Session code trying to take len() of 'SurfaceUpdaters'

[kpwulab@…]

The following bug report has been submitted:
Platform:        macOS-10.14.1-x86_64-i386-64bit
ChimeraX Version: 1.3.dev202109172329 (2021-09-17 23:29:10 UTC)
Description
TypeError: object of type 'SurfaceUpdaters' has no len()

File "/Applications/Science/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/session.py", line 242, in discovery
if sm is None and len(value) == 0:

See log for complete Python traceback.


Log:
UCSF ChimeraX version: 1.3.dev202109172329 (2021-09-17)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open "/Users/kpwu/Documents/Research-IBC-AS/paper-drafts/2021-synyclein
> calcium effect/synuclein-1209 copy.cxs"

Opened aSyn-A53T-Ca-sharpen-job069.mrc as #3, grid size 280,280,280, pixel
0.83, shown at level 0.00781, step 1, values float32  
Opened aSyn-A53T-Ca-sharpen-job069.mrc copy as #5, grid size 280,280,280,
pixel 0.83, shown at level 0.00728, step 1, values float32  
Opened aSyn-no-Ca-sharpen-job022-May5.mrc as #4, grid size 280,280,280, pixel
0.83, shown at level 0.00724, step 1, values float32  
Opened aSyn-no-Ca-sharpen-job022-May5.mrc copy as #7, grid size 280,280,280,
pixel 0.83, shown at level 0.00906, step 1, values float32  
Log from Thu Dec 9 14:42:05 2021UCSF 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 "/Users/kpwu/Documents/Research-IBC-AS/paper-drafts/2021-synyclein
> calcium effect/aSyn A53T Ca-20210723-no water .pdb"

Chain information for aSyn A53T Ca-20210723-no water .pdb #1  
---  
Chain | Description  
A B C D E F G O P Q R S T U | No description available  
  

> hide atoms

> show cartoons

> show atoms

> style sphere

Changed 12964 atom styles  

> color gray #1

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

> color #1 gray

> color #1:/Phe Tyr yellow

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword  

> color #1:phe gray

> color #1:phe yellow

> color #1:phe tyr yellow

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword  

> color #1:phe,tyr yellow

> color #1:phe,tyr,val,leu,ile yellow

> color #1:asp,glu red

> color #1:lys,arg blue

> color #1:asn,gln,his,pro green

> color #1:asn,gln,his,pro lime

> color #1:asn,gln,his,pro,thr,ser lime

> hide cartoons

> color #1:gly,ala pink

> lighting flat

> lighting shadows true intensity 0.5

> lighting shadows false

> graphics silhouettes false

> lighting flat

> set bgColor white

> color #1:lys,arg light seagreen blue

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

> color #1:lys,arg lightseablue

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword  

> color #1:lys,arg liteseablue

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword  

> color #1:lys,arg lightseagreen

> color #1:lys,arg cyan

> lighting full

> lighting soft

> lighting flat

> ui tool show "Color Actions"

> color #1:asp,glu tomato

> color #1:asp,glu crimson

> open "/Users/kpwu/Documents/Research-IBC-AS/paper-drafts/2021-synyclein
> calcium effect/aSyn A53T no Ca 20210708.pdb"

Chain information for aSyn A53T no Ca 20210708.pdb #2  
---  
Chain | Description  
A B C D E F G H I J | No description available  
  

> select #2

9300 atoms, 9320 bonds, 650 residues, 1 model selected  

> color gray

> color phe,tyr,val,leu,ile yellow

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword  

> color asp,glu crimson

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword  

> color lys,arg cyan

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword  

> color asn,gln,his,pro,thr,ser lime

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword  

> color gly,ala pink

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword  

> hide #1 models

> ~select #2

Nothing selected  

> show #1 models

> hide #2 models

> color gly,ala pink

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword  

> color #1,2:phe,tyr,val,leu,ile yellow

> color #1,2:asp,glu crimson

> color #1,2:lys,arg cyan

> color #1,2:asn,gln,his,pro,thr,ser lime

> color #1,2:gly,ala pink

> show #2 models

> hide #1 models

> show #2 cartoons

> hide #2 cartoons

> show #2 cartoons

> show #1 models

> hide #2 models

> open "/Users/kpwu/Documents/Research-IBC-AS/project-synuclein in
> calcium/final-PDB-2021-0816/aSyn-A53T-Ca-200layers-20210817.pdb"

