Problem playing through multiple volume series: object of type 'NoneType' has no len()

[sitins07@…]

The following bug report has been submitted:
Platform:        Linux-4.15.0-42-generic-x86_64-with-debian-buster-sid
ChimeraX Version: 0.9 (2018-12-20)
Description
Moving of Time bar in volume series while opened more than one volume series. Time bar either play both of them even if one is hide (it became visible) or crahes view (both series marked as shown but they are invisible)

Log:
UCSF ChimeraX version: 0.9 (2018-12-20)  
How to cite UCSF ChimeraX  

> toolshed show "Density Map Toolbar"

> set bgColor #888a85

> open /home/vpetryc/Projects/nch/MultiBody/Masks/MultyBody_6.cxs

opened ChimeraX session  
vol ignore padd value None  
m stats None -0.0383734405040741 0.14043882489204407  
vol ignore padd value None  
m stats None 0.0 1.0  
vol ignore padd value None  
m stats None 0.0 1.0  

> hide #!14 models

> hide #!4 models

> show #!4 models

> hide #!1 models

> show #!1 models

> hide #!4 models

> lighting full

> show #!14 models

> hide #!14 models

> hide #!14.1 models

> show #!14.1 models

> hide #!14 models

> show #!14 models

> ui mousemode rightMode select

> show #!10 models

vol ignore padd value None  
m stats None 0.0 0.36819931864738464  

> hide #!10 models

> show #!9 models

vol ignore padd value None  
m stats None 0.0 0.37250685691833496  

> hide #!9 models

Unknown command: history  

> rename #9 id 20

> hide #!20.1 models

> rename #9 id 9.1

> rename #9 Head_masks_30

> hide #!14 models

> show #!14 models

> show #!20 models

> hide #!20 models

> show #!10 models

> hide #!10 models

> rename #20 id 9.1

> rename #9 Head_masks_30

> rename #9 Head_masks_30

> hide #!9 models

> rename #10 id 9.2

> hide #!9.2.1 models

> close #11 #12 #13 #14

> show #!4 models

> hide #!1 models

> select #4

153717 atoms, 166780 bonds, 4796 pseudobonds, 2 models selected  

> show sel ribbons

> lighting simple

> select #4/X

1640 atoms, 1832 bonds, 68 pseudobonds, 1 model selected  

> select #4/Y

1618 atoms, 1806 bonds, 73 pseudobonds, 1 model selected  

Missing or invalid "resolution" argument: Expected a number  

> molmap sel 30 onGrid #1 replace false

vol ignore padd value None  
m stats None 0.0 0.27236494421958923  

> select #4/Z

3061 atoms, 3119 bonds selected  

> molmap sel 30 onGrid #1 replace false

vol ignore padd value None  
m stats None 0.0 0.3247012495994568  

> select #4/Y /Z

4679 atoms, 4925 bonds, 73 pseudobonds, 1 model selected  

> hide #!10 models

> hide #!11 models

> hide sel ribbons

> show sel ribbons

> show #!6 models

> hide #!6.1 models

vol ignore padd value None  
m stats None 0.0 0.32735055685043335  

> show #!10 models

> show #!11 models

> select up

153717 atoms, 166780 bonds, 4795 pseudobonds, 1 model selected  

> select up

613634 atoms, 665641 bonds, 4795 pseudobonds, 11 models selected  

> select up

613634 atoms, 665641 bonds, 4795 pseudobonds, 11 models selected  

> select down

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.6/site-
packages/chimerax/ui/gui.py", line 243, in forward_keystroke  
run(self.session, 'select down')  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.6/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.6/site-
packages/chimerax/core/commands/cli.py", line 2587, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.6/site-
packages/chimerax/std_commands/select.py", line 162, in select_down  
session.selection.demote(session)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.6/site-
packages/chimerax/core/selection.py", line 63, in demote  
self._promotion.demote_selection()  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.6/site-
packages/chimerax/core/selection.py", line 191, in demote_selection  
p.demote()  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.6/site-
packages/chimerax/core/selection.py", line 221, in demote  
m.selected_positions = self._prev_selected  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.6/site-
packages/chimerax/core/graphics/drawing.py", line 228, in __setattr__  
super(Drawing, self).__setattr__(key, value)  
AttributeError: can't set attribute  
  
AttributeError: can't set attribute  
  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.6/site-
packages/chimerax/core/graphics/drawing.py", line 228, in __setattr__  
super(Drawing, self).__setattr__(key, value)  
  
See log for complete Python traceback.  
  

