Opened 4 years ago

Closed 4 years ago

#5269 closed defect (fixed)

fitmap tool: local variable 'msg' referenced before assignment

Reported by: chimerax-bug-report@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Volume Data Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-4.18.0-305.12.1.el8_4.x86_64-x86_64-with-glibc2.14
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open emdb:0436

Summary of feedback from opening 0436 fetched from emdb  
---  
note | Fetching compressed map 0436 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-0436/map/emd_0436.map.gz  
  
Opened emdb 0436 as #1, grid size 1200,1200,1200, pixel 1.62, shown at step 1,
values float32  

> set bgColor white

> volume #1 level -1.353,0 level 12.27,0.8 level 50.99,1

> volume #1 region 0,0,0,1199,1199,1199 step 8

> volume #1 region 0,0,0,1199,1199,1199 step 8

> vop gaussian #1 sDev 3

Opened emdb 0436 gaussian as #2, grid size 1200,1200,1200, pixel 1.62, shown
at step 1, values float32  

> open 6ncl

Summary of feedback from opening 6ncl fetched from pdb  
---  
note | Fetching compressed mmCIF 6ncl from
http://files.rcsb.org/download/6ncl.cif  
  
6ncl title:  
Near-atomic structure of icosahedrally averaged PBCV-1 capsid [more info...]  
  
Chain information for 6ncl #3  
---  
Chain | Description  
a0 | P14  
a1 | P9  
a2 a3 | P10  
a4 | P7  
a5 | P6  
a6 | P1  
a7 | P12  
a8 | P5  
a9 b0 b1 b2 b3 b4 b5 b7 b8 c0 c1 l5 | P11  
b6 | P2  
c2 c3 c4 c5 | P4  
c6 c7 c8 | P3  
c9 | P8  
d0 d1 d2 d3 d4 d5 d6 d7 d8 d9 e0 e1 e2 e3 e4 e5 e6 e7 e8 e9 f0 f1 f2 f3 f4 f5
f6 f7 f8 f9 g0 g1 g2 g3 g4 g5 g6 g7 g8 g9 h0 h1 h2 h3 h4 h5 h6 h7 h8 h9 i0 i1
i2 i3 i4 i5 i6 i7 i8 i9 j0 j1 j2 j3 j4 j5 j6 j7 j8 j9 k0 k1 k2 k3 k4 k5 k6 k7
k8 k9 l0 l1 l2 l3 | Major capsid protein  
l4 | P13  
  
6ncl mmCIF Assemblies  
---  
1| complete icosahedral assembly  
2| icosahedral asymmetric unit  
3| icosahedral pentamer  
4| icosahedral 23 hexamer  
5| icosahedral asymmetric unit, std point frame  
  

> ui tool show "Fit in Map"

Opened 6ncl map 5 as #4, grid size 288,476,255, pixel 1.67, shown at level
0.118, step 1, values float32  
Fit map 6ncl map 5 in map emdb 0436 gaussian using 1098246 points  
correlation = 0.7219, correlation about mean = 0.2355, overlap = 1.125e+06  
steps = 44, shift = 0.203, angle = 0.0812 degrees  
  
Position of 6ncl map 5 (#4) relative to emdb 0436 gaussian (#2) coordinates:  
Matrix rotation and translation  
0.99999952 -0.00026991 -0.00093865 0.54802150  
0.00026895 0.99999944 -0.00102591 0.39957857  
0.00093893 0.00102566 0.99999903 -0.90819321  
Axis 0.72422739 -0.66280409 0.19022465  
Axis point -0.00000000 878.26167035 362.70187940  
Rotation angle (degrees) 0.08115320  
Shift along axis -0.04071087  
  
Average map value = 2.754 for 305842 atoms, 241289 outside contour  

> mask #2 #4

Unknown command: mask #2 #4  

> volume mask #2 surfaces #4

Only empty surfaces specified  

> show #!4 models

> volume mask #2 surfaces #4

Opened emdb 0436 gaussian masked as #5, grid size 281,475,247, pixel 1.62,
shown at step 1, values float32  

> hide #!5 models

> hide #!4 models

> show #!5 models

> hide atoms

> show cartoons

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> volume #2 level 3.703

> hide #!2 models

> show #!2 models

> hide #!2 models

> volume #5 level 0.6356

> volume #5 level 3.605

> close #5

> close #2

> close #4

> close #1

> close #3

> open /data/mcm14/nadishka/run_it015_class001.mrc format mrc

Opened run_it015_class001.mrc as #1, grid size 320,320,320, pixel 1.41, shown
at level 0.0103, step 2, values float32  

> close #1

> open /home/nadishka/Documents/wiv/postprocess.mrc

Opened postprocess.mrc as #1, grid size 1600,1600,1600, pixel 1.39, shown at
step 1, values float32  

> set bgColor black

> open 6ncl

6ncl title:  
Near-atomic structure of icosahedrally averaged PBCV-1 capsid [more info...]  
  
