasta:
Sequence 'DP03824' differs in length from preceding sequences, and it is
therefore impossible to open these sequences as an alignment. If you want to
open the sequences individually, specify 'false' as the value of the
'alignment' keyword in the 'open' command.
> close session
> open 1yjd
Summary of feedback from opening 1yjd fetched from pdb
---
note | Fetching compressed mmCIF 1yjd from http://files.rcsb.org/download/1yjd.cif
1yjd title:
Crystal structure of human CD28 in complex with the Fab fragment of a
mitogenic antibody (5.11A1) [more info...]
Chain information for 1yjd #1
---
Chain | Description | UniProt
C | T-cell-specific surface glycoprotein CD28 | CD28_HUMAN -1-134
H | Fab fragment of 5.11A1 antibody heavy chain |
L | Fab fragment of 5.11A1 antibody light chain |
Non-standard residues in 1yjd #1
---
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
1yjd mmCIF Assemblies
---
1| author_defined_assembly
> select /C
1029 atoms, 1017 bonds, 159 residues, 1 model selected
> select clear
> select /C:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /C:118
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain /C
Alignment identifier is 1/C
> select /C:14
12 atoms, 12 bonds, 1 residue, 1 model selected
> select /C:14
12 atoms, 12 bonds, 1 residue, 1 model selected
> color bfactor sel
12 atoms, 1 residues, atom bfactor range 48.7 to 64.7
> select clear
> color bfactor
4493 atoms, 753 residues, atom bfactor range 25.8 to 100
> delete #1/A,B
> delete #1/A
> delete /A
> select /L:110
8 atoms, 7 bonds, 1 residue, 1 model selected
> delete #1/H
> delete #1/L
> sequence chain #1/C
Destroying pre-existing alignment with identifier 1/C
Alignment identifier is 1/C
> sequence chain #1/C
Destroying pre-existing alignment with identifier 1/C
Alignment identifier is 1/C
> setattr /C uniprot
Missing or invalid "attrName" argument: Expected a text string
> setattr /C
Missing or invalid "target" argument: Expected a text string
> setattr #1/C uniprot
Missing or invalid "attrName" argument: Expected a text string
> setattr uniprot
Missing or invalid "attrName" argument: Expected a text string
> resnumbering
Unknown command: resnumbering
> setattr 1/C resnumbeirng
Missing or invalid "attrValue" argument: Expected a text string
> setattr 1/C resnumbering
Missing or invalid "attrValue" argument: Expected a text string
> setattr 1/C resnumbering=uniprot
Missing or invalid "attrValue" argument: Expected a text string
> open P10747 fromDatabase uniprot
Summary of feedback from opening P10747 fetched from uniprot
---
notes | Fetching compressed P10747 UniProt info from https://www.uniprot.org/uniprot/P10747.xml
Alignment identifier is P10747
Associated 1yjd chain C to P10747 with 4 mismatches
Opened UniProt P10747
> select /C:22,48,68,94
24 atoms, 22 bonds, 4 residues, 1 model selected
> select /C:1-118
949 atoms, 972 bonds, 118 residues, 1 model selected
> select /C:22,48,68,94
24 atoms, 22 bonds, 4 residues, 1 model selected
> select /C:86-88
24 atoms, 23 bonds, 3 residues, 1 model selected
> ~select
Nothing selected
> select /C:19,53,74,87,111
40 atoms, 35 bonds, 5 residues, 1 model selected
> select /C:22,48,68,94
24 atoms, 22 bonds, 4 residues, 1 model selected
> select /C:106
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /C:106-112
52 atoms, 51 bonds, 7 residues, 1 model selected
> select clear
> select /C:102
7 atoms, 7 bonds, 1 residue, 1 model selected
> select /C:102-118
135 atoms, 138 bonds, 17 residues, 1 model selected
> close session
> open "/Users/hwu/Desktop/HeightDB/result-0nvi6/3GJF and 0nvi6.cxs" format
> session
No such file/path: /Users/hwu/Desktop/HeightDB/result-0nvi6/3GJF and 0nvi6.cxs
> open
> /Users/hwu/Desktop/HeightDB/test_77ace/test_77ace_relaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb
> format pdb
No such file/path:
/Users/hwu/Desktop/HeightDB/test_77ace/test_77ace_relaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb
> open "/Users/hwu/Desktop/Structure prediction for
> HeightDB/Boltz2/result-0nvi6/3GJF and 0nvi6.cxs"
> view name session-start
opened ChimeraX session
> hide #!2 models
> show #!2 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> open "/Users/hwu/Desktop/Structure prediction for
> HeightDB/AF2/test_d6f2a/test_d6f2a_relaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb"
Chain information for
test_d6f2a_relaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb #3
---
Chain | Description
A | No description available
Computing secondary structure
> matchmaker #3 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3gjf, chain M (#2) with
test_d6f2a_relaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb, chain A (#3),
sequence alignment score = 631.1
RMSD between 101 pruned atom pairs is 0.315 angstroms; (across all 218 pairs:
26.487)
> hide #3 models
> show #3 models
> hide #3 models
> hide #!2 models
> show #3 models
> show #!2 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #3 models
> color bfactor #3
4550 atoms, 307 residues, atom bfactor range 30.4 to 98.6
> select #3/A:251
22 atoms, 21 bonds, 1 residue, 1 model selected
> sequence chain #3/A
Alignment identifier is 3/A
> select #3/A:58
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/A:58-59
18 atoms, 17 bonds, 2 residues, 1 model selected
> select
> #3/A:5-9,12-14,20-27,35-41,47-53,60-62,70-75,80-85,94-101,115-119,147-150,156-161,173-178,185-188,202-207,210-215,224-232,235-238,242-246,268-270,288-290
1790 atoms, 1791 bonds, 114 residues, 1 model selected
> select clear
> select #3/A:251
22 atoms, 21 bonds, 1 residue, 1 model selected
> info residues sel attribute bfactor
> info residues sel attribute bfactor
> ui tool show "Render/Select by Attribute"
> select #3/A:199
14 atoms, 14 bonds, 1 residue, 1 model selected
Populating font family aliases took 175 ms. Replace uses of missing font
family "Times" with one that exists to avoid this cost.