Summary of feedback from opening /Users/kpwu/Documents/Research-IBC-
AS/project-synuclein in calcium/final-
PDB-2021-0816/aSyn-A53T-Ca-200layers-20210817.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK Created by DsigNA  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
270395 messages similar to the above omitted  
  
Chain information for aSyn-A53T-Ca-200layers-20210817.pdb #3  
---  
Chain | Description  
B O | No description available  
  

> hide #1 models

> show #1 models

> hide #3 models

> open "/Users/kpwu/Documents/Research-IBC-AS/project-synuclein in
> calcium/maps/aSyn-Ca/aSyn-A53T-Ca-sharpen-job069-logfile.pdf"

Unrecognized file suffix '.pdf'  

> open "/Users/kpwu/Documents/Research-IBC-AS/project-synuclein in
> calcium/maps/aSyn-Ca/aSyn-A53T-Ca-sharpen-job069.mrc"

Opened aSyn-A53T-Ca-sharpen-job069.mrc as #4, grid size 280,280,280, pixel
0.83, shown at level 0.000817, step 2, values float32  

> volume #4 step 1

> volume #4 level 0.1

> volume #4 level 0.009875

> surface dust #4 size 8.3

> close #3

> close #4

> open "/Users/kpwu/Documents/Research-IBC-AS/project-synuclein in
> calcium/maps/aSyn-Ca/aSyn-A53T-Ca-sharpen-job069.mrc"

Opened aSyn-A53T-Ca-sharpen-job069.mrc as #3, grid size 280,280,280, pixel
0.83, shown at level 0.000817, step 2, values float32  

> volume #3 level 0.004655

> volume #3 step 1

> surface dust #3 size 8.3

> color zone #3 near #1 range 3

Expected a keyword  

> color zone #3 near #1 distance 3

> hide #1 models

> color zone #3 near #1 distance 7

> color zone #3 near #1 distance 5

> volume zone #3 nearAtoms #1 range 5

> surface dust #3 size 8.3

> volume zone #3 nearAtoms #1 range 7

> volume zone #3 nearAtoms #1 range 4

> volume zone #3 nearAtoms #1 range 3.5

> volume #3 level 0.008856

> volume zone #3 nearAtoms #1 range 4

> volume zone #3 nearAtoms #1 range 3

> graphics silhouettes false

> lighting flat

> lighting flat

> graphics silhouettes false

> lighting full

> lighting soft

> graphics silhouettes true

> graphics silhouettes false

> lighting shadows true intensity 0.5

> graphics silhouettes true

> lighting soft

> lighting simple

> volume zone #3 nearAtoms #1 range 6

> surface dust #3 size 8.3

> volume zone #3 nearAtoms #1 range 8

> surface dust #3 size 8.3

> volume #3 level 0.007806

> show #1 models

> hide #!3 models

> show #!3 models

> hide #1 models

> ui tool show "Map Eraser"

> volume erase #3 center 119.77,70.448,140.06 radius 8.4004

Opened aSyn-A53T-Ca-sharpen-job069.mrc copy as #5, grid size 280,280,280,
pixel 0.83, shown at step 1, values float32  

> volume zone #3 nearAtoms #1 range 8

> color zone #3 near #1 distance 5

> color zone #5 near #1 distance 5

> close #5

> show #1 models

> hide #1 models

> show #!3 models

> surface dust #3 size 8.3

> volume erase #3 center 119.78,70.997,139.77 radius 8.3664

Opened aSyn-A53T-Ca-sharpen-job069.mrc copy as #5, grid size 280,280,280,
pixel 0.83, shown at step 1, values float32  

