boltz predict: RuntimeError

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-15.6-arm64-arm-64bit
ChimeraX Version: 1.12.dev202601080343 (2026-01-08 03:43:52 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  

> open calc_level_ChimeraX/calc_level.py

Error running startup command 'open calc_level_ChimeraX/calc_level.py ': No
such file/path: calc_level_ChimeraX/calc_level.py  
UCSF ChimeraX version: 1.12.dev202601080343 (2026-01-08)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> ui tool show Boltz

Populating font family aliases took 147 ms. Replace uses of missing font
family "-webkit-standard" with one that exists to avoid this cost.  

> boltz predict protein
> MLANENSLLTMFRELGSGKLPLQIEQFERGKTIFFPGDPAERVYLLVKGAVKLSRVYESGEEITVALLRENSVFGVLSLLTGQRSDRFYHAVAFTPVQLFSVPIEFMQKALIERPELANVMLQGLSSRILQTEMMIETLAHRDMGSRLVSFLLILCRDFGIPSPDGITIDLKLSHQAIAEAIGSTRVTVTRLLGDLRESKLIAIHKKRITVFNPVALSQQFS
> name ntca useServer true serverHost 213.173.109.9 serverPort 11329

Running Boltz prediction of protein with 222 residues on gpu  
Using cached multiple sequence alignment
/Users/justinsim/Downloads/ChimeraX/BoltzMSA/ntca  
Sending job request to server (656449 bytes)  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/boltz_gui.py", line 595, in _predict  
self._run_prediction(options = ' '.join(options))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/boltz_gui.py", line 612, in _run_prediction  
br = run(self.session, cmd)  
^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/predict.py", line 87, in boltz_predict  
br.start()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/predict.py", line 559, in start  
self._run_boltz()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/predict.py", line 669, in _run_boltz  
self._run_on_server()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/predict.py", line 706, in _run_on_server  
job_id = predict_on_server(run_dir, self._server_host, self._server_port)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/server.py", line 298, in predict_on_server  
raise RuntimeError(msg.decode('utf-8'))  
RuntimeError  
  
RuntimeError  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/server.py", line 298, in predict_on_server  
raise RuntimeError(msg.decode('utf-8'))  
  
See log for complete Python traceback.  
  

> boltz predict protein
> MLANENSLLTMFRELGSGKLPLQIEQFERGKTIFFPGDPAERVYLLVKGAVKLSRVYESGEEITVALLRENSVFGVLSLLTGQRSDRFYHAVAFTPVQLFSVPIEFMQKALIERPELANVMLQGLSSRILQTEMMIETLAHRDMGSRLVSFLLILCRDFGIPSPDGITIDLKLSHQAIAEAIGSTRVTVTRLLGDLRESKLIAIHKKRITVFNPVALSQQFS
> name ntca useServer true serverHost 213.173.109.9 serverPort 11329

You need to install Boltz by pressing the "Install Boltz" button on the
ChimeraX Boltz user interface, or using the ChimeraX command "boltz install".
If you already have Boltz installed, you can set the Boltz installation
location in the user interface under Options, or use the installLocation
option of the ChimeraX boltz command "boltz predict ... installLocation
/path/to/boltz"  

> boltz predict protein
> MLANENSLLTMFRELGSGKLPLQIEQFERGKTIFFPGDPAERVYLLVKGAVKLSRVYESGEEITVALLRENSVFGVLSLLTGQRSDRFYHAVAFTPVQLFSVPIEFMQKALIERPELANVMLQGLSSRILQTEMMIETLAHRDMGSRLVSFLLILCRDFGIPSPDGITIDLKLSHQAIAEAIGSTRVTVTRLLGDLRESKLIAIHKKRITVFNPVALSQQFS
> name ntca useServer true serverHost 213.173.109.9 serverPort 11329

You need to install Boltz by pressing the "Install Boltz" button on the
ChimeraX Boltz user interface, or using the ChimeraX command "boltz install".
If you already have Boltz installed, you can set the Boltz installation
location in the user interface under Options, or use the installLocation
option of the ChimeraX boltz command "boltz predict ... installLocation
/path/to/boltz"  