> select clear
> select #3/A:248
7 atoms, 6 bonds, 1 residue, 1 model selected
> select clear
> select #3/A:233
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/A:269
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #3/A:270
15 atoms, 14 bonds, 1 residue, 1 model selected
> select clear
> select #3/A:248
7 atoms, 6 bonds, 1 residue, 1 model selected
> close session
> open "/Users/hwu/Desktop/Structure prediction for
> HeightDB/Boltz2/result-0nvi6/3GJF and 0nvi6.cxs" format session
No such file/path: /Users/hwu/Desktop/Structure prediction for
HeightDB/Boltz2/result-0nvi6/3GJF and 0nvi6.cxs
> open "/Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for
> Young-wook/Harry Wu/Collaborations/Structure prediction for
> HeightDB/ChimeraX/3GJF and 0nvi6.cxs"
> view name session-start
opened ChimeraX session
> open "/Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for
> Young-wook/Harry Wu/Collaborations/Structure prediction for
> HeightDB/AF2/test_d6f2a/test_d6f2a_pae.png"
Image mode RGBA is not supported (L, P, I;16, I;16B, I;16L, I;16S, F, F;32BF,
I, RGB)
> open "/Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for
> Young-wook/Harry Wu/Collaborations/Structure prediction for
> HeightDB/AF2/test_d6f2a/test_d6f2a_relaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb"
Chain information for
test_d6f2a_relaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb #3
---
Chain | Description
A | No description available
Computing secondary structure
> matchmaker #3 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3gjf, chain M (#2) with
test_d6f2a_relaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb, chain A (#3),
sequence alignment score = 631.1
RMSD between 101 pruned atom pairs is 0.315 angstroms; (across all 218 pairs:
26.487)
> hide #1 models
> hide #3 models
> show #3 models
> hide #!2 models
> show #!2 models
> hide #3 models
> show #3 models
> save "/Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for
> Young-wook/Harry Wu/Collaborations/Structure prediction for
> HeightDB/ChimeraX/3GJF 0nvi6 d6f2a.cxs"
> hide #!2 models
> color bfactor #3
4550 atoms, 307 residues, atom bfactor range 30.4 to 98.6
> ui tool show Distances
Exactly two atoms must be selected!
> select #3/A:181
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/A:263
12 atoms, 11 bonds, 1 residue, 1 model selected
> select add #3/A:180
26 atoms, 25 bonds, 2 residues, 1 model selected
> select add #3/A:181
33 atoms, 31 bonds, 3 residues, 1 model selected
> select subtract #3/A:180
19 atoms, 17 bonds, 2 residues, 1 model selected
Exactly two atoms must be selected!
> select clear
> select #3/A:181
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3/A:181
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/A:181 @Ca
1 atom, 1 residue, 1 model selected
> select add #3/A:262
13 atoms, 11 bonds, 2 residues, 1 model selected
> show sel atoms
> select #3/A:181 @Ca #3/A:262 @Ca
2 atoms, 2 residues, 1 model selected
> distance #3/A:181@CA #3/A:262@CA
Distance between
test_d6f2a_relaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb #3/A GLY 181
CA and ASP 262 CA: 31.177Å
> ~distance #3/A:181@CA #3/A:262@CA
> sequence chain #3/A
Alignment identifier is 3/A
> show #!2 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> copy #2
Unknown command: copy #2
> combine #2
> hide #!2 models
> hide #3 models
> select #4/M:48
7 atoms, 6 bonds, 1 residue, 1 model selected
> delete #4/M
> select #4/K:107
7 atoms, 6 bonds, 1 residue, 1 model selected
> delete #4/K
> show #3 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> hide #3 models
> hide #!2 models
> show #!4 models
> show #!2 models
> hide #!2 models
> show #3 models
> combine #23
No structures specified
> combine #3
> combine #4 #5
> hide #5 models
> hide #!4 models
> hide #3 models
> save "/Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for
> Young-wook/Harry Wu/Collaborations/Structure prediction for
> HeightDB/ChimeraX/3GJF 0nvi6 d6f2a.cxs"
> show #1 models
> show #!2 models
> hide #!2 models
> hide #1 models
> show #1 models
> show #!2 models
> show #3 models
> hide #3 models
> hide #!6 models
> hide #!2 models
> hide #1 models
> select add #1
5078 atoms, 5211 bonds, 640 residues, 1 model selected
> select add #2
12262 atoms, 11770 bonds, 2257 residues, 2 models selected
> select add #3
16812 atoms, 16378 bonds, 2564 residues, 3 models selected
> select add #4
20378 atoms, 19635 bonds, 3351 residues, 4 models selected
> select add #5
24928 atoms, 24243 bonds, 3658 residues, 5 models selected
> select subtract #5
20378 atoms, 19635 bonds, 3351 residues, 4 models selected
> select add #5
24928 atoms, 24243 bonds, 3658 residues, 5 models selected
> close #5
> close #1
> close #2
> close #3
> close #4
> show #!6 models
> select add #6
8116 atoms, 7865 bonds, 1094 residues, 1 model selected
> select clear
> open "/Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for
> Young-wook/Harry Wu/Collaborations/Structure prediction for
> HeightDB/Sequences/rcsb_pdb_3GJF.fasta"
Failed opening file /Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group
Folder/Data for Young-wook/Harry Wu/Collaborations/Structure prediction for
HeightDB/Sequences/rcsb_pdb_3GJF.fasta:
Sequence '3GJF_4|Chains G[auth K], H[auth L]|Antibody light chain|Homo sapiens
(9606)' differs in length from preceding sequences, and it is therefore
impossible to open these sequences as an alignment. If you want to open the
sequences individually, specify 'false' as the value of the 'alignment'
keyword in the 'open' command.
