Bug 1539225

Summary:	Pymol loads wrong coordinates from PDB files in some locales
Product:	[Fedora] Fedora	Reporter:	Sebastian Keller <sebastian-keller>
Component:	pymol	Assignee:	Tim Fenn <tim.fenn>
Status:	CLOSED ERRATA	QA Contact:	Fedora Extras Quality Assurance <extras-qa>
Severity:	unspecified	Docs Contact:
Priority:	unspecified
Version:	28	CC:	tim.fenn
Target Milestone:	---
Target Release:	---
Hardware:	Unspecified
OS:	Unspecified
Whiteboard:
Fixed In Version:	pymol-1.9.0-1.20180224svn4178.fc26 pymol-1.9.0-1.20180224svn4178.fc27	Doc Type:	If docs needed, set a value
Doc Text:		Story Points:	---
Clone Of:		Environment:
Last Closed:	2018-03-11 19:59:07 UTC	Type:	Bug
Regression:	---	Mount Type:	---
Documentation:	---	CRM:
Verified Versions:		Category:	---
oVirt Team:	---	RHEL 7.3 requirements from Atomic Host:
Cloudforms Team:	---	Target Upstream Version:
Embargoed:

Description Sebastian Keller 2018-01-27 00:24:07 UTC

Pymol in rawhide uses wrong coordinates for atoms when loading a PDB file with LC_NUMERIC=de_DE.utf8. It works as expected when using LC_NUMERIC=C.

It seems like pymol attempts to parse floating point coordinates in the PDB file using the LC_NUMERIC specified formatting rather than always using decimal points. This leads to the fractional part of the coordinates being ignored in languages such as German which use commas as decimal separators.

This bug probably is probably triggered by some changes to a different package modifying some default behavior. So far I've not been able to find the responsible package. There were some LC_NUMERIC related changes to the python3 package recently, but downgrading to a previous version does not seem to fix the issue.

Pymol upstream apparently already has a patch to always use "C" which should fix this issue:
https://sourceforge.net/p/pymol/code/4174/

Comment 1 Fedora End Of Life 2018-02-20 15:33:20 UTC

This bug appears to have been reported against 'rawhide' during the Fedora 28 development cycle.
Changing version to '28'.

Comment 2 Fedora Update System 2018-02-27 17:03:31 UTC

pymol-1.9.0-1.20180224svn4178.fc27 has been submitted as an update to Fedora 27. https://bodhi.fedoraproject.org/updates/FEDORA-2018-42ac8c298a

Comment 3 Fedora Update System 2018-02-27 17:03:39 UTC

pymol-1.9.0-1.20180224svn4178.fc26 has been submitted as an update to Fedora 26. https://bodhi.fedoraproject.org/updates/FEDORA-2018-0e9b210941

Comment 4 Fedora Update System 2018-02-28 17:37:23 UTC

pymol-1.9.0-1.20180224svn4178.fc26 has been pushed to the Fedora 26 testing repository. If problems still persist, please make note of it in this bug report.
See https://fedoraproject.org/wiki/QA:Updates_Testing for
instructions on how to install test updates.
You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2018-0e9b210941

Comment 5 Fedora Update System 2018-02-28 18:08:32 UTC

pymol-1.9.0-1.20180224svn4178.fc27 has been pushed to the Fedora 27 testing repository. If problems still persist, please make note of it in this bug report.
See https://fedoraproject.org/wiki/QA:Updates_Testing for
instructions on how to install test updates.
You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2018-42ac8c298a

Comment 6 Fedora Update System 2018-03-11 19:59:07 UTC

pymol-1.9.0-1.20180224svn4178.fc26 has been pushed to the Fedora 26 stable repository. If problems still persist, please make note of it in this bug report.

Comment 7 Fedora Update System 2018-03-11 22:18:33 UTC

pymol-1.9.0-1.20180224svn4178.fc27 has been pushed to the Fedora 27 stable repository. If problems still persist, please make note of it in this bug report.