> boltz predict protein
> MLANENSLLTMFRELGSGKLPLQIEQFERGKTIFFPGDPAERVYLLVKGAVKLSRVYESGEEITVALLRENSVFGVLSLLTGQRSDRFYHAVAFTPVQLFSVPIEFMQKALIERPELANVMLQGLSSRILQTEMMIETLAHRDMGSRLVSFLLILCRDFGIPSPDGITIDLKLSHQAIAEAIGSTRVTVTRLLGDLRESKLIAIHKKRITVFNPVALSQQFS
> name ntca useServer true serverHost 213.173.109.9 serverPort 11329

You need to install Boltz by pressing the "Install Boltz" button on the
ChimeraX Boltz user interface, or using the ChimeraX command "boltz install".
If you already have Boltz installed, you can set the Boltz installation
location in the user interface under Options, or use the installLocation
option of the ChimeraX boltz command "boltz predict ... installLocation
/path/to/boltz"  

> boltz predict protein
> MLANENSLLTMFRELGSGKLPLQIEQFERGKTIFFPGDPAERVYLLVKGAVKLSRVYESGEEITVALLRENSVFGVLSLLTGQRSDRFYHAVAFTPVQLFSVPIEFMQKALIERPELANVMLQGLSSRILQTEMMIETLAHRDMGSRLVSFLLILCRDFGIPSPDGITIDLKLSHQAIAEAIGSTRVTVTRLLGDLRESKLIAIHKKRITVFNPVALSQQFS
> name ntca useServer true serverHost 213.173.109.9 serverPort 30172

You need to install Boltz by pressing the "Install Boltz" button on the
ChimeraX Boltz user interface, or using the ChimeraX command "boltz install".
If you already have Boltz installed, you can set the Boltz installation
location in the user interface under Options, or use the installLocation
option of the ChimeraX boltz command "boltz predict ... installLocation
/path/to/boltz"  

> boltz predict protein
> MLANENSLLTMFRELGSGKLPLQIEQFERGKTIFFPGDPAERVYLLVKGAVKLSRVYESGEEITVALLRENSVFGVLSLLTGQRSDRFYHAVAFTPVQLFSVPIEFMQKALIERPELANVMLQGLSSRILQTEMMIETLAHRDMGSRLVSFLLILCRDFGIPSPDGITIDLKLSHQAIAEAIGSTRVTVTRLLGDLRESKLIAIHKKRITVFNPVALSQQFS
> name ntca useServer true serverHost 213.173.109.9 serverPort 30172

Running Boltz prediction of protein with 222 residues on gpu  
Using cached multiple sequence alignment
/Users/justinsim/Downloads/ChimeraX/BoltzMSA/ntca  
Sending job request to server (656449 bytes)  
Could not connect to 213.173.109.9:30172, connection refused  

> boltz predict protein
> MLANENSLLTMFRELGSGKLPLQIEQFERGKTIFFPGDPAERVYLLVKGAVKLSRVYESGEEITVALLRENSVFGVLSLLTGQRSDRFYHAVAFTPVQLFSVPIEFMQKALIERPELANVMLQGLSSRILQTEMMIETLAHRDMGSRLVSFLLILCRDFGIPSPDGITIDLKLSHQAIAEAIGSTRVTVTRLLGDLRESKLIAIHKKRITVFNPVALSQQFS
> name ntca useServer true serverHost 213.173.109.9 serverPort 30172

Running Boltz prediction of protein with 222 residues on gpu  
Using cached multiple sequence alignment
/Users/justinsim/Downloads/ChimeraX/BoltzMSA/ntca  
Sending job request to server (656450 bytes)  
Could not connect to 213.173.109.9:30172, connection refused  