> sequence chain #6/D
Alignment identifier is 6/D
> sequence chain #6/E
Alignment identifier is 6/E
> sequence chain #6/F
Alignment identifier is 6/F
> sequence chain #6/A
Alignment identifier is 6/A
> select /A:248
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:248-307
919 atoms, 935 bonds, 60 residues, 1 model selected
> delete #6/A:248-307
> sequence chain #6/D
Alignment identifier is 6/D
> sequence chain #6/E
Alignment identifier is 6/E
> sequence chain #6/F
Alignment identifier is 6/F
> sequence chain #6/A
Destroying pre-existing alignment with identifier 6/A
Alignment identifier is 6/A
> select /D:251
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /D:251-276
217 atoms, 224 bonds, 26 residues, 1 model selected
> select /D:1
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /D:1-60
495 atoms, 512 bonds, 60 residues, 1 model selected
> select clear
> color bfactor
7197 atoms, 1034 residues, atom bfactor range 14.8 to 98.6
> save "/Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for
> Young-wook/Harry Wu/Collaborations/Structure prediction for
> HeightDB/ChimeraX/3GJF d6f2a.cxs"
> save "/Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for
> Young-wook/Harry Wu/Collaborations/Structure prediction for
> HeightDB/ChimeraX/3GJF d6f2a.cif" relModel #6
Not saving entity_poly_seq for non-authoritative sequences
> open "/Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for
> Young-wook/Harry Wu/Collaborations/Structure prediction for
> HeightDB/ChimeraX/3GJF_d6f2a_measure.cxc"
> open 3GJF_d6f2a.cif
Failed opening file /Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group
Folder/Data for Young-wook/Harry Wu/Collaborations/Structure prediction for
HeightDB/ChimeraX/3GJF_d6f2a_measure.cxc:
No such file/path: 3GJF_d6f2a.cif
> close session
> open "/Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for
> Young-wook/Harry Wu/Collaborations/Structure prediction for
> HeightDB/ChimeraX/3GJF_d6f2a_measure.cxc"
> open 3GJF_d6f2a.cif
No such file/path: 3GJF_d6f2a.cif
> open /Users/hwu/Desktop/measure_ecd.py
Traceback (most recent call last):
File "/Users/hwu/Desktop/measure_ecd.py", line 26, in
from Bio.PDB import PDBParser, MMCIFParser
ModuleNotFoundError: No module named 'Bio'
Failed opening file /Users/hwu/Desktop/measure_ecd.py:
Error opening python file /Users/hwu/Desktop/measure_ecd.py
> open "/Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for
> Young-wook/Harry Wu/Collaborations/Structure prediction for
> HeightDB/ChimeraX/3GJF_d6f2a_measure.cxc"
> open 3GJF_d6f2a.cif
Summary of feedback from opening 3GJF_d6f2a.cif
---
warnings | Unknown polymer entity '4' on line 4488
Missing or incorrect sequence information. Inferred polymer connectivity.
Atom H is not in the residue template for MET /A:1
Chain information for 3GJF_d6f2a.cif #1
---
Chain | Description
A | No description available
D | HLA class I histocompatibility antigen, A-2 alpha chain
E | Beta-2-microglobulin
F | NYESO-1 peptide
> color #1 bychain
> color ~#1:0-276 #808080 transparency 70 target ac
> shape cylinder radius 1.0 fromPoint 38.94,2.55,29.79 toPoint
> -52.11,43.45,48.41 color yellow
> shape sphere radius 2.5 center 38.94,2.55,29.79 color red
> shape sphere radius 2.5 center -52.11,43.45,48.41 color red
> 2dlabels text "3GJF_d6f2a: 10.15 nm" xpos 0.05 ypos 0.9 color black size 24
> view
executed 3GJF_d6f2a_measure.cxc
> ui tool show Distances
> close session
> open "/Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for
> Young-wook/Harry Wu/Collaborations/Structure prediction for
> HeightDB/ChimeraX/3GJF d6f2a.cif" format mmcif
No such file/path: /Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group
Folder/Data for Young-wook/Harry Wu/Collaborations/Structure prediction for
HeightDB/ChimeraX/3GJF d6f2a.cif
> open 3gjf
3gjf title:
Rational development of high-affinity T-cell receptor-like antibodies [more
info...]
