Boltz structures distorted

[dominik.oberthuer@…]

The following bug report has been submitted:
Platform:        macOS-14.7.6-arm64-arm-64bit
ChimeraX Version: 1.10rc202506032143 (2025-06-03 21:43:02 UTC)
Description
I'm playing around with boltz in chimera and all the resulting molecules look strangely squeezed together. I tried with various proteins and it always looks completely messed up. If I do the same sequence in the boltz colab I do not have this issue.

OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M2 Pro
OpenGL vendor: Apple

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
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      Model Name: MacBook Pro
      Model Identifier: Mac14,9
      Model Number: Z17G0012PD/A
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      System Firmware Version: 11881.121.1
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[Tom Goddard]

Can you attach a Boltz predicted structure that appears distorted? I have not seen that in dozens of predictions. And could you tell me the sequences and ligands so I can run it myself to see if I also get a distorted structure?

We don't develop Boltz so it may be something that needs to be reported to the Boltz developers.

[dominik.oberthuer@…]

Hi Tom,

thanks for looking into it!

Attached are the Boltz-Colab structure and the chimera-boltz-Structure
and the sequence. The Colab-structure looks as expected (can be used for
molecular replacement).

I could also send you other examples, because it is happening for almost
all proteins so far.

Cheers, Dominik

protein1_colab.cif​

protein1_chimera.cif​

protein1.fasta​

[dominik.oberthuer@…]

Added by email2trac

[dominik.oberthuer@…]

Added by email2trac

[dominik.oberthuer@…]

Added by email2trac

[dominik.oberthuer@…]

Hi Tom,

this for example is lysozyme.

Cheers, Dominik

lysozyme_model_0.cif​

[dominik.oberthuer@…]

Added by email2trac

[Tom Goddard]

Hi Dominik,

Thanks for the files. My Mac M2 machine predicts your protein1.fasta sequence producing a very reasonable looking protein with ChimeraX Boltz. Your protein1_chimera.cif has all the residues within a few Angstroms of the origin. I'll attach the correct prediction.

So something is probably broken with your Boltz installation. Maybe the Boltz network parameters (in ~/.boltz) are corrupted. I suggest you reinstall Boltz. Delete directories ~/boltz and ~/.boltz that ChimeraX created, then start the ChimeraX Boltz tool (menu Tools / Structure Prediction / Boltz) and press the "Install Boltz" button that should appear at the bottom of the Boltz panel. After it has installed Boltz try your protein1.fasta prediction again.

Let me know if that fixes the problem.

Tom

[dominik.oberthuer@…]

Hi Tom,

thanks!

Will try that!

Dominik

[dominik.oberthuer@…]

Hi Tom,

I re-installed twice. Problem persists. Here is the install log:

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Dominik

On 10.06.25 10:44, Dominik Oberthuer wrote:
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>> #17915: Boltz structures distorted
>> -------------------------------------------+-------------------------
>>            Reporter:  dominik.oberthuer@\u2026   |      Owner:  Tom Goddard
>>                Type:  defect                |     Status: assigned
>>            Priority:  normal                |  Milestone:
>>           Component:  Structure Prediction  |    Version:
>>          Resolution:                        |   Keywords:
>>          Blocked By:                        |   Blocking:
>> Notify when closed:                        |   Platform:  all
>>             Project:  ChimeraX              |
>> -------------------------------------------+-------------------------
>> Comment (by Tom Goddard):
>>
>>   Hi Dominik,
>>
>>     Thanks for the files.  My Mac M2 machine predicts your 
>> protein1.fasta
>>   sequence producing a very reasonable looking protein with ChimeraX 
>> Boltz.
>>   Your protein1_chimera.cif has all the residues within a few 
>> Angstroms of
>>   the origin. I'll attach the correct prediction.
>>
>>     So something is probably broken with your Boltz installation.  
>> Maybe the
>>   Boltz network parameters (in ~/.boltz) are corrupted.  I suggest you
>>   reinstall Boltz.  Delete directories ~/boltz and ~/.boltz that 
>> ChimeraX
>>   created, then start the ChimeraX Boltz tool (menu Tools / Structure
>>   Prediction / Boltz) and press the "Install Boltz" button that should
>>   appear at the bottom of the Boltz panel.  After it has installed 
>> Boltz try
>>   your protein1.fasta prediction again.
>>
>>     Let me know if that fixes the problem.
>>
>>       Tom
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[Tom Goddard]

Ok, so reinstalling boltz did not help. There is likely something installed on your computer that is effecting Boltz and messing up the predictions. No one else has reported this problem and there are probably at least 100 Mac ChimeraX Boltz users. Because the possiblities are so numerous it will be hard to figure out.

The next step would be to zip the entire directory of a ChimeraX Boltz run and send that. You also can look at the files stdout and stderr in that directory to see if you spot anything unusual, although there is lots of junk output so it will probably be hard for you to tell if something is unusual.

Other ideas for why it is broken for you include: You have some ChimeraX extension installed that installed a Python package that boltz uses but is a different version and breaks boltz. You have environment variables set for example for PyTorch by other machine learning packages and those break boltz.

[dominik.oberthuer@…]

Dear Tom,

I upgraded my Mac to macOs 15.5 and installed an empty version of 
ChimeraX (latest built, no plug-ins) and it works.

Cheers, Dominik

On 10.06.25 19:51, ChimeraX wrote:
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[Tom Goddard]

Glad you got it to work. Maybe there was a conflict between a ChimeraX extension you installed and Boltz. I think it is very unlikely that updating to macOS 15.5 fixed it.