> boltz predict protein
> MLANENSLLTMFRELGSGKLPLQIEQFERGKTIFFPGDPAERVYLLVKGAVKLSRVYESGEEITVALLRENSVFGVLSLLTGQRSDRFYHAVAFTPVQLFSVPIEFMQKALIERPELANVMLQGLSSRILQTEMMIETLAHRDMGSRLVSFLLILCRDFGIPSPDGITIDLKLSHQAIAEAIGSTRVTVTRLLGDLRESKLIAIHKKRITVFNPVALSQQFS
> name ntca useServer true serverHost 213.173.109.9 serverPort 11329

Running Boltz prediction of protein with 222 residues on gpu  
Using cached multiple sequence alignment
/Users/justinsim/Downloads/ChimeraX/BoltzMSA/ntca  
Sending job request to server (656450 bytes)  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/boltz_gui.py", line 595, in _predict  
self._run_prediction(options = ' '.join(options))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/boltz_gui.py", line 612, in _run_prediction  
br = run(self.session, cmd)  
^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/predict.py", line 87, in boltz_predict  
br.start()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/predict.py", line 559, in start  
self._run_boltz()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/predict.py", line 669, in _run_boltz  
self._run_on_server()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/predict.py", line 706, in _run_on_server  
job_id = predict_on_server(run_dir, self._server_host, self._server_port)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/server.py", line 298, in predict_on_server  
raise RuntimeError(msg.decode('utf-8'))  
RuntimeError  
  
RuntimeError  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/server.py", line 298, in predict_on_server  
raise RuntimeError(msg.decode('utf-8'))  
  
See log for complete Python traceback.  
  

> open 4v6i format mmcif fromDatabase pdb

4v6i title:  
Localization of the small subunit ribosomal proteins into a 6.1 A cryo-EM map
of Saccharomyces cerevisiae translating 80S ribosome [more info...]  
  