> select down

464596 atoms, 503786 bonds, 73 pseudobonds, 9 models selected  

> select down

464596 atoms, 503786 bonds, 73 pseudobonds, 9 models selected  

> rename #10 tRNA_mask_30

> rename #11 EF-Tu_mask_30

> rename #11 id 6.3

> rename #10 id 6.4

> save session /home/vpetryc/Projects/nch/MultiBody/Masks/MultyBody_7.cxs

Session file format is not finalized, and thus might not be restorable in
other versions of ChimeraX.  

> save session ~/Projects/nch/MultiBody/Masks/Session_with_maps.cxs
includeMaps true

Session file format is not finalized, and thus might not be restorable in
other versions of ChimeraX.  

> save map ~/Projects/nch/MultiBody/Masks/EF-Tu-mask.mrc models #6.3

> save map ~/Projects/nch/MultiBody/Masks/tRNA-TC-mask.mrc models #6.4

> open /home/vpetryc/Projects/nch/MultiBody/Masks/MBR_tRNA-TC_mask.mrc

Summary of feedback from opening
/home/vpetryc/Projects/nch/MultiBody/Masks/MBR_tRNA-TC_mask.mrc  
---  
notes | vol ignore padd value None  
m stats None 0.0 1.0  
  
Opened MBR_tRNA-TC_mask.mrc, grid size 128,128,128, pixel 2.32, shown at level
0.642, step 1, values float32  

> hide #!6.3 models

> hide #!6.2 models

vol ignore padd value None  
m stats None 0.0 0.37256354093551636  

> open /home/vpetryc/Projects/nch/MultiBody/Masks/MBR_tRNA-TC_mask.mrc

Summary of feedback from opening
/home/vpetryc/Projects/nch/MultiBody/Masks/MBR_tRNA-TC_mask.mrc  
---  
notes | vol ignore padd value None  
m stats None 0.0 1.0  
  
Opened MBR_tRNA-TC_mask.mrc, grid size 128,128,128, pixel 2.32, shown at level
0.642, step 1, values float32  

> close #12

> hide #!13 models

> show #!13 models

> close #13

> open /home/vpetryc/Projects/nch/MultiBody/Masks/MBR_tRNA-TC_mask.mrc

Summary of feedback from opening
/home/vpetryc/Projects/nch/MultiBody/Masks/MBR_tRNA-TC_mask.mrc  
---  
notes | vol ignore padd value None  
m stats None 0.0 1.0  
  
Opened MBR_tRNA-TC_mask.mrc, grid size 128,128,128, pixel 2.32, shown at level
0.002, step 1, values float32  

> open /home/vpetryc/Projects/nch/MultiBody/Masks/MBR_EF-Tu-TC_mask.mrc

Summary of feedback from opening
/home/vpetryc/Projects/nch/MultiBody/Masks/MBR_EF-Tu-TC_mask.mrc  
---  
notes | vol ignore padd value None  
m stats None 0.0 1.0  
  
Opened MBR_EF-Tu-TC_mask.mrc, grid size 128,128,128, pixel 2.32, shown at
level 0.132, step 1, values float32  

> save session /home/vpetryc/Projects/nch/MultiBody/Masks/MultyBody_7.1.cxs

Session file format is not finalized, and thus might not be restorable in
other versions of ChimeraX.  

