Meeting error in debugging code that checks for null bytes in messages

[goddard@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19041
ChimeraX Version: 1.2.dev202010160427 (2020-10-16 04:27:26 UTC)
Description
3 person vr test with Phil and Victor.  Phil's bandwidth became very slow, lagging minutes in ChimeraX and he tried to rejoin.  I think this null bytes might have happened when he quit and then rejoined.

Log:
UCSF ChimeraX version: 1.2.dev202010160427 (2020-10-16)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open C:\cygwin64\home\goddard\ucsf\data\sars-cov-2-spike\spike2.cxs format
> session

Log from Fri Oct 16 10:33:28 2020UCSF ChimeraX version: 1.2.dev202010160427
(2020-10-16)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open C:\cygwin64\home\goddard\ucsf\data\sars-cov-2-spike\spike1.cxs format
> session

Log from Thu Oct 15 18:43:57 2020UCSF ChimeraX version: 1.2.dev202010081722
(2020-10-14)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/goddard/ucsf/data/sars-cov-2-spike/6vsb_glycosylated.pdb

Chain information for 6vsb_glycosylated.pdb #1  
---  
Chain | Description  
A B C | No description available  
  

> open /Users/goddard/ucsf/data/sars-cov-2-spike/6vsb_6vw1_ace2.pdb

Chain information for 6vsb_6vw1_ace2.pdb #2  
---  
Chain | Description  
A B C | No description available  
D | No description available  
  

> open /Users/goddard/ucsf/data/sars-
> cov-2-spike/6vsb_6wpt_6wps_S309_antibody.pdb

Chain information for 6vsb_6wpt_6wps_S309_antibody.pdb #3  
---  
Chain | Description  
A B C | No description available  
D F | No description available  
E G | No description available  
  

> open /Users/goddard/ucsf/data/sars-cov-2-spike/6vsb_6z43_H11-D4_nanobody.pdb

Chain information for 6vsb_6z43_H11-D4_nanobody.pdb #4  
---  
Chain | Description  
A B C | No description available  
D E F | No description available  
  

> open /Users/goddard/ucsf/data/sars-cov-2-spike/1qmo_fril_lectin.cif

1qmo_fril_lectin.cif title:  
Structure of FRIL, a legume lectin that delays hematopoietic progenitor
maturation [more info...]  
  
Chain information for 1qmo_fril_lectin.cif #5  
---  
Chain | Description  
A B C D | mannose binding lectin, fril  
E F G H | mannose binding lectin, fril  
  
Non-standard residues in 1qmo_fril_lectin.cif #5  
---  
CA — calcium ion  
MAN — alpha-D-mannopyranose  
MN — manganese (II) ion  
  

> mmaker #3/A,B,C to #1/A,B,C

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6vsb_glycosylated.pdb, chain C (#1) with
6vsb_6wpt_6wps_S309_antibody.pdb, chain C (#3), sequence alignment score =
6629  
RMSD between 1273 pruned atom pairs is 0.003 angstroms; (across all 1273
pairs: 0.003)  
  