Chain information for 4v6i #1  
---  
Chain | Description | UniProt  
AA | 40S ribosomal protein rpS0 (S2p) | RSSA1_YEAST 1-252  
AB | 40S ribosomal protein rpS3 (S3p) | RS3_YEAST 1-240  
AC | 40S ribosomal protein rpS9 (S4p) | RS9A_YEAST 1-197  
AD | 40S ribosomal protein rpS4 (S4e) | RS4_YEAST 1-261  
AE | 40S ribosomal protein rpS2 (S5p) | RS2_YEAST 1-254  
AF | 40S ribosomal protein rpS5 (S7p) | RS5_YEAST 1-225  
AG | 40S ribosomal protein rpS7 (S7e) |   
AH | 40S ribosomal protein rpS22 (S8p) | RS22A_YEAST 1-130  
AI | 40S ribosomal protein rpS16 (S9p) | RS16_YEAST 1-143  
AJ | 40S ribosomal protein rpS20 (S10p) | RS20_YEAST 1-121  
AK | 40S ribosomal protein rpS14 (S11p) | RS14A_YEAST 1-137  
AL | 40S ribosomal protein rpS23 (S12p) | RS23_YEAST 1-145  
AM | 40S ribosomal protein rpS18 (S13p) | RS18_YEAST 1-146  
AN | 40S ribosomal protein rpS29 (S14p) | RS29A_YEAST 1-56  
AO | 40S ribosomal protein rpS13 (S15p) | RS13_YEAST 1-151  
AP | 40S ribosomal protein rpS11 (S17p) | RS11_YEAST 1-156  
AQ | 40S ribosomal protein rpS17 (S17e) | RS17A_YEAST 1-136  
AR | 40S ribosomal protein rpS15 (S19p) | RS15_YEAST 1-142  
AS | 40S ribosomal protein rpS19 (S19e) | RS19A_YEAST 1-144  
AT | 40S ribosomal protein rpS21 (S21e) | RS21A_YEAST 1-87  
AU | 40S ribosomal protein S24 | RS24_YEAST 1-135  
AV | 40S ribosomal protein rpS25 (S25e) | RS25A_YEAST 1-108  
AW | 40S ribosomal protein rpS26 (S26e) |   
AX | 40S ribosomal protein rpS27 (S27e) | RS27_YEAST 1-82  
AY | 40S ribosomal protein rpS28 (S28e) | RS28A_YEAST 1-67  
AZ | 40S ribosomal protein rpS30 (S30e) | RS30_YEAST 1-63  
Aa | 40S ribosomal protein RACK1 (RACK1) | GBLP_YEAST 1-319  
Ab | Unknown 40S ribosomal protein XS1 |   
Ac | Unknown 40S ribosomal protein XS2 |   
BA | 60S ribosomal protein rpL1 (L1p) | RL1_YEAST 1-217  
BB | 60S ribosomal protein rpL2 (L2p) | RL2_YEAST 1-254  
BC | 60S ribosomal protein rpL3 (L3p) | RL3_YEAST 1-387  
BD | 60S ribosomal protein rpL4 (L4p) | RL4A_YEAST 1-362  
BE | 60S ribosomal protein rpL11 (L5p) | RL11A_YEAST 1-174  
BF | 60S ribosomal protein rpL9 (L6p) | RL9A_YEAST 1-191  
BG | 60S ribosomal protein rpL6 (L6e) | RL6A_YEAST 1-176  
BH | 60S ribosomal protein rpL8 (L7ae) | RL8A_YEAST 1-256  
BI | 60S ribosomal protein rpL10 (L10e) | RL10_YEAST 1-221  
BJ | 60S ribosomal protein rpL12 (L11p) | RL12_YEAST 1-165  
BK | 60S ribosomal protein rpL16 (L13p) | RL16A_YEAST 1-199  
BL | 60S ribosomal protein rpL13 (L13e) |   
BM | 60S ribosomal protein rpL23 (L14p) | RL23_YEAST 1-137  
BN | 60S ribosomal protein rpL14 (L14e) | RL14A_YEAST 1-138  
BO | 60S ribosomal protein rpL28 (L15p) | RL28_YEAST 1-149  
BP | 60S ribosomal protein rpL15 (L15e) | RL15A_YEAST 1-204  
BQ | 60S ribosomal protein rpL5 (L18p) | RL5_YEAST 1-297  
BR | 60S ribosomal protein rpL18 (L18e) | RL18_YEAST 1-186  
BS | 60S ribosomal protein rpL20 (L18ae) | Q0JJA0_ORYSJ 1-167  
BT | 60S ribosomal protein rpL19 (L19e) | RL19_YEAST 1-189  
BU | 60S ribosomal protein rpL21 (L21e) | RL21A_YEAST 1-160  
BV | 60S ribosomal protein rpL17 (L22p) | RL17A_YEAST 1-170  
BW | 60S ribosomal protein rpL22 (L22e) | RL22A_YEAST 1-121  
BX | 60S ribosomal protein rpL25 (L23p) | RL25_YEAST 1-142  
BY | 60S ribosomal protein rpL26 (L24p) | RL26A_YEAST 1-123  
BZ | 60S ribosomal protein rpL24 (L24e) | RL24A_YEAST 1-155  
Ba | 60S ribosomal protein rpL27 (L27e) | RL27A_YEAST 1-136  
Bc | 60S ribosomal protein rpL35 (L29p) | RL35_YEAST 1-120  
Bd | 60S ribosomal protein rpL29 (L29e) | RL29_YEAST 1-59  
Be | 60S ribosomal protein rpL7 (L30p) | RL7A_YEAST 1-244  
Bf | 60S ribosomal protein rpL30 (L30e) | RL30_YEAST 1-105  
Bg | 60S ribosomal protein rpL31 (L31e) | RL31A_YEAST 1-113  
Bh | 60S ribosomal protein pL32 (L32e) | RL32_YEAST 1-130  
Bi | 60S ribosomal protein rpL34 (L34e) | RL34A_YEAST 1-118  
Bj | 60S ribosomal protein rpL33 (L35ae) | RL33A_YEAST 1-107  
Bk | 60S ribosomal protein rpL36 (L36e) | RL36A_YEAST 1-100  
Bl | 60S ribosomal protein rpL37 (L37e) | RL37A_YEAST 1-88  
Bm | 60S ribosomal protein rpL43 (L37ae) | RL43_YEAST 1-92  
Bn | 60S ribosomal protein rpL38 (L38e) | RL38_YEAST 1-78  
Bo | 60S ribosomal protein rpL39 (L39e) | RL39_YEAST 1-51  
Bp | 60S ribosomal protein rpL40 (L40e) | RL401_YEAST 1-52  
Bq | 60S ribosomal protein rpL41 (L41e) | RL41_YEAST 1-25  
Br | 60S ribosomal protein rpL42 (L44e) | RL44_YEAST 1-106  
Bs | 60S acidic ribosomal protein rpP0 (L10P) | RLA0_YEAST 1-312  
Bt Bu | 60S acidic ribosomal protein rpP11 (P1) | RLA1_YEAST 1-106  
Bv Bw | 60S acidic ribosomal protein (P2) | RLA2_YEAST 1-106  
Bx By | Unknown protein |   
Bz | Unknown protein |   
CA | 18S rRNA |   
CB | P-SITE TRNA ASP |   
CC | MRNA, RNA (5'-R(P*AP*AP*AP*AP*GP*AP*CP*UP*UP*CP*A)-3') |   
DA | 25S rRNA |   
DB | 5.8S rRNA |   
DC | 5S rRNA |   
  