Chain information for 3gjf #1
---
Chain | Description | UniProt
A D | HLA class I histocompatibility antigen, A-2 alpha chain | 1A02_HUMAN 1-276
B E | Beta-2-microglobulin | B2MG_HUMAN 1-99
C F | NYESO-1 peptide |
H M | Antibody heavy chain |
K L | Antibody light chain |
3gjf mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> hide surfaces
> select ::name="HOH"
1603 atoms, 1603 residues, 1 model selected
> select /D:1380@O
1 atom, 1 residue, 1 model selected
> select ::name="HOH"
1603 atoms, 1603 residues, 1 model selected
> hide sel
> hide sel atoms
> select clear
> hide cartoons
> show cartoons
> hide surfaces
> hide atoms
> select clear
> select /H:164
5 atoms, 4 bonds, 1 residue, 1 model selected
> delete #1/H
> select /L:73
5 atoms, 4 bonds, 1 residue, 1 model selected
> delete #1/L
> select /A:116
12 atoms, 12 bonds, 1 residue, 1 model selected
> delete #1/A
> select clear
> select /C:3
8 atoms, 7 bonds, 1 residue, 1 model selected
> delete #1/C
> select /B:55
6 atoms, 5 bonds, 1 residue, 1 model selected
> delete #1/B
> select /M:48
7 atoms, 6 bonds, 1 residue, 1 model selected
> delete #1/M
> select /K:76
7 atoms, 6 bonds, 1 residue, 1 model selected
> delete #1/K
> save "/Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for
> Young-wook/Harry Wu/Collaborations/Structure prediction for
> HeightDB/ChimeraX/3GJF_HLA A*2:01_only.cif" relModel #1
> close session
> open "/Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for
> Young-wook/Harry Wu/Collaborations/Structure prediction for
> HeightDB/ChimeraX/3GJF_HLA_A*201_only_measure.cxc"
> open 3GJF_HLA_A*201_only.cif
Chain information for 3GJF_HLA_A*201_only.cif #1
---
Chain | Description
D | HLA class I histocompatibility antigen, A-2 alpha chain
E | Beta-2-microglobulin
F | NYESO-1 peptide
3GJF_HLA_A*201_only.cif mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> color #1 bychain
> color ~#1:0-276 #808080 transparency 70 target ac
> shape cylinder radius 1.0 fromPoint 39.24,8.14,34.22 toPoint
> -26.71,25.38,37.76 color yellow
> shape sphere radius 2.5 center 39.24,8.14,34.22 color red
> shape sphere radius 2.5 center -26.71,25.38,37.76 color red
> 2dlabels text "3GJF_HLA_A*201_only: 6.83 nm" xpos 0.05 ypos 0.9 color black
> size 24
> view
executed 3GJF_HLA_A*201_only_measure.cxc
> open "/Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for
> Young-wook/Harry Wu/Collaborations/Structure prediction for
> HeightDB/ChimeraX/CD2CD58merge_measure.cxc"
> open CD2CD58merge.cif
Summary of feedback from opening CD2CD58merge.cif
---
warnings | Unknown polymer entity '1' on line 112
Unknown polymer entity '2' on line 1374
Missing or incorrect sequence information. Inferred polymer connectivity.
Chain information for CD2CD58merge.cif #6
---
Chain | Description
A | HUMAN CD2 PROTEIN
B | HUMAN CD58 PROTEIN
> color #1 bychain
> color ~#1:1-215 #808080 transparency 70 target ac
> shape cylinder radius 1.0 fromPoint 6.92,-7.59,89.20 toPoint
> 68.86,44.41,-34.22 color yellow
> shape sphere radius 2.5 center 6.92,-7.59,89.20 color red
> shape sphere radius 2.5 center 68.86,44.41,-34.22 color red
> 2dlabels text "CD2CD58merge: 14.76 nm" xpos 0.05 ypos 0.9 color black size
> 24
> view
executed CD2CD58merge_measure.cxc
> select add #1
3566 atoms, 3257 bonds, 787 residues, 1 model selected
> select add #2
3566 atoms, 3257 bonds, 787 residues, 2 models selected
> select add #3
3566 atoms, 3257 bonds, 787 residues, 3 models selected
> select add #4
3566 atoms, 3257 bonds, 787 residues, 4 models selected
> select add #5
3566 atoms, 3257 bonds, 787 residues, 7 models selected
> select clear
> hide #1 models
> hide #2 models
> hide #4 models
> hide #3 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> close session
> open /Users/hwu/Desktop/HeightDB/CD2CD58merge_measure.cxc format cmd
No such file/path: /Users/hwu/Desktop/HeightDB/CD2CD58merge_measure.cxc
> open "/Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for
> Young-wook/Harry Wu/Collaborations/Structure prediction for
> HeightDB/ChimeraX/CD2CD58merge_measure.cxc"
> open CD2CD58merge.cif
Summary of feedback from opening CD2CD58merge.cif
---
warnings | Unknown polymer entity '1' on line 112
Unknown polymer entity '2' on line 1374
Missing or incorrect sequence information. Inferred polymer connectivity.
Chain information for CD2CD58merge.cif #1
---
Chain | Description
A | HUMAN CD2 PROTEIN
B | HUMAN CD58 PROTEIN
> color #1 bychain
> color ~#1:1-215 #808080 transparency 70 target ac
> shape cylinder radius 1.0 fromPoint 6.92,-7.59,89.20 toPoint
> 68.86,44.41,-34.22 color yellow
> shape sphere radius 2.5 center 6.92,-7.59,89.20 color red
> shape sphere radius 2.5 center 68.86,44.41,-34.22 color red
> 2dlabels text "CD2CD58merge: 14.76 nm" xpos 0.05 ypos 0.9 color black size
> 24
> view
executed CD2CD58merge_measure.cxc
> close session
> alphafold fetch AF-Q9Y287-F1
Unrecognized format for AlphaFold id "AF-Q9Y287-F1". Example AlphaFold ids
P29474, Q8N9C0-2, IGS22_HUMAN, AF-Q8N9C0-F1-v6, AF-Q8N9C0-2-F1-v6.
