Bug 2369728

Summary:	Data files are not in the correct path
Product:	[Fedora] Fedora	Reporter:	davidoskky
Component:	pymol	Assignee:	Antonio T. sagitter <trpost>
Status:	CLOSED ERRATA	QA Contact:	Fedora Extras Quality Assurance <extras-qa>
Severity:	medium	Docs Contact:
Priority:	unspecified
Version:	42	CC:	trpost
Target Milestone:	---	Keywords:	Desktop, Regression
Target Release:	---
Hardware:	x86_64
OS:	Linux
Whiteboard:
Fixed In Version:	pymol-3.1.0-8.fc42	Doc Type:	---
Doc Text:		Story Points:	---
Clone Of:		Environment:
Last Closed:	2025-06-14 01:10:28 UTC	Type:	---
Regression:	---	Mount Type:	---
Documentation:	---	CRM:
Verified Versions:		Category:	---
oVirt Team:	---	RHEL 7.3 requirements from Atomic Host:
Cloudforms Team:	---	Target Upstream Version:
Embargoed:

Description davidoskky 2025-06-02 09:31:54 UTC

Several problems arise from this, a good way to test is by loading two PDB archives containing proteins and then running align.
In this case the following error is generated 
PyMOL>align AF-P22303-F1-model_v4, protein_processed
 Match-Error: unable to open matrix file '/usr/lib64/python3.13/site-packages/pymol/data/pymol/matrices/BLOSUM62'.

The software is searching for data in the data folder, however in that folder only an icon is present.
The data is located at /usr/lib64/python3.13/site-packages/pymol/pymol_path/data

The following can be used as a temporary fix.
mv /usr/lib64/python3.13/site-packages/pymol/data /usr/lib64/python3.13/site-packages/pymol/old_data 
ln -s /usr/lib64/python3.13/site-packages/pymol/pymol_path/data /usr/lib64/python3.13/site-packages/pymol/data

Reproducible: Always

Steps to Reproduce:
1. Open pymol preferrably from terminal to read the output
2. Load two archives containing protein data
3. Run the command aling <protein1>, <oriteub2>
Actual Results:
Match-Error: unable to open matrix file '/usr/lib64/python3.13/site-packages/pymol/data/pymol/matrices/BLOSUM62'.

Expected Results:
Aligned protein

Comment 1 Fedora Update System 2025-06-05 19:34:09 UTC

FEDORA-2025-1df4860ed0 (pymol-3.1.0-8.fc42) has been submitted as an update to Fedora 42.
https://bodhi.fedoraproject.org/updates/FEDORA-2025-1df4860ed0

Comment 2 Fedora Update System 2025-06-06 02:22:30 UTC

FEDORA-2025-1df4860ed0 has been pushed to the Fedora 42 testing repository.
Soon you'll be able to install the update with the following command:
`sudo dnf upgrade --enablerepo=updates-testing --refresh --advisory=FEDORA-2025-1df4860ed0`
You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2025-1df4860ed0

See also https://fedoraproject.org/wiki/QA:Updates_Testing for more information on how to test updates.

Comment 3 Fedora Update System 2025-06-14 01:10:28 UTC

FEDORA-2025-1df4860ed0 (pymol-3.1.0-8.fc42) has been pushed to the Fedora 42 stable repository.
If problem still persists, please make note of it in this bug report.