Opened 7 years ago

Closed 7 years ago

#1313 closed enhancement (not a bug)

misleading error message

Reported by: huter@… Owned by: Greg Couch
Priority: normal Milestone:
Component: Command Line Version:
Keywords: Cc: Tom Goddard, pett
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description (last modified by pett) 

The following bug report has been submitted:
Platform:        Windows-10-10.0.17134
ChimeraX Version: 0.8 (2018-09-15)
Description
Cant save any images. Says Expected a models specifier or a keyword.
Neither the symbol nor command line works

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 0.8 (2018-09-15)  
How to cite UCSF ChimeraX  

open "C:\Users\HUT Privat\Desktop\bookchapter\translocation\efgaction.cxs" ↵

File not found: C:\Users\HUT Privat\Desktopookchapter
ranslocation\efgaction.cxs  

open "C:/Users/HUT Privat/Desktop/bookchapter/translocation/efgaction.cxs" ↵

Summary of feedback from opening C:/Users/HUT
Privat/Desktop/bookchapter/translocation/efgaction.cxs  
---  
error | Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 584, in restore  
obj = sm.restore_snapshot(self, data)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\bond_rot\manager.py", line 154, in restore_snapshot  
mgr._ses_restore(data)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\bond_rot\manager.py", line 168, in _ses_restore  
self.bond_rotations = data['rotations']  
KeyError: 'rotations'  
  
opened ChimeraX session  

open "C:/Users/HUT Privat/Desktop/bookchapter/translocation/4v7d-pdb-
bundle_brilotandEFG.tar/4v7d-pdb-bundle/4v7d-pdb-bundle2.pdb" ↵

Summary of feedback from opening C:/Users/HUT
Privat/Desktop/bookchapter/translocation/4v7d-pdb-
bundle_brilotandEFG.tar/4v7d-pdb-bundle/4v7d-pdb-bundle2.pdb  
---  
warning | Ignored bad PDB record found on line 1  
HEADER TRANSLATION/ANTIBIOTIC 2013-11-21 XXXX  
  
Chain information for 4v7d-pdb-bundle2.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
V W | No description available  
X | No description available  
Y | No description available  
Z | No description available  
  

color #1/A yellow ↵

color #1/A & sideonly khaki ↵

select #1/B-U ↵

18543 atoms, 18811 bonds selected  

hide selAtoms ↵

select #1/Y ↵

5301 atoms, 5400 bonds selected  

color #1/Y ↵

color #1/Y red ↵

show selAtoms ribbons ↵

hide selAtoms ↵

set silhouettes false ↵

set silhouettes true ↵

color #1/V sienna ↵

color #1/V & sideonly tan ↵

color #1/W salmon ↵

color #1/W & sideonly pink ↵

select #1/X cyan

Expected a keyword  

color #1/X cyan ↵

color #1/X & sideonly aquamarine ↵

hide #1/A ↵

open "C:/Users/HUT Privat/Desktop/bookchapter/translocation/4v7b-pdb-
bundle_ApP_pePnew.tar/4v7b-pdb-bundle/4v7b-pdb-
bundle1-coot-0_aligned4v7dSSU.pdb" ↵

Summary of feedback from opening C:/Users/HUT
Privat/Desktop/bookchapter/translocation/4v7b-pdb-
bundle_ApP_pePnew.tar/4v7b-pdb-bundle/4v7b-pdb-
bundle1-coot-0_aligned4v7dSSU.pdb  
---  
warning | Ignored bad PDB record found on line 65057  
END  
  
Chain information for 4v7b-pdb-bundle1-coot-0_aligned4v7dSSU.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
V W | No description available  
X | No description available  
Y | No description available  
Z | No description available  
a | No description available  
  

hide #!1 models ↵

select #2/B-U ↵

18558 atoms, 18827 bonds selected  

hide selAtoms ↵

select #2/Z ↵

2529 atoms, 2828 bonds selected  

hide selAtoms ↵

select #2/a ↵

2082 atoms, 2121 bonds selected  

hide selAtoms ↵

color #27A yellow

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons',
'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