> volume erase #5 center 126.69,70.255,143.27 radius 8.3664

> volume erase #5 center 118.59,81.735,141.08 radius 8.3664

> color zone #5 near #1 distance 5

> volume erase #5 center 114.66,87.213,140.69 radius 8.3664

> volume erase #5 center 103.11,91.288,140.31 radius 8.3664

> volume erase #5 center 108.5,93.989,140.39 radius 8.3664

> surface dust #5 size 8.3

> lighting flat

> lighting shadows true intensity 0.5

> lighting full

> lighting soft

> lighting simple

> volume #5 level 0.007543

> volume #5 level 0.007281

> surface dust #5 size 8.3

> surface dust #5 size 8.3

> transparency #5.1 50

> transparency #5.1 0

> volume erase #5 center 115.7,97.565,143.3 radius 8.3664

> color zone #5 near #1 distance 5

> hide #4 models

> show #4 models

> volume erase #5 center 92.383,124.85,89.273 radius 8.3664

> volume erase #5 center 90.4,131.65,89.466 radius 8.3664

> volume erase #5 center 89.797,133.19,90.199 radius 8.3664

> volume erase #5 center 94.927,137.69,89.964 radius 8.3664

> hide #4 models

> save /Users/kpwu/Desktop/aSyn-map-structure-1209.cxs

> color zone #5 near #1 distance 6

> show #!3 models

> hide #!5 models

> hide #!3 models

> close #4

> show #!5 models

> open "/Users/kpwu/Documents/Research-IBC-AS/project-synuclein in
> calcium/maps/aSyn-no-Ca-May-5-KP/aSyn-no-Ca-sharpen-job022-May5.mrc"

Opened aSyn-no-Ca-sharpen-job022-May5.mrc as #4, grid size 280,280,280, pixel
0.83, shown at level 0.00114, step 2, values float32  

> volume #4 step 1

> volume #4 level 0.007244

Color zone shortcut requires 1 displayed atomic model and 1 map, got 0 atomic
models, 1 maps.  

> surface dust #4 size 8.3

> show #2 models

> color zone #4 near #2 distance 4.98

> hide #2 models

> color zone #4 near #2 distance 6

> volume #4 level 0.009389

> show #2 models

> hide #!4 models

> show #2 cartoons

> show #!4 models

> volume #4 level 0.01302

> volume #4 level 0.0117

> hide #2 models

> volume #4 level 0.01021

> volume #4 level 0.008564

> volume #4 level 0.007244

> color zone #4 near #2 distance 8

> volume #4 level 0.008069

> ui tool show "Map Eraser"

> volume erase #4 center 90.412,121.63,93.244 radius 9.0636

Opened aSyn-no-Ca-sharpen-job022-May5.mrc copy as #7, grid size 280,280,280,
pixel 0.83, shown at step 1, values float32  

> volume erase #7 center 86.795,113.78,93.17 radius 9.0636

> color zone #7 near #2 distance 8

> volume erase #7 center 85.746,108.63,93.521 radius 9.0636

> surface dust #7 size 8.3

> volume erase #7 center 80.487,135.12,118.73 radius 9.0636

> volume erase #7 center 109.18,99.66,94.641 radius 9.0636

> volume erase #7 center 108.83,93.308,94.51 radius 9.0636

> volume erase #7 center 108.94,85.827,94.35 radius 9.0636

> volume erase #7 center 130.13,86.831,92.39 radius 9.0636

> volume erase #7 center 134.7,85.407,95.281 radius 9.0636

> volume erase #7 center 136.69,85.693,96.759 radius 9.0636

> volume erase #7 center 146.83,86.936,98.911 radius 9.0636

> volume erase #7 center 139.03,72.01,95.564 radius 9.0636

> volume erase #7 center 127.78,78.501,93.884 radius 9.0636

> show #2 models

> hide #!7 models

> show #!7 models

> hide #2 models

> volume #4 level 0.009059

> color zone #7 near #2 distance 10

> volume #4 level 0.007244

> hide #!7 models

> hide #6 models

> show #!5 models

> hide #!4 models

> show #1 models

> hide #!5 models

> lighting flat

> show #2 models

> hide #1 models

> hide #2 cartoons

> show #!3 models

> hide #2 models

> show #6 models

> show #!5 models

> hide #6 models

> show #!4 models

> hide #!5 models

> hide #!4 models

> show #!5 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!5 models

> show #!5 models

> hide #!3 models

> show #6 models

> show #!7 models

> hide #6 models

> hide #!5 models

> show #6 models

> volume #7 level 0.009059

> volume erase #7 center 119.42,95.73,132.9 radius 2.7888

> surface dust #7 size 8.3

> volume erase #7 center 111.49,110.34,132.37 radius 2.7888

> show #!5 models

> hide #!7 models

> hide #6 models

> graphics silhouettes false

> lighting full

> hide #!5 models

> show #2 models

> lighting flat

> graphics silhouettes false

> graphics silhouettes true

> open "/Users/kpwu/Documents/Research-IBC-AS/paper-drafts/2021-synyclein
> calcium effect/aSyn A53T Ca-20210723-no water.pdb"