> close session

> open vseries /home/vpetryc/Projects/nch/MultiBody/trna-tu/

File not found: vseries  

> open vseries /home/vpetryc/Projects/nch/MultiBody/trna-
tu/analyse_component001_bin001.mrc

File not found: vseries  
Summary of feedback from opening files  
---  
notes | vol ignore padd value None  
m stats None -0.044876329600811005 0.13861683011054993  
vol ignore padd value None  
m stats None -0.044438619166612625 0.13865229487419128  
vol ignore padd value None  
m stats None -0.04341156780719757 0.13866519927978516  
vol ignore padd value None  
m stats None -0.04397549852728844 0.13867239654064178  
vol ignore padd value None  
m stats None -0.04455660656094551 0.13867761194705963  
vol ignore padd value None  
m stats None -0.045073989778757095 0.13868235051631927  
vol ignore padd value None  
m stats None -0.045113418251276016 0.1386876404285431  
vol ignore padd value None  
m stats None -0.04406735673546791 0.13869497179985046  
vol ignore padd value None  
m stats None -0.042945150285959244 0.1387079507112503  
vol ignore padd value None  
m stats None -0.04530459642410278 0.13874366879463196  
  
Opened analyse_component001_bin001.mrc, grid size 128,128,128, pixel 2.32,
shown at level 0.0858, step 1, values float32  

> close session

> open vseries /home/vpetryc/Projects/nch/MultiBody/trna-
tu/analyse_component001_bin001.mrc

File not found: vseries  

> open vseries /home/vpetryc/Projects/nch/MultiBody/trna-
tu/analyse_component001_bin00*

File not found: vseries  

> open vseries true /home/vpetryc/Projects/nch/MultiBody/trna-
tu/analyse_component001_bin00*

File not found: vseries  

> open vseries true /home/vpetryc/Projects/nch/MultiBody/trna-
tu/analyse_component001_bin0??.mrc

File not found: vseries  

> open /home/vpetryc/Projects/nch/MultiBody/trna-
tu/analyse_component001_bin0??.mrc

Summary of feedback from opening files  
---  
notes | vol ignore padd value None  
m stats None -0.044876329600811005 0.13861683011054993  
vol ignore padd value None  
m stats None -0.044438619166612625 0.13865229487419128  
vol ignore padd value None  
m stats None -0.04341156780719757 0.13866519927978516  
vol ignore padd value None  
m stats None -0.04397549852728844 0.13867239654064178  
vol ignore padd value None  
m stats None -0.04455660656094551 0.13867761194705963  
vol ignore padd value None  
m stats None -0.045073989778757095 0.13868235051631927  
vol ignore padd value None  
m stats None -0.045113418251276016 0.1386876404285431  
vol ignore padd value None  
m stats None -0.04406735673546791 0.13869497179985046  
vol ignore padd value None  
m stats None -0.042945150285959244 0.1387079507112503  
vol ignore padd value None  
m stats None -0.04530459642410278 0.13874366879463196  
  
Opened analyse_component001_bin001.mrc, grid size 128,128,128, pixel 2.32,
shown at level 0.0858, step 1, values float32  

> open /home/vpetryc/Projects/nch/MultiBody/trna-
tu/analyse_component001_bin0??.mrc vseries true

Summary of feedback from opening files  
---  
notes | vol ignore padd value None  
m stats None -0.044876329600811005 0.13861683011054993  
  
Opened map series analyse_component001_bin001.mrc, 10 images, grid size
128,128,128, pixel 2.32, shown at level 0.0858, step 1, values float32  

> close #1.1,2,3,4,5,6,7,8,9,10,0 #2

> close

> open /home/vpetryc/Projects/nch/MultiBody/trna-
tu/analyse_component001_bin0??.mrc vseries true

Summary of feedback from opening files  
---  
notes | vol ignore padd value None  
m stats None -0.044876329600811005 0.13861683011054993  
  