color #2/A yellow ↵

color #2/A & sideonly tan ↵

color #2/Y red ↵

select #2/Y ↵

5259 atoms, 5362 bonds selected  

show selAtoms ribbons ↵

hide selAtoms ↵

select #2/V ↵

1640 atoms, 1832 bonds selected  

color#2/V sienna

Unknown command: color#2/V sienna  

color #2/V sienna ↵

color #2/V & sideonly tan ↵

color #2/W salmon ↵

color #2/W & sideonly pink ↵

hide #2/A ↵

color #2/X cyan ↵

color #2/X & sideonly aquamarine ↵

select #2/A:1485-1500 ↵

349 atoms, 391 bonds selected  

show selAtoms ribbons ↵

select up ↵

23 atoms, 25 bonds selected  

select up ↵

1640 atoms, 1832 bonds selected  

show selAtoms ribbons ↵

hide selAtoms ↵

color #2/V sienna ↵

color #2/W salmon ↵

select up ↵

65014 atoms, 70100 bonds selected  

show selAtoms ribbons ↵

hide selAtoms ↵

select up ↵

20 atoms, 21 bonds selected  

select up ↵

1635 atoms, 1827 bonds selected  

show selAtoms ribbons ↵

hide selAtoms ↵

select up ↵

22 atoms, 24 bonds selected  

select up ↵

416 atoms, 469 bonds selected  

show selAtoms ribbons ↵

hide selAtoms ↵

color #2/X cyan ↵

lighting full ↵

lighting shadows false ↵

lighting soft ↵

lighting full ↵

lighting soft ↵

lighting full ↵

lighting simple ↵

lighting shadows true ↵

lighting soft ↵

style selAtoms sphere ↵

Changed 44 atom styles  

show selAtoms ↵

style selAtoms stick ↵

Changed 44 atom styles  

select up ↵

22 atoms, 24 bonds selected  

select up ↵

32895 atoms, 36834 bonds selected  

select up ↵

32895 atoms, 36834 bonds selected  

color sel yellow ↵

color sel khaki ↵

show #1/W ↵

show #!1 models ↵

hide #1 ↵

show #1/w ↵

select up ↵

20 atoms, 21 bonds selected  

select up ↵

1622 atoms, 1812 bonds selected  

show selAtoms ribbons ↵

hide selAtoms ↵

hide #1/w ↵

select up ↵

1622 atoms, 1812 bonds selected  

hide selAtoms ribbons ↵

show #2/A:1335-1345 ↵

select #2/A:1335-1345 ↵

233 atoms, 259 bonds selected  

show selAtoms ribbons ↵

hide selAtoms ↵

select #1/A:1335-1345 ↵

233 atoms, 259 bonds selected  

show selAtoms ribbons ↵

select #1/A:1330-1345 ↵

343 atoms, 383 bonds selected  

show selAtoms ribbons ↵

color #1/A:1330-1345 khaki ↵

color #1/A:1330-1345 grey ↵

color #1/A:1330-1345 light grey ↵

select #1/1485-1500 ↵

Nothing selected  

select #1/A:1485-1500 ↵

349 atoms, 391 bonds selected  

show selAtoms ribbons ↵

style selAtoms stick ↵

Changed 44 atom styles  

show selAtoms ↵

hide#1/A:1485-1500

Unknown command: hide#1/A:1485-1500  

hide #1/A:1485-1500 ↵

select #1/A:1485-1500 ↵

349 atoms, 391 bonds selected  

hide selAtoms ribbons ↵

style selAtoms stick ↵

Changed 42 atom styles  

show selAtoms ↵

style selAtoms stick ↵

Changed 22 atom styles  

show selAtoms ↵

hide selAtoms ↵

select #1/W ↵

1622 atoms, 1812 bonds selected  

show selAtoms ribbons ↵

hide selAtoms ribbons ↵

select #1/V ↵

1619 atoms, 1809 bonds selected  

show selAtoms ribbons ↵

select #1/W ↵

1622 atoms, 1812 bonds selected  

show selAtoms ribbons ↵

hide selAtoms ribbons ↵

select #1/V ↵

1619 atoms, 1809 bonds selected  

hide selAtoms ribbons ↵

toolshed show "Side View"

save C:\Users\HUT Privat/Desktop\image13.png supersample 3

Expected a models specifier or a keyword  

Expected a models specifier or a keyword  

save C:\Users\HUT Privat/Desktop\image13.png supersample 3

Expected a models specifier or a keyword  

Expected a models specifier or a keyword  

save image efgaction.png ↵

save C:\Users\HUT Privat/Desktop\image13.png supersample 3

Expected a models specifier or a keyword  

Expected a models specifier or a keyword  

save image yolo.png ↵

save image C:\Users\HUT Privat\Desktop\yolo.png

Expected a keyword  

save image C:\Users\HUTPrivat\Desktop\yolo.png ↵

Directory "C:\Users\HUTPrivat\Desktop" does not exist  

save image C:\Users\HUT Privat\Desktop\yolo.png

Expected a keyword  

save image C:\Users\HUT Privat\Desktop\yolo.png supersample 3

Expected a keyword  

save C:\Users\HUT Privat/Desktop\image13.png supersample 3

Expected a models specifier or a keyword  

Expected a models specifier or a keyword  




OpenGL version: 3.3.0 - Build 10.18.10.4425
OpenGL renderer: Intel(R) HD Graphics 4000
OpenGL vendor: Intel

Change History (3)

comment:1 by pett, 7 years ago

Cc: Tom Goddard pett added
Component: Unassigned → Command Line
Description: modified (diff)
Owner: set to Greg Couch
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → misleading error message
Type: defect → enhancement

Hi Paul,

The real problem with your image-save command is the space in the middle of the file path. The error message unfortunately isn't much help in diagnosing the problem, I know. Anyway, you need to put quotes around the whole file name, and it would probably be best to use forward slashes instead of back slashes (you would have to use double back slashes to prevent them from being handled specially).

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

in reply to:  2 ; comment:2 by goddard@…, 7 years ago 

save C:\Users\HUT Privat/Desktop\image13.png supersample 3
Expected a models specifier or a keyword

A more informative message that would probably allow the user to see the unquoted space problem might be:

Expected a models specifier or a keyword, got "Privat/Desktop\image13.png"

comment:3 by Greg Couch, 7 years ago

Resolution: → not a bug
Status: assigned → closed

I don't consider this a bug. In the log window, the part of the command line where the error was found (after the space in the file name) is highlighted in red. So it is explicitly shown where the problem is. Would it help to change the error message to "Expected a models specifier or a keyword argument" -- i.e, "keyword" argument instead of just "keyword"? I have asked that the documentation for the save and open commands remind users about the need to quote filenames with a space or semicolon in them.

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