Opened 6 years ago

Closed 6 years ago

#2741 closed enhancement (fixed)

nicer form for ligand-table selection command, when possible

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

Description (last modified by Eric Pettersen)

The following bug report has been submitted:
Platform:        Darwin-19.2.0-x86_64-i386-64bit
ChimeraX Version: 0.92 (2020-01-11)
Description
Selecting ADP in Log ligand table of 6n2y issues command

select ::name="ADP"

Would be better to issue the command a user would actually type

select :ADP

and only use the more complicated syntax if necessary (for an all numeric residue name).


Log:
UCSF ChimeraX version: 0.92 (2020-01-11)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/goddard/ucsf/presentations/stanford-jul2019/tutorial2.html

Opened tutorial2.html  

> open 6n2y

6n2y title:  
Bacillus PS3 ATP synthase class 1 [more info...]  
  
Chain information for 6n2y #1  
---  
Chain | Description  
A B C | ATP synthase subunit α  
D E F | ATP synthase subunit β  
G | ATP synthase γ chain  
H | ATP synthase ε chain  
I | ATP synthase subunit δ  
a | ATP synthase subunit a  
b1 | ATP synthase subunit b  
b2 | ATP synthase subunit b  
c0 c1 c2 c3 c4 c5 c6 c7 c8 c9 | ATP synthase subunit c  
  
Non-standard residues in 6n2y #1  
---  
ADP — adenosine-5'-diphosphate  
ATP — adenosine-5'-triphosphate  
MG — magnesium ion  
PO4 — phosphate ion  
  
  

> select /A:2-501

3827 atoms, 3888 bonds, 1 model selected  

> select clear

> sequence chain #1/A#1/B#1/C

Alignment identifier is 1  

> sequence chain #1/A

Alignment identifier is 1.A  

> log metadata #1

Metadata for 6n2y #1  
---  
Title | Bacillus PS3 ATP synthase class 1  
Citation | Guo, H., Suzuki, T., Rubinstein, J.L. (2019). Structure of a
bacterial ATP synthase. Elife, 8. PMID: 30724163. DOI: 10.7554/eLife.43128  
Non-standard residues | ADP — adenosine-5'-diphosphate  
ATP — adenosine-5'-triphosphate  
MG — magnesium ion  
PO4 — phosphate ion  
Gene source | Bacillus sp. (strain PS3)  
Experimental method | Electron microscopy  
Resolution | 3.0Å  
  
> ui dockable true "Help Viewer"

> show cartoons

> show cartoons

> hide atoms

> show ligand

> hide ligand

> select ::name="ADP"

27 atoms, 29 bonds, 1 model selected  




OpenGL version: 4.1 ATI-3.4.19
OpenGL renderer: AMD Radeon Pro 580 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Change History (2)

comment:1 by Eric Pettersen, 6 years ago

Component: UnassignedGeneral Controls
Description: modified (diff)
Platform: all
Project: ChimeraX
Summary: ChimeraX bug report submissionnicer form for ligand-table selection command, when possible
Type: defectenhancement

comment:2 by Eric Pettersen, 6 years ago

Resolution: fixed
Status: newclosed

Now only uses ::name="123" when needed

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