Opened map series analyse_component001_bin001.mrc, 10 images, grid size
128,128,128, pixel 2.32, shown at level 0.0858, step 1, values float32  
vol ignore padd value None  
m stats None -0.044876329600811005 0.13861683011054993  
vol ignore padd value None  
m stats None -0.04406735673546791 0.13869497179985046  

> open /home/vpetryc/Projects/nch/MultiBody/trna-
tu/analyse_component002_bin0??.mrc vseries true

Summary of feedback from opening files  
---  
notes | vol ignore padd value None  
m stats None -0.042903754860162735 0.13848410546779633  
  
Opened map series analyse_component002_bin001.mrc, 10 images, grid size
128,128,128, pixel 2.32, shown at level 0.0859, step 1, values float32  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.6/site-
packages/chimerax/map/series/slider.py", line 120, in slider_moved_cb  
self.update_time(t)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.6/site-
packages/chimerax/map/series/slider.py", line 132, in update_time  
s.show_time(t)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.6/site-
packages/chimerax/map/series/series.py", line 97, in show_time  
self.unshow_time(t)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.6/site-
packages/chimerax/map/series/series.py", line 120, in unshow_time  
v.display = False  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.6/site-
packages/chimerax/core/graphics/drawing.py", line 228, in __setattr__  
super(Drawing, self).__setattr__(key, value)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.6/site-
packages/chimerax/map/volume.py", line 607, in _set_display  
if display == self.display:  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.6/site-
packages/chimerax/core/graphics/drawing.py", line 311, in get_display  
return self._any_displayed_positions and len(self._positions) > 0  
TypeError: object of type 'NoneType' has no len()  
  
TypeError: object of type 'NoneType' has no len()  
  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.6/site-
packages/chimerax/core/graphics/drawing.py", line 311, in get_display  
return self._any_displayed_positions and len(self._positions) > 0  
  
See log for complete Python traceback.  
  

> close #1

> close #2

> open /home/vpetryc/Projects/nch/MultiBody/trna-
tu/analyse_component002_bin0??.mrc vseries true

Summary of feedback from opening files  
---  
notes | vol ignore padd value None  
m stats None -0.042903754860162735 0.13848410546779633  
  
Opened map series analyse_component002_bin001.mrc, 10 images, grid size
128,128,128, pixel 2.32, shown at level 0.0859, step 1, values float32  
vol ignore padd value None  
m stats None -0.04308639094233513 0.1385905146598816  

> close #1

> open /home/vpetryc/Projects/nch/MultiBody/trna-
tu/analyse_component003_bin0??.mrc vseries true

Summary of feedback from opening files  
---  
notes | vol ignore padd value None  
m stats None -0.041694317013025284 0.13819000124931335  
  
Opened map series analyse_component003_bin001.mrc, 10 images, grid size
128,128,128, pixel 2.32, shown at level 0.0858, step 1, values float32  
vol ignore padd value None  
m stats None -0.04363901913166046 0.1386757791042328  

> open /home/vpetryc/Projects/nch/MultiBody/trna-
tu/analyse_component002_bin0??.mrc vseries true

Summary of feedback from opening files  
---  
notes | vol ignore padd value None  
m stats None -0.042903754860162735 0.13848410546779633  
  
Opened map series analyse_component002_bin001.mrc, 10 images, grid size
128,128,128, pixel 2.32, shown at level 0.0859, step 1, values float32  
vol ignore padd value None  
m stats None -0.04507127031683922 0.13867123425006866  




OpenGL version: 3.3.0 NVIDIA 390.87
OpenGL renderer: Quadro 2000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

[Tom Goddard]

Fixed.

Attempting to use map series slider after first map in series was deleted (probably using the "-" delete button on the volume viewer panel) caused an error. Added code to handle deleted maps in series.

When you open two series of the same length ChimeraX controls both with the same slider since the most common case is the two series are related data such as two channels in light microscopy. If you want a separate slider for each map series then close the automatically created slider (x button on slider panel), and use commands to create the separate sliders

vseries slider #1
vseries slider #2