Opened 5 years ago

Closed 5 years ago

#3399 closed defect (duplicate)

Session save error caused by deleted Structure

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

Description 

The following bug report has been submitted:
Platform:        Darwin-19.5.0-x86_64-i386-64bit
ChimeraX Version: 1.1.dev202006100038 (2020-06-10 00:38:38 UTC)
Description
Error saving session.  Deleted atomic model long before saving.

Log:
Startup Messages  
---  
note | Updating list of available bundles failed: [Errno 8] nodename nor
servname provided, or not known  
  
UCSF ChimeraX version: 1.1.dev202006100038 (2020-06-10)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 1808 fromDatabase emdb

Fetching url
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-1808/map/emd_1808.map.gz
failed: <urlopen error [Errno 8] nodename nor servname provided, or not known>  

> open 1080 fromDatabase emdb

Opened emd_1080.map, grid size 100,100,100, pixel 2.7, shown at level 1.68,
step 1, values float32  

> open 1grl

1grl title:  
The crystal structure of the bacterial chaperonin groel At 2.8 angstroms [more
info...]  
  
Chain information for 1grl #2  
---  
Chain | Description  
A B C D E F G | groel (HSP60 class)  
  
1grl mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| software_defined_assembly  
  

> fitmap #2 inMap #1

Fit molecule 1grl (#2) to map emdb 1080 (#1) using 29274 atoms  
average map value = 1.33, steps = 160  
shifted from previous position = 43.6  
rotated from previous position = 25.7 degrees  
atoms outside contour = 23229, contour level = 1.6751  
  
Position of 1grl (#2) relative to emdb 1080 (#1) coordinates:  
Matrix rotation and translation  
0.90168160 -0.43226797 -0.01070926 39.38378225  
0.43239643 0.90128739 0.02672781 18.93321539  
-0.00190145 -0.02873062 0.99958538 -0.07505929  
Axis -0.06400385 -0.01016498 0.99789788  
Axis point -21.87971538 95.67332351 0.00000000  
Rotation angle (degrees) 25.67354134  
Shift along axis -2.78807077  
  

> delete ~/A

> molmap /A 20

> volume #3 level 0.1183

> delete #2

> volume #3 showOutlineBox true

> ui mousemode right "crop volume"

> volume #1 region 0,0,0,99,99,99

> volume #3 region 0,0,0,26,26,26

> volume #3 region 0,0,0,26,26,24

> volume #3 region 0,0,0,26,26,23

> volume #3 region 8,0,0,26,26,23

> volume #3 region 8,0,0,19,26,23

> volume #3 region 8,7,0,19,26,23

> volume #3 region 8,7,0,19,25,23

> volume #3 region 8,7,0,19,26,23

> volume #3 region 8,7,0,19,26,23

> volume #3 region 8,7,0,19,26,23

> volume #3 region 8,7,8,19,26,23

> volume #3 region 8,7,8,19,26,23

> volume #3 region 8,8,8,19,26,23

> volume #3 region 8,8,8,19,26,23

> volume #3 region 8,8,8,19,26,22

> volume #3 region 8,8,8,19,26,22

> volume #3 region 8,8,8,19,26,22

> volume #3 region 8,8,8,19,26,22

> volume #3 region 8,17,8,19,26,22

> ui mousemode right "move planes"

> volume #3 region 8,17,8,19,26,22

> volume #3 region 8,9,8,19,18,22

> volume copy #3

> close #2

> usage volume copy

volume copy volumes [valueType numeric value type] [subregion map region]
[step map step] [modelId modelId]  
— Copy a map or a map subregio  
modelId: a model id  

> volume copy #3 subregion shown

> close #3

> volume resample #1 onGrid #2

> select #2

2 models selected  

> ui mousemode right "translate selected models"

> fitmap #2 inMap #1

Fit map 1grl map 20 copy in map emdb 1080 using 261 points  
correlation = 0.9743, correlation about mean = 0.713, overlap = 79.03  
steps = 148, shift = 6.88, angle = 102 degrees  
  
Position of 1grl map 20 copy (#2) relative to emdb 1080 (#1) coordinates:  
Matrix rotation and translation  
0.23200220 0.97020135 0.06988792 9.96635886  
-0.97270326 0.23175663 0.01171445 -40.21686890  
-0.00483161 -0.07069799 0.99748607 -0.41495000  
Axis -0.04234778 0.03839476 -0.99836492  
Axis point -20.44336829 -26.38741052 0.00000000  
Rotation angle (degrees) 76.66627933  
Shift along axis -1.55189869  
  

> volume resample #1 onGrid #2

> hide #!4 models

> fitmap #2 inMap #1

Fit map 1grl map 20 copy in map emdb 1080 using 261 points  
correlation = 0.9746, correlation about mean = 0.7164, overlap = 79.08  
steps = 48, shift = 5.57, angle = 19.1 degrees  
  