> alphafold fetch AF-Q9Y287-F1-v6
Fetching compressed AlphaFold database settings from
https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database6.json
Fetching compressed AlphaFold Q9Y287 from
https://alphafold.ebi.ac.uk/files/AF-Q9Y287-F1-model_v6.cif
Chain information for AlphaFold Q9Y287 #1
---
Chain | Description | UniProt
A | Integral membrane protein 2B | ITM2B_HUMAN 1-266
Color AlphaFold Q9Y287 by residue attribute pLDDT_score
> ui tool show Distances
> select clear
> select /A:80
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel atoms
> select /A:200
10 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select /A:200
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/A:200 @Ca
1 atom, 1 residue, 1 model selected
> select #1/A:80 @Ca
1 atom, 1 residue, 1 model selected
Exactly two atoms must be selected!
> select clear
> select #1/A:200 @Ca
1 atom, 1 residue, 1 model selected
> select #1/A:80 @Ca
1 atom, 1 residue, 1 model selected
Exactly two atoms must be selected!
> select #1/A:80@Ca
1 atom, 1 residue, 1 model selected
> select #1/A:80@Ca #1/A:200 @Ca
2 atoms, 2 residues, 1 model selected
> distance /A:80@CA /A:200@CA
Distance between /A ALA 80 CA and HIS 200 CA: 40.325Å
> close session
> open "/Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for
> Young-wook/Harry Wu/Collaborations/Structure prediction for
> HeightDB/ChimeraX/CD2CD58merge_measure.cxc" format cmd
> open CD2CD58merge.cif
Summary of feedback from opening CD2CD58merge.cif
---
warnings | Unknown polymer entity '1' on line 112
Unknown polymer entity '2' on line 1374
Missing or incorrect sequence information. Inferred polymer connectivity.
Chain information for CD2CD58merge.cif #1
---
Chain | Description
A | HUMAN CD2 PROTEIN
B | HUMAN CD58 PROTEIN
> color #1 bychain
> color ~#1:1-215 #808080 transparency 70 target ac
> shape cylinder radius 1.0 fromPoint 6.92,-7.59,89.20 toPoint
> 68.86,44.41,-34.22 color yellow
> shape sphere radius 2.5 center 6.92,-7.59,89.20 color red
> shape sphere radius 2.5 center 68.86,44.41,-34.22 color red
> 2dlabels text "CD2CD58merge: 14.76 nm" xpos 0.05 ypos 0.9 color black size
> 24
> view
executed CD2CD58merge_measure.cxc
> close session
> open "/Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for
> Young-wook/Harry Wu/Collaborations/Structure prediction for
> HeightDB/ChimeraX/3GJF_HLA A*2:01_only.cif" format mmcif
No such database '/users/hwu/library/cloudstorage/box-box/jun lab group
folder/data for young-wook/harry wu/collaborations/structure prediction for
heightdb/chimerax/3gjf_hla a*2'
> open "/Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for
> Young-wook/Harry Wu/Collaborations/Structure prediction for
> HeightDB/ChimeraX/3GJF_HLA_A*201_only_measure.cxc" format cmd
> open 3GJF_HLA_A*201_only.cif
Chain information for 3GJF_HLA_A*201_only.cif #1
---
Chain | Description
D | HLA class I histocompatibility antigen, A-2 alpha chain
E | Beta-2-microglobulin
F | NYESO-1 peptide
3GJF_HLA_A*201_only.cif mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> color #1 bychain
> color ~#1:0-276 #808080 transparency 70 target ac
> shape cylinder radius 1.0 fromPoint 39.24,8.14,34.22 toPoint
> -26.71,25.38,37.76 color yellow
> shape sphere radius 2.5 center 39.24,8.14,34.22 color red
> shape sphere radius 2.5 center -26.71,25.38,37.76 color red
> 2dlabels text "3GJF_HLA_A*201_only: 6.83 nm" xpos 0.05 ypos 0.9 color black
> size 24
> view
executed 3GJF_HLA_A*201_only_measure.cxc
> close session
> open "/Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for
> Young-wook/Harry Wu/Collaborations/Structure prediction for
> HeightDB/ChimeraX/3GJF_d6f2a_measure.cxc" format cmd
> open 3GJF_d6f2a.cif
Summary of feedback from opening 3GJF_d6f2a.cif
---
warnings | Unknown polymer entity '4' on line 4488
Missing or incorrect sequence information. Inferred polymer connectivity.
Atom H is not in the residue template for MET /A:1
Chain information for 3GJF_d6f2a.cif #1
---
Chain | Description
A | No description available
D | HLA class I histocompatibility antigen, A-2 alpha chain
E | Beta-2-microglobulin
F | NYESO-1 peptide
> color #1 bychain
> color ~#1:0-276 #808080 transparency 70 target ac
> shape cylinder radius 1.0 fromPoint 38.94,2.55,29.79 toPoint
> -52.11,43.45,48.41 color yellow
> shape sphere radius 2.5 center 38.94,2.55,29.79 color red
> shape sphere radius 2.5 center -52.11,43.45,48.41 color red
> 2dlabels text "3GJF_d6f2a: 10.15 nm" xpos 0.05 ypos 0.9 color black size 24
> view
executed 3GJF_d6f2a_measure.cxc
> close session
> open "/Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for
> Young-wook/Harry Wu/Collaborations/Structure prediction for
> HeightDB/ChimeraX/3GJF 0nvi6 d6f2a.cxs" format session
> view name session-start
opened ChimeraX session
> close session
> open "/Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for
> Young-wook/Harry Wu/Collaborations/Structure prediction for
> HeightDB/ChimeraX/3GJF_d6f2a_measure.cxc" format cmd
> open 3GJF_d6f2a.cif
Summary of feedback from opening 3GJF_d6f2a.cif
---
warnings | Unknown polymer entity '4' on line 4488
Missing or incorrect sequence information. Inferred polymer connectivity.