> boltz predict protein
> MLANENSLLTMFRELGSGKLPLQIEQFERGKTIFFPGDPAERVYLLVKGAVKLSRVYESGEEITVALLRENSVFGVLSLLTGQRSDRFYHAVAFTPVQLFSVPIEFMQKALIERPELANVMLQGLSSRILQTEMMIETLAHRDMGSRLVSFLLILCRDFGIPSPDGITIDLKLSHQAIAEAIGSTRVTVTRLLGDLRESKLIAIHKKRITVFNPVALSQQFS
> name ntca useServer true serverHost 213.173.109.9 serverPort 11329

Running Boltz prediction of protein with 222 residues on gpu  
Using cached multiple sequence alignment
/Users/justinsim/Downloads/ChimeraX/BoltzMSA/ntca  
Sending job request to server (656450 bytes)  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/boltz_gui.py", line 595, in _predict  
self._run_prediction(options = ' '.join(options))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/boltz_gui.py", line 612, in _run_prediction  
br = run(self.session, cmd)  
^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/predict.py", line 87, in boltz_predict  
br.start()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/predict.py", line 559, in start  
self._run_boltz()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/predict.py", line 669, in _run_boltz  
self._run_on_server()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/predict.py", line 706, in _run_on_server  
job_id = predict_on_server(run_dir, self._server_host, self._server_port)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/server.py", line 298, in predict_on_server  
raise RuntimeError(msg.decode('utf-8'))  
RuntimeError  
  
RuntimeError  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/server.py", line 298, in predict_on_server  
raise RuntimeError(msg.decode('utf-8'))  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M2
OpenGL vendor: Apple

Python: 3.11.9
Locale: en_US.UTF-8
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Air
      Model Identifier: Mac14,2
      Model Number: MLXW3LL/A
      Chip: Apple M2
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 8 GB
      System Firmware Version: 11881.140.96
      OS Loader Version: 11881.140.96

Software:

    System Software Overview:

      System Version: macOS 15.6 (24G84)
      Kernel Version: Darwin 24.6.0
      Time since boot: 1 day, 17 hours, 24 minutes

Graphics/Displays:

    Apple M2:

      Chipset Model: Apple M2
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 8
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina Display
          Resolution: 2560 x 1664 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    aiohappyeyeballs: 2.6.1
    aiohttp: 3.13.1
    aiosignal: 1.4.0
    alabaster: 1.0.0
    annotated-types: 0.7.0
    anyio: 4.12.1
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.1
    attrs: 25.4.0
    babel: 2.17.0
    beautifulsoup4: 4.13.5
    blockdiag: 3.0.0
    blosc2: 3.12.2
    build: 1.3.0
    certifi: 2025.7.14
    cftime: 1.6.5
    charset-normalizer: 3.4.4
    ChimeraX-AddCharge: 1.5.20
    ChimeraX-AddH: 2.2.8
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 3.1.1
    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: 1.61.5
    ChimeraX-AtomicLibrary: 14.2.3
    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
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.3
    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.dev202601080343
    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: 1.1.4
    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
    ChimeraX-Label: 1.3
    ChimeraX-LightingGUI: 1.0
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.2
    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-MatchMaker: 2.2.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MCPServer: 0.1.0
    ChimeraX-MDcrds: 2.17.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-Minimize: 1.3.3
    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
    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: 1.15.2
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.12
    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: 1.4.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.7
    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: 3.5.10
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17.3
    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: 1.19.2
    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: 2.5.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.50
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDock: 1.5.2
    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: 8.3.1
    colorama: 0.4.6
    comm: 0.2.3
    contourpy: 1.3.3
    coverage: 7.13.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.1.4
    debugpy: 1.8.19
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.1
    filelock: 3.19.1
    fonttools: 4.61.1
    frozenlist: 1.8.0
    funcparserlib: 2.0.0a0
    glfw: 2.10.0
    grako: 3.16.5
    h11: 0.16.0
    h5py: 3.15.1
    html2text: 2025.4.15
    httpcore: 1.0.9
    httpx: 0.28.1
    httpx-sse: 0.4.3
    idna: 3.11
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.3.0
    ipykernel: 7.1.0
    ipython: 9.9.0
    ipython_pygments_lexers: 1.1.1
    ipywidgets: 8.1.8
    jedi: 0.19.2
    Jinja2: 3.1.6
    jsonschema: 4.26.0
    jsonschema-specifications: 2025.9.1
    jupyter_client: 8.7.0
    jupyter_core: 5.9.1
    jupyterlab_widgets: 3.0.16
    kiwisolver: 1.4.9
    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: 0.2.1
    mcp: 1.18.0
    msgpack: 1.1.1
    multidict: 6.7.0
    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: 0.8.5
    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: 4.5.1
    pluggy: 1.6.0
    prompt_toolkit: 3.0.52
    propcache: 0.4.1
    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: 2.12.5
    pydantic-settings: 2.12.0
    pydantic_core: 2.41.5
    pydicom: 2.4.4
    Pygments: 2.18.0
    pynmrstar: 3.3.6
    pynrrd: 1.0.0
    PyOpenGL: 3.1.10
    PyOpenGL-accelerate: 3.1.10
    pyopenxr: 1.1.4501
    pyparsing: 3.3.1
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.9.1
    PyQt6-Qt6: 6.9.2
    PyQt6-WebEngine-commercial: 6.9.0
    PyQt6-WebEngine-Qt6: 6.9.2
    PyQt6_sip: 13.10.2
    pytest: 9.0.2
    pytest-cov: 7.0.0
    python-dateutil: 2.9.0.post0
    python-dotenv: 1.2.1
    python-multipart: 0.0.21
    pytz: 2025.2
    pyzmq: 27.1.0
    qtconsole: 5.7.0
    QtPy: 2.4.3
    qtshim: 1.2
    RandomWords: 0.4.0
    referencing: 0.37.0
    requests: 2.32.5
    roman-numerals: 4.1.0
    roman-numerals-py: 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: 2.8.1
    Sphinx: 8.2.3
    sphinx-autodoc-typehints: 3.2.0
    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: 3.1.2
    stack-data: 0.6.3
    starlette: 0.50.0
    superqt: 0.7.6
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.5
    tornado: 6.5.4
    traitlets: 5.14.3
    typing-inspection: 0.4.2
    typing_extensions: 4.15.0
    tzdata: 2025.3
    urllib3: 2.6.3
    uvicorn: 0.40.0
    wcwidth: 0.2.14
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.15
    yarl: 1.22.0

[Tom Goddard]

Duplicate of #19698