Handle Boltz prediction out of memory

[goddard@…]

The following bug report has been submitted:
Platform:        macOS-15.4.1-arm64-arm-64bit
ChimeraX Version: 1.10.dev202504050547 (2025-04-05 05:47:37 UTC)
Description
This is the boltz prediction error when it runs out of memory.  Apparently the boltz process exits with exit code 0 and the stderr contains no error indication and stdout contains a "ran out of memory, skipping batch" warning.


Log:
UCSF ChimeraX version: 1.10.dev202504050547 (2025-04-05)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 9moj format mmcif fromDatabase pdb

9moj title:  
Saccharolobus solfataricus GINS tetramer [more info...]  
  
Chain information for 9moj #1  
---  
Chain | Description | UniProt  
A B | SsoGINS51 | Q97Z82_SACS2 1-151  
C D | GINS subunit domain-containing protein | D0KTH8_SACS9 1-179  
  

> ui tool show Boltz

> boltz predict protein /A protein /B protein /C protein /D name 9moj

Running Boltz prediction of 2 proteins with 660 residues  
Using cached multiple sequence alignment
/Users/goddard/Downloads/ChimeraX/BoltzMSA/9moj  
Please cite Boltz-1 Democratizing Biomolecular Interaction Modeling. BioRxiv
https://doi.org/10.1101/2024.11.19.624167 if you use these predictions.  
Boltz prediction completed in 218 seconds  

> open /Users/goddard/Desktop/boltz_9moj_1/9moj_model_0.cif logInfo false

> matchmaker #2 to #1 logParameters false

Computing secondary structure  
Matchmaker 9moj, chain C (#1) with 9moj_model_0.cif, chain C (#2), sequence
alignment score = 868.2  
RMSD between 151 pruned atom pairs is 1.101 angstroms; (across all 176 pairs:
1.517)  
  

> color bfactor #2 palette alphafold

5408 atoms, 660 residues, atom bfactor range 35.7 to 98.2  

> close

> open 9h1k

Summary of feedback from opening 9h1k fetched from pdb  
---  
note | Fetching compressed mmCIF 9h1k from http://files.rcsb.org/download/9h1k.cif  
  
9h1k title:  
RlmR 23S rRNA methyltransferase from Thermus thermophilus in complex with rRNA
and S-adenosyl-L-homocysteine (SAH) [more info...]  
  
Chain information for 9h1k #1  
---  
Chain | Description | UniProt  
A B | 23S rRNA methyltransferase | Q72GY4_THET2 1-260  
C | RNA (59-MER) |   
  
Non-standard residues in 9h1k #1  
---  
SAH — S-adenosyl-L-homocysteine  
  

> boltz predict protein /A protein /B rna /C ligandCcd SAH(2) name 9h1k

Running Boltz prediction of protein with 560 residues, nucleic acid sequence
with 59 residues, 2 ligands SAH (2)  
Using multiple sequence alignment server https://api.colabfold.com  
Boltz prediction completed in 274 seconds  

> open /Users/goddard/Desktop/boltz_9h1k/9h1k_model_0.cif logInfo false

> matchmaker #2 to #1 logParameters false

Computing secondary structure  
Matchmaker 9h1k, chain A (#1) with 9h1k_model_0.cif, chain A (#2), sequence
alignment score = 1375.3  
RMSD between 260 pruned atom pairs is 0.651 angstroms; (across all 261 pairs:
0.662)  
  

> color bfactor #2 palette alphafold

5575 atoms, 621 residues, atom bfactor range 12.7 to 94.4  

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> close

> open 1hho format mmcif fromDatabase pdb

1hho title:  
Structure of human oxyhaemoglobin At 2.1 angstroms resolution [more info...]  
  