Chain information for 6ncl #2  
---  
Chain | Description  
a0 | P14  
a1 | P9  
a2 a3 | P10  
a4 | P7  
a5 | P6  
a6 | P1  
a7 | P12  
a8 | P5  
a9 b0 b1 b2 b3 b4 b5 b7 b8 c0 c1 l5 | P11  
b6 | P2  
c2 c3 c4 c5 | P4  
c6 c7 c8 | P3  
c9 | P8  
d0 d1 d2 d3 d4 d5 d6 d7 d8 d9 e0 e1 e2 e3 e4 e5 e6 e7 e8 e9 f0 f1 f2 f3 f4 f5
f6 f7 f8 f9 g0 g1 g2 g3 g4 g5 g6 g7 g8 g9 h0 h1 h2 h3 h4 h5 h6 h7 h8 h9 i0 i1
i2 i3 i4 i5 i6 i7 i8 i9 j0 j1 j2 j3 j4 j5 j6 j7 j8 j9 k0 k1 k2 k3 k4 k5 k6 k7
k8 k9 l0 l1 l2 l3 | Major capsid protein  
l4 | P13  
  
6ncl mmCIF Assemblies  
---  
1| complete icosahedral assembly  
2| icosahedral asymmetric unit  
3| icosahedral pentamer  
4| icosahedral 23 hexamer  
5| icosahedral asymmetric unit, std point frame  
  

> open /home/nadishka/Documents/wiv/gauss_sdev5_wiv.mrc

Opened gauss_sdev5_wiv.mrc as #3, grid size 1600,1600,1600, pixel 1.39, shown
at step 1, values float32  

> hide #!1 models

> volume #3 region 0,0,0,1599,1599,1599 step 8

> volume #3 region 0,0,0,1599,1599,1599 step 8

> volume #3 step 2

> ui mousemode right select

Drag select of 81568 atoms  
Drag select of 302724 atoms, 2 pseudobonds  
Drag select of 305842 atoms, 2 pseudobonds, 3 gauss_sdev5_wiv.mrc  

> select clear

Drag select of 305842 atoms, 2 pseudobonds  

> ui mousemode right "translate selected models"

Traceback (most recent call last):  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.8/site-
packages/chimerax/map_fit/fitgui.py", line 302, in _model_moved  
self._update_metric_values()  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.8/site-
packages/chimerax/map_fit/fitgui.py", line 569, in _update_metric_values  
self._show_average_map_value(fatoms, bmap, log=log)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.8/site-
packages/chimerax/map_fit/fitgui.py", line 616, in _show_average_map_value  
self.status(msg)  
UnboundLocalError: local variable 'msg' referenced before assignment  
  
Error processing trigger "model position changed":  
UnboundLocalError: local variable 'msg' referenced before assignment  
  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.8/site-
packages/chimerax/map_fit/fitgui.py", line 616, in _show_average_map_value  
self.status(msg)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.8/site-
packages/chimerax/map_fit/fitgui.py", line 302, in _model_moved  
self._update_metric_values()  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.8/site-
packages/chimerax/map_fit/fitgui.py", line 569, in _update_metric_values  
self._show_average_map_value(fatoms, bmap, log=log)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.8/site-
packages/chimerax/map_fit/fitgui.py", line 616, in _show_average_map_value  
self.status(msg)  
UnboundLocalError: local variable 'msg' referenced before assignment  
  
Error processing trigger "model position changed":  
UnboundLocalError: local variable 'msg' referenced before assignment  
  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.8/site-
packages/chimerax/map_fit/fitgui.py", line 616, in _show_average_map_value  
self.status(msg)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.8/site-
packages/chimerax/map_fit/fitgui.py", line 302, in _model_moved  
self._update_metric_values()  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.8/site-
packages/chimerax/map_fit/fitgui.py", line 569, in _update_metric_values  
self._show_average_map_value(fatoms, bmap, log=log)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.8/site-
packages/chimerax/map_fit/fitgui.py", line 616, in _show_average_map_value  
self.status(msg)  
UnboundLocalError: local variable 'msg' referenced before assignment  
  
Error processing trigger "model position changed":  
UnboundLocalError: local variable 'msg' referenced before assignment  
  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.8/site-
packages/chimerax/map_fit/fitgui.py", line 616, in _show_average_map_value  
self.status(msg)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.8/site-
packages/chimerax/map_fit/fitgui.py", line 302, in _model_moved  
self._update_metric_values()  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.8/site-
packages/chimerax/map_fit/fitgui.py", line 569, in _update_metric_values  
self._show_average_map_value(fatoms, bmap, log=log)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.8/site-
packages/chimerax/map_fit/fitgui.py", line 616, in _show_average_map_value  
self.status(msg)  
UnboundLocalError: local variable 'msg' referenced before assignment  
  