Position of 1grl map 20 copy (#2) relative to emdb 1080 (#1) coordinates:  
Matrix rotation and translation  
0.21691947 -0.97380327 -0.06821386 8.47751241  
-0.97615549 -0.21579836 -0.02348470 -40.65917067  
0.00814904 0.07168162 -0.99739427 0.39451342  
Axis 0.77980420 -0.62572671 -0.01927434  
Axis point 0.00000000 -16.94816177 -0.10149097  
Rotation angle (degrees) 176.50167441  
Shift along axis 32.04472470  
  

> volume resample #1 onGrid #2

> save test.cxs

Traceback (most recent call last):  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 69, in <lambda>  
lambda *args, qual=ses_func: self._ses_call(qual)))  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/molobject.py", line 1792, in _ses_call  
f(self._c_pointer)  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 43, in _getattr_  
return base.__getattr__(self, attr_name, look_in_class=base)  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_  
return look_in_class._attr_registration.get_attr(attr_name)  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
AttributeError: 'Structure' object has no attribute '_c_pointer'  
  
Error processing trigger "begin save session":  
AttributeError: 'Structure' object has no attribute '_c_pointer'  
  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 69, in <lambda>  
lambda *args, qual=ses_func: self._ses_call(qual)))  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/molobject.py", line 1792, in _ses_call  
f(self._c_pointer)  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 43, in _getattr_  
return base.__getattr__(self, attr_name, look_in_class=base)  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_  
return look_in_class._attr_registration.get_attr(attr_name)  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
AttributeError: 'Structure' object has no attribute '_c_pointer'  
  
Error processing trigger "end save session":  
AttributeError: 'Structure' object has no attribute '_c_pointer'  
  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
  
See log for complete Python traceback.  
  

Failed to send bug report. Error while sending follows:  

Traceback (most recent call last):  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/bug_reporter/bug_reporter_gui.py", line 240, in submit  
errcode, errmsg, headers, body = post_multipart_formdata(BUG_HOST,
BUG_SELECTOR, fields)  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/webservices/post_form.py", line 40, in
post_multipart_formdata  
h.request('POST', url, body=body, headers=headers)  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py",
line 1252, in request  
self._send_request(method, url, body, headers, encode_chunked)  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py",
line 1298, in _send_request  
self.endheaders(body, encode_chunked=encode_chunked)  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py",
line 1247, in endheaders  
self._send_output(message_body, encode_chunked=encode_chunked)  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py",
line 1026, in _send_output  
self.send(msg)  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py",
line 966, in send  
self.connect()  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py",
line 938, in connect  
(self.host,self.port), self.timeout, self.source_address)  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/socket.py",
line 707, in create_connection  
for res in getaddrinfo(host, port, 0, SOCK_STREAM):  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/socket.py",
line 752, in getaddrinfo  
for res in _socket.getaddrinfo(host, port, family, type, proto, flags):  
socket.gaierror: [Errno 8] nodename nor servname provided, or not known  




OpenGL version: 4.1 ATI-3.9.15
OpenGL renderer: AMD Radeon Pro Vega 20 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro15,3
      Processor Name: 8-Core Intel Core i9
      Processor Speed: 2.4 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache (per Core): 256 KB
      L3 Cache: 16 MB
      Hyper-Threading Technology: Enabled
      Memory: 32 GB
      Boot ROM Version: 1037.120.87.0.0 (iBridge: 17.16.15300.0.0,0)

Software:

    System Software Overview:

      System Version: macOS 10.15.5 (19F101)
      Kernel Version: Darwin 19.5.0
      Time since boot: 5 days 20:54

Graphics/Displays:

    Intel UHD Graphics 630:

      Chipset Model: Intel UHD Graphics 630
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3e9b
      Revision ID: 0x0002
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal: Supported, feature set macOS GPUFamily2 v1

    Radeon Pro Vega 20:

      Chipset Model: Radeon Pro Vega 20
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x8
      VRAM (Total): 4 GB
      Vendor: AMD (0x1002)
      Device ID: 0x69af
      Revision ID: 0x00c0
      ROM Revision: 113-D2060I-087
      VBIOS Version: 113-D20601MA0T-016
      Option ROM Version: 113-D20601MA0T-016
      EFI Driver Version: 01.01.087
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal: Supported, feature set macOS GPUFamily2 v1
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2880 x 1800 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal

PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.8

Change History (3)

comment:1 by Tom Goddard, 5 years ago

Platform: → all
Project: → ChimeraX

Repeated all the same steps and did not get the error. Looks like Structure.delete() was not called. It should be called explicitly by Models.close().

comment:2 by Tom Goddard, 5 years ago

Component: Unassigned → Sessions
Owner: set to Tom Goddard
Status: new → assigned
Summary: ChimeraX bug report submission → Session save error caused by deleted Structure

comment:3 by Tom Goddard, 5 years ago

Resolution: → duplicate
Status: assigned → closed

Simpler case reported in #3401.

Just "delete #1" to close a structure instead of "close #1" then save a session.

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