id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
20506	Modeller results worse	roberto@…	Eric Pettersen	"I am using the ChimeraX modeller comparative command in both ChimeraX
1.7 and ChimeraX 1.11.1. The command executes successfully in both
versions, but the results are significantly different. The model
generated with ChimeraX 1.7 appears correct, whereas the model
generated with ChimeraX 1.11.1 appears incorrect.

One notable difference is the GA341 ""correlation"" score: it is close
to 1.0 (high confidence) in ChimeraX 1.7, but close to 0.0 (very low
confidence) in ChimeraX 1.11.1.

The test data is:

Sequence: UniProt P69905 (human hemoglobin)
Template structure: PDB 2DHB (horse hemoglobin)
Alignment: attached file

The exact command used was generated using chimerax GUI:

modeller comparative aligned_1.fasta:2 numModels 5 fast false
multichain true hetPreserve false hydrogens false waterPreserve false"	defect	closed	moderate		Structure Prediction		fixed		Elaine Meng				all	ChimeraX