Chain information for aSyn A53T Ca-20210723-no water.pdb #8  
---  
Chain | Description  
A B C D E F G O P Q R S T U | No description available  
  

> show #1 models

> hide #2 models

> hide #8 models

> show #8 models

> hide #1 models

> show #8 cartoons

> hide #8 atoms

> select #8

12964 atoms, 12992 bonds, 910 residues, 1 model selected  

> color sel dim gray

> select clear

> show #1 models

> hide #1 models

> save /Users/kpwu/Desktop/001.png width 751 height 741 supersample 3
> transparentBackground true

> show #1 models

> hide #8 models

> save /Users/kpwu/Desktop/002.png width 751 height 741 supersample 3
> transparentBackground true

> hide #1 models

> show #8 models

> select #8

12964 atoms, 12992 bonds, 910 residues, 1 model selected  

> hide sel cartoons

> select #8/G,U

1852 atoms, 1856 bonds, 130 residues, 1 model selected  

> show sel cartoons

> show #1 models

> hide #8 models

> show #8 models

> hide #1 models

> select clear

> setattr #8/U:87-92 res ss_type 2

Assigning ss_type attribute to 6 items  

> setattr #8:87-92 res ss_type 2

Assigning ss_type attribute to 84 items  

> setattr #8:89-92 res ss_type 2

Assigning ss_type attribute to 56 items  

> setattr #8:87-88 res ss_type 0

Assigning ss_type attribute to 28 items  

> setattr #8:88-92 res ss_type 2

Assigning ss_type attribute to 70 items  

> select #8

12964 atoms, 12992 bonds, 910 residues, 1 model selected  

> show sel cartoons

> select clear

> setattr #8:94-97 res ss_type 2

Assigning ss_type attribute to 56 items  

> select #8

12964 atoms, 12992 bonds, 910 residues, 1 model selected  

> setattr #8:94-97 res ss_type 2

Assigning ss_type attribute to 56 items  

> show sel cartoons

> show sel cartoons

> hide sel cartoons

> show sel cartoons

> ~select #8

Nothing selected  

> setattr #8:94-96 res ss_type 2

Assigning ss_type attribute to 42 items  

> setattr #8:94-97 res ss_type 2

Assigning ss_type attribute to 56 items  

> setattr #8:94-97 res ss_type 0

Assigning ss_type attribute to 56 items  

> setattr #8:94-97 res ss_type 2

Assigning ss_type attribute to 56 items  

> setattr #8:94-98 res ss_type 2

Assigning ss_type attribute to 70 items  

> select #8

12964 atoms, 12992 bonds, 910 residues, 1 model selected  

> style sel stick

Changed 12964 atom styles  

> show sel atoms

> setattr #8:94-98 res ss_type 0

Assigning ss_type attribute to 70 items  

> setattr #8:94-96 res ss_type 2

Assigning ss_type attribute to 42 items  

> hide sel atoms

> select clear

> setattr #8:63-66 res ss_type 2

Assigning ss_type attribute to 56 items  

> setattr #8:62-66 res ss_type 2

Assigning ss_type attribute to 70 items  

> show #8 cartoons

> show #1 models

> show #!7 models

> hide #8 models

> show #!3 models

> hide #1 models

> hide #!3 models

> show #2 models

> hide #2 models

> show #6 models

> volume erase #7 center 90.892,120.55,133.13 radius 2.7888

> volume erase #7 center 94.629,125.15,133.25 radius 2.7888

> volume erase #7 center 101.3,123.81,133.16 radius 2.7888

> volume erase #7 center 101.11,128.47,131.95 radius 2.7888

> volume erase #7 center 101.57,133.49,130.84 radius 2.7888

> volume erase #7 center 103.51,135.92,132.4 radius 2.7888

> volume erase #7 center 105.4,137.78,132.21 radius 2.7888

> volume erase #7 center 101.16,140.63,132.39 radius 2.7888

> volume erase #7 center 102.05,144.16,132.22 radius 2.7888

> volume erase #7 center 101.64,146.21,133.37 radius 2.7888

> volume erase #7 center 104.9,148.97,132.53 radius 2.7888

> volume erase #7 center 106.18,145.71,132.94 radius 2.7888

> volume erase #7 center 106.49,143.11,133.35 radius 2.7888

> volume erase #7 center 105.96,143.22,132.28 radius 2.7888

> volume erase #7 center 109.65,151.29,131.16 radius 2.7888

> volume erase #7 center 113.67,154.16,130.44 radius 2.7888

> volume erase #7 center 111.43,148.96,131.59 radius 2.7888

> volume erase #7 center 111.07,144.45,131.34 radius 2.7888

> volume erase #7 center 107.31,140.03,132.29 radius 2.7888

> volume erase #7 center 109.76,139.72,132.27 radius 2.7888

> volume erase #7 center 108.8,139.44,131 radius 2.7888

> volume erase #7 center 111.5,140.11,131.09 radius 2.7888

> save /Users/kpwu/Desktop/synuclein-1209.cxs includeMaps true

——— End of log from Thu Dec 9 14:42:05 2021 ———

opened ChimeraX session  

> save /Users/kpwu/Desktop/xxx.cxs includeMaps true

Traceback (most recent call last):  
File
"/Applications/Science/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 887, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/Science/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 616, in save  
mgr.discovery(self._state_containers)  
File
"/Applications/Science/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 242, in discovery  
if sm is None and len(value) == 0:  
TypeError: object of type 'SurfaceUpdaters' has no len()  
  
TypeError: object of type 'SurfaceUpdaters' has no len()  
  
File
"/Applications/Science/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 242, in discovery  
if sm is None and len(value) == 0:  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/Science/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 116, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File
