Opened 6 years ago

Closed 6 years ago

#3008 closed defect (fixed)

Residues not organized correctly

Reported by: Ben Webb Owned by: Greg Couch
Priority: normal Milestone:
Component: Input/Output Version:
Keywords: Cc: Tom Goddard
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Darwin-19.4.0-x86_64-i386-64bit
ChimeraX Version: 0.93 (2020-04-01)
Description
Each atom gets its own Residue object.

Testing the fix for bug #2979, loading the same file as in that bug,

PDBDEV_00000018.cif​


Each atom is placed in its own residue object. This gives duplicate Residue objects for each residue number and certain properties (such as Residue.principal_atom) don't work correctly (principal_atom is None for every "residue" except for the objects that wrap a CA atom).

This is easy to demonstrate from the Python shell:

In [1]: m=session.models[0]

In [2]: len(m.atoms), len(m.residues)
Out[2]: (55796, 55796)

OpenGL version: 4.1 ATI-3.8.24
OpenGL renderer: AMD Radeon Pro 560 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Change History (2)

comment:1 by Eric Pettersen, 6 years ago

Cc: Tom Goddard added
Component: Unassigned → Input/Output
Owner: set to Greg Couch
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Residues not organized correctly

comment:2 by Greg Couch, 6 years ago

Resolution: → fixed
Status: assigned → closed

Sorry about that. Should be fixed now.

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