Opened 6 years ago

Closed 6 years ago

#2168 closed defect (fixed)

Graphics context menu: spurious drag select; also delete hydrogens

Reported by: tic20@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: General Controls Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description

The following bug report has been submitted:
Platform:        Linux-3.10.0-957.12.2.el7.x86_64-x86_64-with-centos-7.6.1810-Core
ChimeraX Version: 0.91 (2019-07-02)
Description
I really like the new (or new to me, at least!) ctrl-double-click mouse mode to bring up a context menu. A minor bug, though: if I ctrl-double-click on an atom, then (after releasing ctrl) click somewhere outside the drop-down menu to dismiss it, ChimeraX acts as if I've done a ctrl-left-drag and selects everything between the original double-click point and the final click.

Also, a suggestion: for the "delete atom(s)" options in the menu, it would probably make sense to automatically remove any hydrogens attached to the deleted heavy atoms.

Log:
Startup Messages  
---  
warning | 'clip' is a prefix of an existing command 'clipper'  
  
UCSF ChimeraX version: 0.91 (2019-07-02)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 1a0m format mmCIF fromDatabase pdb structureFactors true

Summary of feedback from opening 1a0m fetched from pdb  
---  
warning | No free flags detected in this dataset! Automatically generated a
new random set with 484 free from 9265 observed reflections. You should save
your data to a new MTZ file and use this for any future rebuilding/refinement.  
notes | Resolution: 1.0944213038232693  
  
1a0m title:  
1.1 angstrom crystal structure of A-conotoxin [TYR15]-epi [more info...]  
  
Chain information for 1a0m  
---  
Chain | Description  
1.3/A 1.3/B | α-conotoxin [TYR15]-epi  
  
Non-standard residues in 1a0m #1.3  
---  
NH2 — amino group  
  
  

> select /B:16@O

1 atom, 1 model selected  

> select clear

> select /B:11@O

1 atom, 1 model selected  

> select clear

> select /B:11@OD1

1 atom, 1 model selected  

> select /B:11@OD1

1 atom, 1 model selected  

> select clear

> select /B:11@OD1

1 atom, 1 model selected  

> select clear

> select /B:11@OD1

1 atom, 1 model selected  

> select /B:10@SD

1 atom, 1 model selected  

> select clear

> select /B:10@SD

1 atom, 1 model selected  

> select clear

> select /B:10@SD

1 atom, 1 model selected  

> select clear

> select clear

> select /B:10@CG

1 atom, 1 model selected  

> select /B:10@SD

1 atom, 1 model selected  

> select clear

> select /B:7@CG

1 atom, 1 model selected  

> select clear

> addh

Summary of feedback from adding hydrogens to 1a0m #1.3  
---  
warning | Not adding hydrogens to /A ARG 7 CB because it is missing heavy-atom
bond partners  
notes | Termini for 1a0m (#1.3) chain A determined from SEQRES records  
Termini for 1a0m (#1.3) chain B determined from SEQRES records  
Chain-initial residues that are actual N termini: /A GLY 1, /B GLY 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A NH2 17, /B NH2 17  
Chain-final residues that are not actual C termini:  
107 hydrogen bonds  
271 hydrogens added  
  

> select /B:7@CG

1 atom, 1 model selected  

> delete atoms sel

> select /B:7@HG2

1 atom, 1 model selected  

> delete atoms sel




OpenGL version: 3.3.0 NVIDIA 415.27
OpenGL renderer: TITAN Xp/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Change History (3)

comment:1 by Eric Pettersen, 6 years ago

Component: UnassignedGeneral Controls
Owner: set to Eric Pettersen
Platform: all
Project: ChimeraX
Status: newaccepted
Summary: ChimeraX bug report submissionGraphics context menu: spurious drag select; also delete hydrogens

comment:2 by Eric Pettersen, 6 years ago

Okay, the 'delete' command (which this context menu uses) now defaults to also deleting attached hydrogens (controlled by the 'attachedHyds' keyword).

comment:3 by Eric Pettersen, 6 years ago

Resolution: fixed
Status: acceptedclosed

Spurious drag selection also fixed.

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