Atom H is not in the residue template for MET /A:1
Chain information for 3GJF_d6f2a.cif #1
---
Chain | Description
A | No description available
D | HLA class I histocompatibility antigen, A-2 alpha chain
E | Beta-2-microglobulin
F | NYESO-1 peptide
> color #1 bychain
> color ~#1:0-276 #808080 transparency 70 target ac
> shape cylinder radius 1.0 fromPoint 38.94,2.55,29.79 toPoint
> -52.11,43.45,48.41 color yellow
> shape sphere radius 2.5 center 38.94,2.55,29.79 color red
> shape sphere radius 2.5 center -52.11,43.45,48.41 color red
> 2dlabels text "3GJF_d6f2a: 10.15 nm" xpos 0.05 ypos 0.9 color black size 24
> view
executed 3GJF_d6f2a_measure.cxc
> close session
> open "/Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for
> Young-wook/Harry Wu/Collaborations/Structure prediction for
> HeightDB/ChimeraX/CD2CD58merge_measure.cxc" format cmd
> open CD2CD58merge.cif
Summary of feedback from opening CD2CD58merge.cif
---
warnings | Unknown polymer entity '1' on line 112
Unknown polymer entity '2' on line 1374
Missing or incorrect sequence information. Inferred polymer connectivity.
Chain information for CD2CD58merge.cif #1
---
Chain | Description
A | HUMAN CD2 PROTEIN
B | HUMAN CD58 PROTEIN
> color #1 bychain
> color ~#1:1-215 #808080 transparency 70 target ac
> shape cylinder radius 1.0 fromPoint 6.92,-7.59,89.20 toPoint
> 68.86,44.41,-34.22 color yellow
> shape sphere radius 2.5 center 6.92,-7.59,89.20 color red
> shape sphere radius 2.5 center 68.86,44.41,-34.22 color red
> 2dlabels text "CD2CD58merge: 14.76 nm" xpos 0.05 ypos 0.9 color black size
> 24
> view
executed CD2CD58merge_measure.cxc
> select /B:186
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:182
10 atoms, 9 bonds, 1 residue, 1 model selected
> sequence chain #1/A
Alignment identifier is 1/A
> select /B:172
6 atoms, 5 bonds, 1 residue, 1 model selected
> close session
> open /Users/hwu/Desktop/HeightDB/CD2CD58merge.cif format mmcif
No such file/path: /Users/hwu/Desktop/HeightDB/CD2CD58merge.cif
> open "/Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for
> Young-wook/Harry Wu/Collaborations/Structure prediction for
> HeightDB/ChimeraX/CD2CD58merge.cxs"
> view name session-start
opened ChimeraX session
> select /B:209
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /B:209-215
58 atoms, 59 bonds, 7 residues, 1 model selected
> select clear
> select /B:209
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /B:209-215
58 atoms, 59 bonds, 7 residues, 1 model selected
> delete sel
> select clear
> save "/Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for
> Young-wook/Harry Wu/Collaborations/Structure prediction for
> HeightDB/ChimeraX/CD2CD58merge.cif" relModel #5
Not saving entity_poly_seq for non-authoritative sequences
> close session
> open "/Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for
> Young-wook/Harry Wu/Collaborations/Structure prediction for
> HeightDB/ChimeraX/CD2CD58merge_measure.cxc"
> open CD2CD58merge.cif
Summary of feedback from opening CD2CD58merge.cif
---
warnings | Unknown polymer entity '1' on line 112
Unknown polymer entity '2' on line 1374
Missing or incorrect sequence information. Inferred polymer connectivity.
Chain information for CD2CD58merge.cif #1
---
Chain | Description
A | HUMAN CD2 PROTEIN
B | HUMAN CD58 PROTEIN
> color #1 bychain
> color ~#1:1-208 #808080 transparency 70 target ac
> shape cylinder radius 1.0 fromPoint 6.45,-6.16,90.14 toPoint
> 62.15,36.49,-20.74 color yellow
> shape sphere radius 2.5 center 6.45,-6.16,90.14 color red
> shape sphere radius 2.5 center 62.15,36.49,-20.74 color red
> 2dlabels text "CD2CD58merge: 13.12 nm" xpos 0.05 ypos 0.9 color black size
> 24
> view
executed CD2CD58merge_measure.cxc
> close session
> open "/Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for
> Young-wook/Harry Wu/Collaborations/Structure prediction for
> HeightDB/AF2/test_0d0a1/test_0d0a1_relaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb"
Chain information for
test_0d0a1_relaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb #1
---
Chain | Description
A | No description available
Computing secondary structure
> color bfactor
4547 atoms, 311 residues, atom bfactor range 33.2 to 98.7
> close session
> open /Users/hwu/Downloads/ChimeraX/AlphaFold/AF-Q9Y287-F1-model_v6.cif
> format mmcif
Chain information for AF-Q9Y287-F1-model_v6.cif #1
---
Chain | Description | UniProt
A | Integral membrane protein 2B | ITM2B_HUMAN 1-266
Color AF-Q9Y287-F1-model_v6.cif by residue attribute pLDDT_score
> color bfactor
2134 atoms, 266 residues, atom bfactor range 24.6 to 98
> close session
> open "/Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for
> Young-wook/Harry Wu/Collaborations/Structure prediction for
> HeightDB/AF2/test_14818 (IgG1 CAR
> ECD)/test_14818_relaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb"
Chain information for
test_14818_relaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb #1
---
Chain | Description
A | No description available
Computing secondary structure
> color bfactor
5811 atoms, 394 residues, atom bfactor range 24.4 to 98.4
> sequence chain #1/A
Alignment identifier is 1/A
> select /A:1
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /A:1-101
1478 atoms, 1491 bonds, 101 residues, 1 model selected
> select clear
> select /A:120-121
22 atoms, 21 bonds, 2 residues, 1 model selected
> select /A:118-120
41 atoms, 40 bonds, 3 residues, 1 model selected
> select /A:120-146
416 atoms, 418 bonds, 27 residues, 1 model selected
> select /A:301
15 atoms, 14 bonds, 1 residue, 1 model selected
> select /A:301-388