Chain information for 1hho #1  
---  
Chain | Description | UniProt  
A | HEMOGLOBIN A (OXY) (ALPHA CHAIN) | HBA_HUMAN 1-141  
B | HEMOGLOBIN A (OXY) (BETA CHAIN) | HBB_HUMAN 1-146  
  
Non-standard residues in 1hho #1  
---  
HEM — protoporphyrin IX containing Fe (HEME)  
OXY — oxygen molecule  
PO4 — phosphate ion  
  
1hho mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  

> boltz predict protein /A protein /B ligandCcd PO4(1),HEM(2),OXY(2) name 1hho

Running Boltz prediction of 2 proteins with 287 residues, 5 ligands HEM (2),
OXY (2), PO4  
Using cached multiple sequence alignment
/Users/goddard/Downloads/ChimeraX/BoltzMSA/1hho  
Boltz prediction completed in 126 seconds  

> open /Users/goddard/Desktop/boltz_1hho/1hho_model_0.cif logInfo false

> matchmaker #2 to #1 logParameters false

Computing secondary structure  
Matchmaker 1hho, chain B (#1) with 1hho_model_0.cif, chain B (#2), sequence
alignment score = 749.5  
RMSD between 146 pruned atom pairs is 0.424 angstroms; (across all 146 pairs:
0.424)  
  

> color bfactor #2 palette alphafold

2285 atoms, 292 residues, atom bfactor range 35.2 to 99  

> close

> open 8sa0

Summary of feedback from opening 8sa0 fetched from pdb  
---  
notes | Fetching compressed mmCIF 8sa0 from http://files.rcsb.org/download/8sa0.cif  
Fetching CCD I6H from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/H/I6H/I6H.cif  
  
8sa0 title:  
CryoEM structure of P-Glycoprotein in occluded closed state under continuous
turnover conditions with verapamil [more info...]  
  
Chain information for 8sa0 #1  
---  
Chain | Description | UniProt  
A | ATP-dependent translocase ABCB1 | MDR1_HUMAN 1-1274  
  
Non-standard residues in 8sa0 #1  
---  
ATP — adenosine-5'-triphosphate  
I6H — Dexverapamil  
MG — magnesium ion  
  

> boltz predict protein /A ligandCcd ATP(2),MG(2),I6H(1) name 8sa0

Running Boltz prediction of protein with 1274 residues, 5 ligands ATP (2),
I6H, MG (2)  
Using multiple sequence alignment server https://api.colabfold.com  
Boltz prediction completed in 1153 seconds  
Traceback (most recent call last):  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/predict.py", line 437, in _check_process_completion  
self._process_completed(stdout, stderr)  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/predict.py", line 455, in _process_completed  
self._open_predictions()  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/predict.py", line 485, in _open_predictions  
self._copy_predictions()  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/predict.py", line 524, in _copy_predictions  
for filename in listdir(pdir):  
^^^^^^^^^^^^^  
FileNotFoundError: [Errno 2] No such file or directory:
'/Users/goddard/Desktop/boltz_8sa0/boltz_results_8sa0/predictions/8sa0'  
  
Error processing trigger "new frame":  
FileNotFoundError: [Errno 2] No such file or directory:
'/Users/goddard/Desktop/boltz_8sa0/boltz_results_8sa0/predictions/8sa0'  
  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/predict.py", line 524, in _copy_predictions  
for filename in listdir(pdir):  
^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M1 Max
OpenGL vendor: Apple

Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,2
      Model Number: MK1H3LL/A
      Chip: Apple M1 Max
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 32 GB
      System Firmware Version: 11881.101.1
      OS Loader Version: 11881.101.1

Software:

    System Software Overview:

      System Version: macOS 15.4.1 (24E263)
      Kernel Version: Darwin 24.4.0
      Time since boot: 10 days, 23 hours, 5 minutes

Graphics/Displays:

    Apple M1 Max:

      Chipset Model: Apple M1 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 32
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3456 x 2234 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal


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[Tom Goddard]

Fixed.

Added error message when "ran out of memory" detected in stdout.