> preset "initial styles" cartoon

Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> hide #!5 models

> hide #4 models

> hide #!3 models

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> select #2/D

10529 atoms, 10711 bonds, 638 residues, 1 model selected  

> delete #2 & ~/D

> hide #2 models

> show #2 models

> select clear

> select #1:333-527

9009 atoms, 9153 bonds, 585 residues, 1 model selected  

> select #1/A:333-527

3003 atoms, 3051 bonds, 195 residues, 1 model selected  

> color list

No custom colors.  
248 builtin colors: alice blue

, aliceblue

, antique white

, antiquewhite

, aqua

, aquamarine

, azure

, beige

, bisque

, black

, blanched almond

, blanchedalmond

, blue

, blue violet

, blueviolet

, brown

, burly wood

, burlywood

, cadet blue

, cadetblue

, chartreuse

, chocolate

, coral

, cornflower blue

, cornflowerblue

, cornsilk

, crimson

, cyan

, dark blue

, dark cyan

, dark goldenrod

, dark gray

, dark green

, dark grey

, dark khaki

, dark magenta

, dark olive green

, dark orange

, dark orchid

, dark red

, dark salmon

, dark sea green

, dark seagreen

, dark slate blue

, dark slate gray

, dark slate grey

, dark turquoise

, dark violet

, darkblue

, darkcyan

, darkgoldenrod

, darkgray

, darkgreen

, darkgrey

, darkkhaki

, darkmagenta

, darkolivegreen

, darkorange

, darkorchid

, darkred

, darksalmon

, darkseagreen

, darkslateblue

, darkslategray

, darkslategrey

, darkturquoise

, darkviolet

, deep pink

, deep sky blue

, deep skyblue

, deeppink

, deepskyblue

, dim gray

, dim grey

, dimgray

, dimgrey

, dodger blue

, dodgerblue

, fire brick

, firebrick

, floral white

, floralwhite

, forest green

, forestgreen

, fuchsia

, gainsboro

, ghost white

, ghostwhite

, gold

, goldenrod

, gray

, green

, green yellow

, greenyellow

, grey

, honeydew

, hot pink

, hotpink

, indian red

, indianred

, indigo

, ivory

, khaki

, lavender

, lavender blush

, lavenderblush

, lawn green

, lawngreen

, lemon chiffon

, lemonchiffon

, light blue

, light coral

, light cyan

, light goldenrod yellow

, light gray

, light green

, light grey

, light pink

, light salmon

, light sea green

, light seagreen

, light sky blue

, light skyblue

, light slate gray

, light slate grey

, light steel blue

, light yellow

, lightblue

, lightcoral

, lightcyan

, lightgoldenrodyellow

, lightgray

, lightgreen

, lightgrey

, lightpink

, lightsalmon

, lightseagreen

, lightskyblue

, lightslategray

, lightslategrey

, lightsteelblue

, lightyellow

, lime

, lime green

, limegreen

, linen

, magenta

, maroon

, medium aquamarine

, medium blue

, medium orchid

, medium purple

, medium sea green

, medium seagreen

, medium slate blue

, medium spring green

, medium turquoise

, medium violet red

, mediumaquamarine

, mediumblue

, mediumorchid

, mediumpurple

, mediumseagreen

, mediumslateblue

, mediumspringgreen

, mediumturquoise

, mediumvioletred

, midnight blue

, midnightblue

, mint cream

, mintcream

, misty rose

, mistyrose

, moccasin

, navajo white

, navajowhite

, navy

, old lace

, oldlace

, olive

, olive drab

, olivedrab

, orange

, orange red

, orangered

, orchid

, pale goldenrod

, pale green

, pale turquoise

, pale violet red

, palegoldenrod

, palegreen

, paleturquoise

, palevioletred

, papaya whip

, papayawhip

, peach puff

, peachpuff

, peru

, pink

, plum

, powder blue

, powderblue

, purple

, rebecca purple

, rebeccapurple

, red

, rosy brown

, rosybrown

, royal blue

, royalblue

, saddle brown

, saddlebrown

, salmon

, sandy brown

, sandybrown

, sea green

, seagreen

, seashell

, sienna

, silver

, sky blue

, skyblue

, slate blue

, slate gray

, slate grey

, slateblue

, slategray

, slategrey

, snow

, spring green

, springgreen

, steel blue

, steelblue

, tan

, teal

, thistle

, tomato

, transparent

, turquoise

, violet

, wheat

, white

, white smoke

, whitesmoke

, yellow

, yellow green

, and yellowgreen

.  