1322 atoms, 1337 bonds, 88 residues, 1 model selected
> select clear
> select /A:248
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:248-249
24 atoms, 23 bonds, 2 residues, 1 model selected
> select /A:248-291
632 atoms, 644 bonds, 44 residues, 1 model selected
> select /A:248
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:248-285
541 atoms, 551 bonds, 38 residues, 1 model selected
> select /A:287
14 atoms, 14 bonds, 1 residue, 1 model selected
> select /A:286
17 atoms, 16 bonds, 1 residue, 1 model selected
> select /A:248-286
558 atoms, 568 bonds, 39 residues, 1 model selected
> select clear
> select /A:286
17 atoms, 16 bonds, 1 residue, 1 model selected
> delete #1A:1-286
Missing or invalid "atoms" argument: invalid atoms specifier
> delete #1/A:1-286
> select /A:394
23 atoms, 22 bonds, 1 residue, 1 model selected
> select /A:387-394
122 atoms, 122 bonds, 8 residues, 1 model selected
> select /A:385-394
146 atoms, 147 bonds, 10 residues, 1 model selected
> select /A:394
23 atoms, 22 bonds, 1 residue, 1 model selected
> select /A:388-394
108 atoms, 108 bonds, 7 residues, 1 model selected
> delete sel
> select clear
> save "/Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for
> Young-wook/Harry Wu/Collaborations/Structure prediction for
> HeightDB/ChimeraX/14818_IgG1_only.cif" relModel #1
Not saving entity_poly_seq for non-authoritative sequences
> open "/Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for
> Young-wook/Harry Wu/Collaborations/Structure prediction for
> HeightDB/ChimeraX/14818_IgG1_only_measure.cxc"
> open 14818_IgG1_only.cif
Summary of feedback from opening 14818_IgG1_only.cif
---
warnings | Unknown polymer entity '1' on line 106
Missing or incorrect sequence information. Inferred polymer connectivity.
Chain information for 14818_IgG1_only.cif #2
---
Chain | Description
A | No description available
> color #1 bychain
> color ~#1:287-387 #808080 transparency 70 target ac
> shape cylinder radius 1.0 fromPoint 7.35,10.76,17.68 toPoint
> -30.85,-9.09,17.28 color yellow
> shape sphere radius 2.5 center 7.35,10.76,17.68 color red
> shape sphere radius 2.5 center -30.85,-9.09,17.28 color red
> 2dlabels text "14818_IgG1_only: 4.31 nm" xpos 0.05 ypos 0.9 color black size
> 24
> view
executed 14818_IgG1_only_measure.cxc
===== Log before crash end =====
Log:
You can double click a model's Name or ID in the model panel to edit those
fields
UCSF ChimeraX version: 1.12 (2026-06-12)
© 2016-2026 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M1
OpenGL vendor: Apple
Python: 3.11.9
Locale: en_US.UTF-8
Qt version: PyQt6 6.10.2, Qt 6.10.0
Qt runtime version: 6.10.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro17,1
Model Number: MYD82LL/A
Chip: Apple M1
Total Number of Cores: 8 (4 Performance and 4 Efficiency)
Memory: 8 GB
System Firmware Version: 18000.120.36
OS Loader Version: 18000.120.36
Software:
System Software Overview:
System Version: macOS 26.5.1 (25F80)
Kernel Version: Darwin 25.5.0
Time since boot: 54 days, 3 hours, 56 minutes
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Support: Metal 4
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
accessible-pygments: 0.0.5
aiohappyeyeballs: 2.6.2
aiohttp: 3.13.4
aiosignal: 1.4.0
alabaster: 1.0.0
annotated-types: 0.7.0
anyio: 4.13.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.1
attrs: 26.1.0
babel: 2.18.0
beautifulsoup4: 4.13.5
blockdiag: 3.0.0
blosc2: 4.4.3
bs4: 0.0.2
build: 1.3.0
certifi: 2025.7.14
cftime: 1.6.5
charset-normalizer: 3.4.7
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.2.8
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.2
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Animations: 1.0
ChimeraX-Aniso: 1.3.2
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.67.1
ChimeraX-AtomicLibrary: 14.4
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.1
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.6.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4.1
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.4
ChimeraX-Cluster: 1.0
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3.1
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.12
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.2.2
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5.3
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.4
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.8.2
ChimeraX-Label: 1.5
ChimeraX-LightingGUI: 1.0
ChimeraX-ListInfo: 1.3.1
ChimeraX-Log: 1.2.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.3
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchAlign: 1.2
ChimeraX-MatchMaker: 2.4.1
ChimeraX-MCopy: 1.0
ChimeraX-MCPServer: 0.2.0
ChimeraX-MDcrds: 2.19
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.3.9
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.23
ChimeraX-ModelPanel: 1.6.1
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0.1
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.15.4
ChimeraX-OpenFold: 1.0
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.13
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.5
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.4
ChimeraX-ProfileGrids: 1.6
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.8.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.3
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.2
ChimeraX-Scenes: 0.3.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.12
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.18
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SNFG: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5.3
