Save options widgets deleted

[caillancm@…]

The following bug report has been submitted:
Platform:        Linux-5.3.0-51-generic-x86_64-with-debian-buster-sid
ChimeraX Version: 1.0 (2020-05-08)
Description
This is an update to bug #3175.

After a model is fitted into density, the save dialogue won't work. This doesn't happen with every model and map, but the commands in the log could repoducibly trigger it on my system.

Log:
Startup Errors  
---  
error | Bundle 'ChimeraX-Registration' custom initialization failed  
warning | Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 432, in initialize  
api._api_caller.initialize(api, session, self)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/toolshed/__init__.py", line 1652, in initialize  
return cls._get_func(api, "initialize")(session, bi)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/registration/__init__.py", line 41, in initialize  
nag(session)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/registration/nag.py", line 28, in nag  
if not check_registration(logger=session.logger):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/registration/nag.py", line 49, in check_registration  
return _check_expiration(param, logger)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/registration/nag.py", line 131, in _check_expiration  
expires = datetime.strptime(param["Expires"], TimeFormat)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/_strptime.py", line 577, in
_strptime_datetime  
tt, fraction, gmtoff_fraction = _strptime(data_string, format)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/_strptime.py", line 359, in
_strptime  
(data_string, format))  
ValueError: time data 'Tue Apr 13 07:53:02 2021' does not match format '%a %b
%d %H:%M:%S %Y'  
  
UCSF ChimeraX version: 1.0rc202005080235 (2020-05-08)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open emdb:1777

Summary of feedback from opening 1777 fetched from emdb  
---  
note | Fetching compressed map 1777 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-1777/map/emd_1777.map.gz  
  
Opened emd_1777.map, grid size 100,100,100, pixel 2.3, shown at level 5.07,
step 1, values float32  

> open 6ha8

6ha8 title:  
Cryo-EM structure of the ABCF protein VmlR bound to the Bacillus subtilis
ribosome [more info...]  
  
Chain information for 6ha8 #2  
---  
Chain | Description  
0 | 50S ribosomal protein L32  
1 | 50S ribosomal protein L33 1  
2 | 50S ribosomal protein L34  
3 | 50S ribosomal protein L35  
4 | 50S ribosomal protein L36  
6 | 50S ribosomal protein L31  
7 | mRNA  
8 | 50S ribosomal protein L1  
A | 23S rRNA  
B | 5S rRNA  
C | 50S ribosomal protein L2  
D | 50S ribosomal protein L3  
E | 50S ribosomal protein L4  
F | 50S ribosomal protein L5  
G | 50S ribosomal protein L6  
J | 50S ribosomal protein L13  
K | 50S ribosomal protein L14  
L | 50S ribosomal protein L15  
M | 50S ribosomal protein L16  
N | 50S ribosomal protein L17  
O | 50S ribosomal protein L18  
P | 50S ribosomal protein L19  
Q | 50S ribosomal protein L20  
R | 50S ribosomal protein L21  
S | 50S ribosomal protein L22  
T | 50S ribosomal protein L23  
U | 50S ribosomal protein L24  
V | Nucleotide-binding protein ExpZ  
W | 50S ribosomal protein L27  
X | 50S ribosomal protein L28  
Y | 50S ribosomal protein L29  
Z | 50S ribosomal protein L30  
a | 16S rRNA  
b | 30S ribosomal protein S2  
c | 30S ribosomal protein S3  
d | 30S ribosomal protein S4  
e | 30S ribosomal protein S5  
f | 30S ribosomal protein S6  
g | 30S ribosomal protein S7  
h | 30S ribosomal protein S8  
i | 30S ribosomal protein S9  
j | 30S ribosomal protein S10  
k | 30S ribosomal protein S11  
l | 30S ribosomal protein S12  
m | 30S ribosomal protein S13  
n | 30S ribosomal protein S14  
o | 30S ribosomal protein S15  
p | 30S ribosomal protein S16  
q | 30S ribosomal protein S17  
r | 30S ribosomal protein S18  
s | 30S ribosomal protein S19  
t | 30S ribosomal protein S20  
x | P-tRNA(Leu)  
  
Non-standard residues in 6ha8 #2  
---  
ATP — adenosine-5'-triphosphate  
TEL — telithromycin ((3R,5S,6S,7R,8S,11S,12R,13S,14R,15S)-12-
[(4-O-acetyl-2,6-dideoxy-3-O-methyl-α-L-arabino-hexopyranosyl) oxy]
-14-{[2-O-acetyl-3,4,6-trideoxy-3-(dimethylamino) β-D-xylo-hexopyranosyl]oxy}
-5,7,8,11,13,15-hexamethyl-4,10-dioxo-1,9-dioxaspiro[2.13]hexadec-6-yl
acetate)  
  

> fitmap #2 inMap #1

Fit molecule 6ha8 (#2) to map emdb 1777 (#1) using 146404 atoms  
average map value = 0.5477, steps = 424  
shifted from previous position = 143  
rotated from previous position = 28.2 degrees  
atoms outside contour = 141327, contour level = 5.0661  
  
Position of 6ha8 (#2) relative to emdb 1777 (#1) coordinates:  
Matrix rotation and translation  
0.93532862 -0.01367671 0.35351565 -102.13486207  
0.12942031 0.94321699 -0.30592824 -61.91711606  
-0.32925787 0.33189555 0.88398790 -59.41255508  
Axis 0.67477558 0.72232944 0.15138723  
Axis point -134.69366845 0.00000000 30.18708013  
Rotation angle (degrees) 28.20444900  
Shift along axis -122.63696893  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/ui/gui.py",
line 1543, in <lambda>  
action.triggered.connect(lambda arg, cb = callback: cb())  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 111, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 122, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 24, in display  
self._customize_dialog(session, dialog)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 86, in _customize_dialog  
self._format_selected(session, dialog)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 98, in _format_selected  
self._options_layout.addWidget(self._current_option)  
RuntimeError: wrapped C/C++ object of type SaveOptionsWidget has been deleted  
  
RuntimeError: wrapped C/C++ object of type SaveOptionsWidget has been deleted  
  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 98, in _format_selected  
self._options_layout.addWidget(self._current_option)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.5 (Core Profile) Mesa 19.2.8
OpenGL renderer: Mesa DRI Intel(R) UHD Graphics 620 (Kabylake GT2) 
OpenGL vendor: Intel Open Source Technology Center
Manufacturer: LENOVO
Model: 20L6S01W00
OS: Ubuntu 18.04 bionic
Architecture: 64bit ELF
CPU: 8 Intel(R) Core(TM) i5-8250U CPU @ 1.60GHz
Cache Size: 6144 KB
Graphics:
	00:02.0 VGA compatible controller [0300]: Intel Corporation UHD Graphics 620 [8086:5917] (rev 07)
	Subsystem: Lenovo UHD Graphics 620 [17aa:225d]
	Kernel driver in use: i915

[pett]

Hi Caillan,

Actually the problem is that the save dialog only works the first time. Subsequent uses fail with the error you saw. Again,sorry! :-(

--Eric