> color #1/A:333-527 tomato

> color #1/B:333-527 salmon

> color #1/C:333-527 coral

> select #1 & ligand

14040 atoms, 14559 bonds, 588 residues, 1 model selected  

> select #1 & ligand & C

4083 atoms, 3240 bonds, 588 residues, 1 model selected  

> color #1 & ligand & C yellow

> select clear

> hide #2 models

> show #!3 models

> delete #2/A,B,C

> delete #3/A,B,C

> hide #!3 models

> show #4 models

> delete #4/A,B,C

> show #2 models

> hide #2 models

> hide #4 models

> show #!5 models

> color #4 bychain

> color #4/B,C orange

> hide #!5 models

> show #4 models

> color #4 lightgreen

> hide #4 models

> show #!5 models

> color #5 bychain

> color #5/A,E,H,D gold

> color #5/B,F,C,G lightyellow

> color #5/B,F gray

> color #5/B,F khaki

> color #5/H,D goldenrod

> color #5/G,C lemonchiffon

> select #5 ligand

Expected a keyword  

> select #5 & ligand

48 atoms, 48 bonds, 4 residues, 1 model selected  

> color #5 & ligand @ C blue

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

> color #5 & ligand & C skyblue

> style sel sphere

Changed 48 atom styles  

> select clear

> color #5 & ligand byhetero

> align #5/D:302@C1,C2,C3,C4,C5 toAtoms #1/A:2025@C1,C2,C3,C4,C5

RMSD between 5 atom pairs is 0.042 angstroms  

> select #5/D:302

12 atoms, 12 bonds, 1 residue, 1 model selected  

> style sel stick

Changed 12 atom styles  

> select clear

> hide #!5 models

> show #!5 models

> surface enclose #1/A,B,C:1-332,528-2000

> lighting soft

> usage color

color [objects] [color [what]] [target characters from 'abcfprs']
[transparency a number] [halfbond true or false]  
— color objects  
objects: an objects specifier or nothing  
color: a color or one of byatom, bychain, byelement, byhetero, bymodel,
bynucleotide, bypolymer, fromatoms, or random  
what: a collection of one of All, atoms, bonds, cartoons, labels, pseudobonds,
ribbons, rings, or surfaces  
Subcommands are:

  * color bfactor
  * color byattribute
  * color cylindrical
  * color delete
  * color electrostatic
  * color gradient
  * color height
  * color image
  * color list
  * color modify
  * color name
  * color radial
  * color sample
  * color sequential
  * color show
  * color zone

  

> color #1/A,B,C:1-332,528-2000 gray surfaces

> lighting simple

> hide #!5 models

> show #2 models

> hide #2 models

> show #!3 models

> hide #!3 models

> show #4 models

> hide #4 models

> show #!5 models

> surface close

> usage cartoon style

cartoon style [atoms] [width a number] [thickness a number] [arrows true or
false] [arrowsHelix true or false] [arrowScale arrowScale] [xsection xsection]
[sides sides] [divisions divisions] [barScale a number] [barSides barSides]
[modeHelix modeHelix] [radius radius]  
— set cartoon style for secondary structures in specified models  
arrowScale: a number ≥ 1.0 and ≤ 5.0  
xsection: one of barbell, oval, piping, rectangle, round, or square  
sides: an even integer ≥ 3 and ≤ 24  
divisions: an integer ≥ 2 and ≤ 40  
barSides: an even integer ≥ 3 and ≤ 24  
modeHelix: one of default, tube, or wrap  
radius: a number or auto  

> caft style #1 modehelix tube

Unknown command: caft style #1 modehelix tube  

> cartoon style #1 modeHelix tube

> hide #!5 models

> save spike1.cxs

——— End of log from Thu Oct 15 18:43:57 2020 ———

opened ChimeraX session  

> usage rename

rename models [name] [id id]  
— rename a model or change its id number  
name: a text string  
id: a model id  

> rename #1 "Spike sars-cov-2"

> rename #2 ACE2

> rename #3 "Antibody S309"

> rename #4 "Nanobody H11-D4"

> rename #5 "FRIL lectin"

> save C:/cygwin64/home/goddard/ucsf/data/sars-cov-2-spike/spike2.cxs

——— End of log from Fri Oct 16 10:33:28 2020 ———

opened ChimeraX session  

> vr true

started SteamVR rendering  

> show #2 models

> meeting start

Meeting at DESKTOP-J8FC2Q4 or 192.168.0.2 port 52194  
Connection accepted from 73.128.52.221 port 59835  
Connection accepted from 68.84.133.89 port 50439  

