Opened 5 days ago

Closed 4 days ago

#20506 closed defect (fixed)

Modeller results worse

Reported by: roberto@… Owned by: Eric Pettersen
Priority: moderate Milestone:
Component: Structure Prediction Version:
Keywords: Cc: Elaine Meng
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description

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

Attachments (1)

aligned_1.fasta​ (305 bytes ) - added by Eric Pettersen 5 days ago.
alignment

Download all attachments as: .zip

Change History (2)

by Eric Pettersen, 5 days ago

Attachment: aligned_1.fasta​ added

alignment

comment:1 by Eric Pettersen, 4 days ago

Resolution: → fixed
Status: assigned → closed

Fix will be in tomorrow's daily build.

Fix: ​https://github.com/RBVI/ChimeraX/commit/feb4e02c9b7d2918a98115a2a48d2ea3e85c51d6

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