"/Applications/Science/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File
"/Applications/Science/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 51, in display  
run(session, cmd)  
File
"/Applications/Science/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/Science/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/Science/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File
"/Applications/Science/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/Science/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 89, in provider_save  
saver_info.save(session, path, **provider_kw)  
File
"/Applications/Science/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core_formats/__init__.py", line 84, in save  
return cxs_save(session, path, **kw)  
File
"/Applications/Science/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 887, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/Science/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 616, in save  
mgr.discovery(self._state_containers)  
File
"/Applications/Science/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 242, in discovery  
if sm is None and len(value) == 0:  
TypeError: object of type 'SurfaceUpdaters' has no len()  
  
TypeError: object of type 'SurfaceUpdaters' has no len()  
  
File
"/Applications/Science/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 242, in discovery  
if sm is None and len(value) == 0:  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-12.2.17
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 655
OpenGL vendor: Intel Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro15,2
      Processor Name: Intel Core i5
      Processor Speed: 2.3 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 6 MB
      Memory: 16 GB
      Boot ROM Version: 1554.80.3.0.0 (iBridge: 18.16.14347.0.0,0)

Software:

    System Software Overview:

      System Version: macOS 10.14.1 (18B75)
      Kernel Version: Darwin 18.2.0
      Time since boot: 38 days 4:35

Graphics/Displays:

    Intel Iris Plus Graphics 655:

      Chipset Model: Intel Iris Plus Graphics 655
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3ea5
      Revision ID: 0x0001
      Metal: Supported, feature set macOS GPUFamily2 v1
      Displays:
        DELL P2719H:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60 Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: DRT2LS2     
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Adapter Type: DVI or HDMI
          Automatically Adjust Brightness: No
        DELL P2719H:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60 Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: 2S0TKS2     
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: No
          Connection Type: DVI or HDMI
          Adapter Firmware Version: 0.00

Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.2
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.5.30
    cftime: 1.5.0
    chardet: 4.0.0
    ChimeraX-AddCharge: 1.1.4
    ChimeraX-AddH: 2.1.10
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.2
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.29.1
    ChimeraX-AtomicLibrary: 4.1.4
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3.dev202109172329
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    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: 1.1
    ChimeraX-Hbonds: 2.1.1
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.1
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2
    ChimeraX-ModelPanel: 1.2
    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: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6.2
    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: 2.1
    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: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6
    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: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-VIPERdb: 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: 0.4.4
    cxservices: 1.1
    cycler: 0.10.0
    Cython: 0.29.24
    decorator: 5.1.0
    distlib: 0.3.2
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.4.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.20
    imagecodecs: 2021.4.28
    imagesize: 1.2.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.8.1
    kiwisolver: 1.3.2
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.7.3
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.0
    ParmEd: 3.2.0
    parso: 0.8.2
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.20
    psutil: 5.8.0
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    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: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.1
    RandomWords: 0.3.0
    requests: 2.25.1
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    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
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.0
    urllib3: 1.26.6
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0

[Eric Pettersen]

Hi Kuen,

Thanks for reporting this problem. It was fixed about 6 days after the release that you have, so if you upgrade to the 1.3 production release you won't run into it anymore.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab