Detect incomplete Boltz installation running predictions

[Tom Goddard]

Connor Ferguson wrote on the ChimeraX mailing list about Boltz failing to prediction due to ALA.cif template file missing. This is no doubt because installation was not completed.

During Boltz install write a sentinel file INSTALL_STARTED and remove it on completion and when running Boltz check if that file exists and give an error about a partial installation if it is found.

[Tom Goddard]

Begin forwarded message:

From: "Ferguson, Connor"
Subject: Re: [chimerax-users] Using Blotz in ChimeraX 1.12 issue
Date: August 19, 2026 at 2:50:43 PM PDT
To: Tom Goddard

I attempted to uninstall and reinstall both Boltz and ChimeraX 1.11 and 1.12 (I had hoped an older model would work). I got the following error again during the download: "Downloading Boltz model parameters and CCD database to ~/.boltz or creating CCD atom counts file failed". I went ahead and also attached the entire log for a time it seemed to work in downloading but threw the same ALA absence error. Any assistance or guidance is greatly appreciated.

Connor Ferguson
Graduate Student
Department of Biological Sciences
University of Tulsa, OK

From: Tom Goddard
Sent: Wednesday, August 19, 2026 7:21 AM
To: Ferguson, Connor
Cc: chimerax-users@…
Subject: Re: [chimerax-users] Using Blotz in ChimeraX 1.12 issue

Hi Connor,

When ChimeraX installs Boltz it downloads the PDB Chemical Component Dictionary (CCD) and puts it in directory ~/.boltz/mols. That contains templates for about 50,000 PDB residues including the standard amino acids. If you quit ChimeraX before it completes that part of the installation then the templates won't be available and it will fail with the kind of error you saw "ALA" (alanine) not found. The full Boltz installation can take 30 or more minutes depending on network speed. In the last step it says "Downloading Boltz model parameters (4 GB) and chemical component database (1.8 GB) to ~/.boltz" and when that completes successfully the ChimeraX Log panel will say "Successfully installed Boltz program and neural net weights.". You may need to delete the ~/.boltz/mols.tar file and ~/.boltz/mols directory if partial versions were installed and delete ~/boltz22 and try reinstalling and make sure it fully completes before quitting ChimeraX. I plan to improve the ChimeraX Boltz install so it detects when the installation is incomplete and explains how to fix it.

The fact that you get an error message about amino acid ALA not found when you are only predicting an RNA, not a protein, seems like a problem. It could be that Boltz always loads the standard 20 amino acids, I'm not sure. Another way to get that error is if you pasted your RNA sequence into the ChimeraX Boltz entry when the menu above the entry field said "protein sequence". You have to choose "RNA sequence" from the menu before pasting the RNA sequence. ChimeraX has no way of knowing if "AGCCGAAG" is a protein or an amino acid sequence, so you have to choose the menu entry to tell it what type of sequence is being pasted.

Tom

On Aug 18, 2026, at 3:59 PM, Ferguson, Connor via ChimeraX-users wrote:

Hello,

I am attempting to examine the interaction of a viral RdRp with single stranded RNA. I downloaded Blotz as prompted, but it ran into an error downloading. I deleted the folder and redownloaded it with seemingly no issue. However, When I put in the RNA alone in an attempt to also get the secondary structure of the ssRNA, or when I put both the RNA and the predicted protein structure, I get the error message "Your Boltz installation does not have a molecular structure for PDB chemical component dictionary code ALA either because that code is new or is mistyped. You can try specifying that ligand using a SMILES string from ​https://www.rcsb.org/ligand/ALA instead of using its CCD code." I do not know why this message is occurring because even with the RNA alone this occurs (which the RNA should not care about alanine?). Any assistance or guidance on this matter would be greatly appreciated.

Connor Ferguson
Graduate Student, Virology Lab
Teaching Assistant
Department of Biological Sciences
The University of Tulsa

[Tom Goddard]

I've attached the Log Connor sent when Python tar extractall fails on mols.tar (CCD entries) with FileNotFoundError.

From: Tom Goddard
Subject: Re: [chimerax-users] Using Blotz in ChimeraX 1.12 issue
Date: August 20, 2026 at 3:24:19 PM PDT
To: "Ferguson, Connor"

Hi Connor,

The error in the ChimeraX Log you sent when installing Boltz says

FileNotFoundError: [Errno 2] No such file or directory: 'C:
Users
conno
.boltz
mols
AUX.pkl'

while it is using Python to extract the mols.tar file. I'm not sure how this error can occur unless the .boltz/mols directory got deleted while it was extracting the files. I am on vacation the past week and for one more week and don't have access to a Windows computer so I can't test until I return after August 26. You might try again deleting ~/.boltz and ~/boltz22. Make sure ~/.boltz really gets deleted. Note the "." in the directory name ~/.boltz. I have never seen this error before so I suspect it is some problem specific to your computer or that the ~/.boltz directory was not deleted and somehow prevented the mols.tar file from being extracted.

Tom

[Tom Goddard]

Log file from Connor showing failed python tar extractall on mols.tar