Error processing trigger "model position changed":  
UnboundLocalError: local variable 'msg' referenced before assignment  
  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.8/site-
packages/chimerax/map_fit/fitgui.py", line 616, in _show_average_map_value  
self.status(msg)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.8/site-
packages/chimerax/map_fit/fitgui.py", line 302, in _model_moved  
self._update_metric_values()  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.8/site-
packages/chimerax/map_fit/fitgui.py", line 569, in _update_metric_values  
self._show_average_map_value(fatoms, bmap, log=log)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.8/site-
packages/chimerax/map_fit/fitgui.py", line 616, in _show_average_map_value  
self.status(msg)  
UnboundLocalError: local variable 'msg' referenced before assignment  
  
Error processing trigger "model position changed":  
UnboundLocalError: local variable 'msg' referenced before assignment  
  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.8/site-
packages/chimerax/map_fit/fitgui.py", line 616, in _show_average_map_value  
self.status(msg)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.8/site-
packages/chimerax/map_fit/fitgui.py", line 302, in _model_moved  
self._update_metric_values()  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.8/site-
packages/chimerax/map_fit/fitgui.py", line 569, in _update_metric_values  
self._show_average_map_value(fatoms, bmap, log=log)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.8/site-
packages/chimerax/map_fit/fitgui.py", line 616, in _show_average_map_value  
self.status(msg)  
UnboundLocalError: local variable 'msg' referenced before assignment  
  
Error processing trigger "model position changed":  
UnboundLocalError: local variable 'msg' referenced before assignment  
  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.8/site-
packages/chimerax/map_fit/fitgui.py", line 616, in _show_average_map_value  
self.status(msg)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.8/site-
packages/chimerax/map_fit/fitgui.py", line 302, in _model_moved  
self._update_metric_values()  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.8/site-
packages/chimerax/map_fit/fitgui.py", line 569, in _update_metric_values  
self._show_average_map_value(fatoms, bmap, log=log)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.8/site-
packages/chimerax/map_fit/fitgui.py", line 616, in _show_average_map_value  
self.status(msg)  
UnboundLocalError: local variable 'msg' referenced before assignment  
  
Error processing trigger "model position changed":  
UnboundLocalError: local variable 'msg' referenced before assignment  
  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.8/site-
packages/chimerax/map_fit/fitgui.py", line 616, in _show_average_map_value  
self.status(msg)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.8/site-
packages/chimerax/map_fit/fitgui.py", line 302, in _model_moved  
self._update_metric_values()  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.8/site-
packages/chimerax/map_fit/fitgui.py", line 569, in _update_metric_values  
self._show_average_map_value(fatoms, bmap, log=log)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.8/site-
packages/chimerax/map_fit/fitgui.py", line 616, in _show_average_map_value  
self.status(msg)  
UnboundLocalError: local variable 'msg' referenced before assignment  
  
Error processing trigger "model position changed":  
UnboundLocalError: local variable 'msg' referenced before assignment  
  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.8/site-
packages/chimerax/map_fit/fitgui.py", line 616, in _show_average_map_value  
self.status(msg)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.8/site-
packages/chimerax/map_fit/fitgui.py", line 302, in _model_moved  
self._update_metric_values()  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.8/site-
packages/chimerax/map_fit/fitgui.py", line 569, in _update_metric_values  
self._show_average_map_value(fatoms, bmap, log=log)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.8/site-
packages/chimerax/map_fit/fitgui.py", line 616, in _show_average_map_value  
self.status(msg)  
UnboundLocalError: local variable 'msg' referenced before assignment  
  
Error processing trigger "model position changed":  
UnboundLocalError: local variable 'msg' referenced before assignment  
  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.8/site-
packages/chimerax/map_fit/fitgui.py", line 616, in _show_average_map_value  
self.status(msg)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.8/site-
packages/chimerax/map_fit/fitgui.py", line 302, in _model_moved  
self._update_metric_values()  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.8/site-
packages/chimerax/map_fit/fitgui.py", line 569, in _update_metric_values  
self._show_average_map_value(fatoms, bmap, log=log)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.8/site-
packages/chimerax/map_fit/fitgui.py", line 616, in _show_average_map_value  
self.status(msg)  
UnboundLocalError: local variable 'msg' referenced before assignment  
  
