Opened 6 years ago

Closed 6 years ago

Last modified 6 years ago

#2535 closed defect (fixed)

Crash on structure with non-unique atom names

Reported by: goddard@… Owned by: pett
Priority: normal Milestone:
Component: Core Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description

The following bug report has been submitted:
Platform:        Windows-10-10.0.18362
ChimeraX Version: 0.91 (2019-10-24)
Description
Running addh on this "structure" crashes ChimeraX.  I realize this is some gruesome 2D structure but still did not expect a crash.

Log:
UCSF ChimeraX version: 0.91 (2019-10-24)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open C:/Users/goddard/Desktop/milk-oct2019/DB13038_triolein.pdb

DB13038_triolein.pdb title:  
NULL [more info...]  
  




OpenGL version: 3.3.0 NVIDIA 398.35
OpenGL renderer: GeForce GTX 1070 with Max-Q Design/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
File attachment: DB13038_triolein.pdb

DB13038_triolein.pdb

Attachments (1)

DB13038_triolein.pdb (10.5 KB ) - added by goddard@… 6 years ago.
Added by email2trac

Download all attachments as: .zip

Change History (4)

by goddard@…, 6 years ago

Attachment: DB13038_triolein.pdb added

Added by email2trac

comment:1 by pett, 6 years ago

Component: UnassignedCore
Owner: set to pett
Platform: all
Project: ChimeraX
Status: newaccepted
Summary: ChimeraX bug report submissionCrash on structure with non-unique atom names

comment:2 by pett, 6 years ago

Resolution: fixed
Status: acceptedclosed

The non-unique naming of the atoms in this large residue caused addh to generate 5-character hydrogen names. Switched to using hybrid-36 for numbers that would exceed the character limit.

in reply to:  4 comment:3 by goddard@…, 6 years ago

These atom name character limits are going to plague ChimeraX forever into the future.  It would be a good move to use std::string and head-off this future burden trying to debug hard to fathom crashes.

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