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.4
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.50.8
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.6.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.5
ChimeraX-Zone: 1.0.1
click: 8.4.1
colorama: 0.4.6
comm: 0.2.3
contourpy: 1.3.3
coverage: 7.14.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.2.4
debugpy: 1.8.21
decorator: 5.3.1
docutils: 0.21.2
executing: 2.2.1
filelock: 3.19.1
fonttools: 4.63.0
frozenlist: 1.8.0
funcparserlib: 2.0.0a0
glfw: 2.10.0
grako: 3.16.5
h11: 0.16.0
h5py: 3.16.0
html2text: 2025.4.15
httpcore: 1.0.9
httpx: 0.28.1
httpx-sse: 0.4.3
idna: 3.18
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 2.0.0
iniconfig: 2.3.0
ipykernel: 7.1.0
ipython: 9.9.0
ipython_pygments_lexers: 1.1.1
jedi: 0.19.2
Jinja2: 3.1.6
jsonschema: 4.26.0
jsonschema-specifications: 2025.9.1
jupyter_client: 8.8.0
jupyter_core: 5.9.1
kiwisolver: 1.5.0
line_profiler: 5.0.0
lxml: 6.0.2
lz4: 4.3.2
Markdown: 3.8.2
MarkupSafe: 3.0.3
matplotlib: 3.10.7
matplotlib-inline: 0.2.2
mcp: 1.18.0
msgpack: 1.1.1
multidict: 6.7.1
narwhals: 2.22.1
ndindex: 1.10.1
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.14.1
numpy: 1.26.4
OpenMM: 8.4.0
openvr: 1.26.701
packaging: 25.0
ParmEd: 4.2.2
parso: 0.8.7
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 11.3.0
pip: 25.2
pkginfo: 1.12.1.2
platformdirs: 4.10.0
plotly: 6.8.0
pluggy: 1.6.0
prompt_toolkit: 3.0.52
propcache: 0.5.2
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pybind11: 3.0.1
pycollada: 0.8
pydantic: 2.13.4
pydantic-settings: 2.14.1
pydantic_core: 2.46.4
pydata-sphinx-theme: 0.18.0
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.5.1
pynrrd: 1.0.0
PyOpenGL: 3.1.10
PyOpenGL-accelerate: 3.1.10
pyopenxr: 1.1.4501
pyparsing: 3.3.2
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.10.2
PyQt6-Qt6: 6.10.2
PyQt6-WebEngine-commercial: 6.10.0
PyQt6-WebEngine-Qt6: 6.10.2
PyQt6_sip: 13.10.3
pytest: 9.0.3
pytest-cov: 7.1.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.2.2
python-multipart: 0.0.32
pyzmq: 27.1.0
qtconsole: 5.7.0
QtPy: 2.4.3
qtshim: 1.2.2
RandomWords: 0.4.0
referencing: 0.37.0
requests: 2.32.5
roman-numerals: 4.1.0
rpds-py: 2026.5.1
scipy: 1.14.0
setuptools: 80.9.0
sfftk-rw: 0.8.1
six: 1.17.0
snowballstemmer: 3.1.1
sortedcontainers: 2.4.0
soupsieve: 2.8.4
Sphinx: 9.0.4
sphinx-autodoc-typehints: 3.6.1
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
sse-starlette: 3.4.4
stack-data: 0.6.3
starlette: 1.3.0
superqt: 0.7.6
tables: 3.10.2
tcia_utils: 3.2.1
threadpoolctl: 3.6.0
tifffile: 2025.3.13
tinyarray: 1.2.5
tornado: 6.5.7
tqdm: 4.68.2
traitlets: 5.14.3
typing-inspection: 0.4.2
typing_extensions: 4.15.0
Unidecode: 1.4.0
urllib3: 2.7.0
uvicorn: 0.49.0
wcwidth: 0.8.1
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
yarl: 1.24.2
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| #20829 | fixed | ChimeraX UI widgets look bad on macOS 26 | ||
| Description |
ChimeraX versions since early July 2026 and also development builds on macOS 26.x have ugly button, table, header appearance on macOS 26. Probably our Github nightly builds which use macos_latest updated causing the newer daily builds to have this bad appearance. The bad appearance is probably what Apple intends on macOS. A way to restore the old appearance is to add the following to the ChimeraX Info.plist:
I'll attach an image showing the Models panel in the new flat, low contrast widgets versus the older widgets. |
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Query Language
query: TracLinks and the [[TicketQuery]] macro both use a mini “query language” for specifying query filters. Filters are separated by ampersands (&). Each filter consists of the ticket field name, an operator and one or more values. More than one value are separated by a pipe (|), meaning that the filter matches any of the values. To include a literal & or | in a value, escape the character with a backslash (\).
The available operators are:
= | the field content exactly matches one of the values |
~= | the field content contains one or more of the values |
^= | the field content starts with one of the values |
$= | the field content ends with one of the values |
All of these operators can also be negated:
!= | the field content matches none of the values |
!~= | the field content does not contain any of the values |
!^= | the field content does not start with any of the values |
!$= | the field content does not end with any of the values |
The date fields created and modified can be constrained by using the = operator and specifying a value containing two dates separated by two dots (..). Either end of the date range can be left empty, meaning that the corresponding end of the range is open. The date parser understands a few natural date specifications like "3 weeks ago", "last month" and "now", as well as Bugzilla-style date specifications like "1d", "2w", "3m" or "4y" for 1 day, 2 weeks, 3 months and 4 years, respectively. Spaces in date specifications can be omitted to avoid having to quote the query string.
created=2007-01-01..2008-01-01 | query tickets created in 2007 |
created=lastmonth..thismonth | query tickets created during the previous month |
modified=1weekago.. | query tickets that have been modified in the last week |
modified=..30daysago | query tickets that have been inactive for the last 30 days |
See also: TracTickets, TracReports, TracGuide, TicketQuery
Last modified
10 years ago
Last modified on Jan 4, 2017, 10:45:36 AM
Note:
See TracWiki
for help on using the wiki.