Error processing trigger "model position changed":  
UnboundLocalError: local variable 'msg' referenced before assignment  
  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.8/site-
packages/chimerax/map_fit/fitgui.py", line 616, in _show_average_map_value  
self.status(msg)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.8/site-
packages/chimerax/map_fit/fitgui.py", line 302, in _model_moved  
self._update_metric_values()  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.8/site-
packages/chimerax/map_fit/fitgui.py", line 569, in _update_metric_values  
self._show_average_map_value(fatoms, bmap, log=log)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.8/site-
packages/chimerax/map_fit/fitgui.py", line 616, in _show_average_map_value  
self.status(msg)  
UnboundLocalError: local variable 'msg' referenced before assignment  
  
Error processing trigger "model position changed":  
UnboundLocalError: local variable 'msg' referenced before assignment  
  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.8/site-
packages/chimerax/map_fit/fitgui.py", line 616, in _show_average_map_value  
self.status(msg)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.8/site-
packages/chimerax/map_fit/fitgui.py", line 302, in _model_moved  
self._update_metric_values()  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.8/site-
packages/chimerax/map_fit/fitgui.py", line 569, in _update_metric_values  
self._show_average_map_value(fatoms, bmap, log=log)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.8/site-
packages/chimerax/map_fit/fitgui.py", line 616, in _show_average_map_value  
self.status(msg)  
UnboundLocalError: local variable 'msg' referenced before assignment  
  
Error processing trigger "model position changed":  
UnboundLocalError: local variable 'msg' referenced before assignment  
  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.8/site-
packages/chimerax/map_fit/fitgui.py", line 616, in _show_average_map_value  
self.status(msg)  
  
See log for complete Python traceback.  
  

> view matrix models #2,1,0,0,101.36,0,1,0,97.737,0,0,1,58.396




OpenGL version: 3.3.0 NVIDIA 470.63.01
OpenGL renderer: NVIDIA GeForce RTX 2080 SUPER/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Micro-Star International Co., Ltd.
Model: MS-7D04
OS: AlmaLinux 8.4 Electric Cheetah
Architecture: 64bit ELF
Virutal Machine: none
CPU: 16 11th Gen Intel(R) Core(TM) i9-11900KF @ 3.50GHz
Cache Size: 16384 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:           62Gi       6.7Gi       3.0Gi        57Mi        53Gi        55Gi
	Swap:          31Gi       1.1Gi        30Gi

Graphics:
	01:00.0 VGA compatible controller [0300]: NVIDIA Corporation TU104 [GeForce RTX 2080 SUPER] [10de:1e81] (rev a1)	
	Subsystem: ASUSTeK Computer Inc. Device [1043:8736]	
	Kernel driver in use: nvidia
Locale: ('en_US', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.12.5
    cftime: 1.5.0
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0.1
    ChimeraX-AddH: 2.1.6
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.13.2
    ChimeraX-AtomicLibrary: 3.1.3
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.2.1
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.5
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.1.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.3
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.0
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-Label: 1.0
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.0.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.2.1
    ChimeraX-MDcrds: 2.2
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0.1
    ChimeraX-ModelPanel: 1.0.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.1
    ChimeraX-OpenCommand: 1.5
    ChimeraX-PDB: 2.4.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.1
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.0.1
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.4
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.3.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.7.6
    ChimeraX-uniprot: 2.1
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.21
    decorator: 5.0.9
    distlib: 0.3.1
    distro: 1.5.0
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.17
    imagecodecs: 2020.5.30
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.7
    jupyter-core: 4.7.1
    kiwisolver: 1.3.1
    line-profiler: 2.1.2
    lxml: 4.6.2
    lz4: 3.1.0
    MarkupSafe: 2.0.1
    matplotlib: 3.3.2
    msgpack: 1.0.0
    netCDF4: 1.5.4
    networkx: 2.5
    numexpr: 2.7.3
    numpy: 1.19.2
    numpydoc: 1.1.0
    openvr: 1.14.1501
    packaging: 20.9
    ParmEd: 3.2.0
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 21.0.1
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.18
    psutil: 5.7.2
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.7.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.1
    pytz: 2021.1
    pyzmq: 22.0.3
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    setuptools: 50.3.2
    sfftk-rw: 0.6.7.dev1
    six: 1.15.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.2.2
    Sphinx: 3.2.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.9.3
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.0.5
    urllib3: 1.25.11
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.0
    wheel-filename: 1.2.0

Change History (2)

comment:1 by Tom Goddard, 4 years ago

Component: Unassigned → Volume Data
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → fitmap tool: local variable 'msg' referenced before assignment

comment:2 by Tom Goddard, 4 years ago

Resolution: → fixed
Status: assigned → closed

Fixed.

Using map fitting gui and reporting realtime average map value for atoms in map while moving atoms generated status message error when map has no surface depiction.

Note: See TracTickets for help on using tickets.