> vr true

VR mode move picked models  

> view matrix models
> #2,0.73532,-0.67739,0.021217,71.061,0.6614,0.71042,-0.24051,-33.272,0.14784,0.19088,0.97042,-35.839

> view matrix models
> #2,0.77383,-0.51135,-0.3738,195.74,0.38986,0.84962,-0.35518,-44.959,0.4992,0.12911,0.85681,19.032

> view matrix models
> #2,0.78773,-0.5731,-0.22597,84.898,0.14345,0.52737,-0.83745,127.23,0.59909,0.62725,0.49763,136.14

> marker segment #6 position -21.85,-131.3,277.1 toPosition -7.903,-113,251.4
> color yellow radius 0.812 label 34.45 labelHeight 3.445 labelColor yellow
> adjust #6:1,2

Socket error Unable to write  
Disconnected from 73.128.52.221:59835  

> marker segment #6 position 12.63,-145.3,298.3 toPosition 57.31,-96.97,225
> color yellow radius 0.812 label 98.53 labelHeight 9.853 labelColor yellow
> adjust #6:3,4

VR mode tape measure  

> marker segment #7 position 10.2,-70.26,227.3 toPosition -6.408,-51.46,-21.91
> color yellow radius 0.812 label 250.5 labelHeight 25.05 labelColor yellow
> adjust #7:1,2

> marker delete #6

Deleted 6 markers  

> marker segment #6 position -26.17,-1.52,283.3 toPosition
> -2.264,-0.2981,-46.88 color yellow radius 0.812 label 331.1 labelHeight
> 33.11 labelColor yellow adjust #6:1,2

> marker delete #7

> marker delete #6

Deleted 4 markers  

> marker segment #6 position 13.43,-20.41,104.1 toPosition -4.646,-25.72,118.4
> color yellow radius 0.812 label 23.64 labelHeight 2.364 labelColor yellow
> adjust #6:1,2

Connection accepted from 73.128.52.221 port 60122  
VR mode move picked models  

> view matrix models
> #2,0.78773,-0.5731,-0.22597,84.898,0.14345,0.52737,-0.83745,127.23,0.59909,0.62725,0.49763,136.14

VR mode move picked models  

> view matrix models
> #2,0.78773,-0.5731,-0.22597,84.898,0.14345,0.52737,-0.83745,127.23,0.59909,0.62725,0.49763,136.14

> marker segment #6 position -17.97,-42.82,111.9 toPosition -29.09,-34.1,114.9
> color yellow radius 0.812 label 14.46 labelHeight 1.624 labelColor yellow
> adjust #6:3,4

> marker segment #6 position -48.05,-68.52,115.1 toPosition -40.9,-66.06,92.25
> color yellow radius 0.812 label 24.08 labelHeight 2.408 labelColor yellow
> adjust #6:5,6

> marker delete #6

Deleted 8 markers  

> marker delete #6

Deleted 2 markers  

> marker delete #6

Deleted 2 markers  

> marker delete #6

Deleted 2 markers  

> marker segment #6 position -43.75,-189.8,186.8 toPosition -20.6,-57.55,191.4
> color yellow radius 0.812 label 134.3 labelHeight 13.43 labelColor yellow
> adjust #6:1,2

> marker delete #6

Deleted 4 markers  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX-Oct-16-2020\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 614, in _data_available  
msg = self._read_message()  
File "C:\Program Files\ChimeraX-Oct-16-2020\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 633, in _read_message  
self._check_for_null_bytes(rbytes) # Debug code. Ticket #3784  
File "C:\Program Files\ChimeraX-Oct-16-2020\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 640, in _check_for_null_bytes  
last_block = self._bytes_list[-1]  
IndexError: list index out of range  
  
IndexError: list index out of range  
  
File "C:\Program Files\ChimeraX-Oct-16-2020\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 640, in _check_for_null_bytes  
last_block = self._bytes_list[-1]  
  
See log for complete Python traceback.  
  

> marker segment #6 position -9.514,-85.22,147.8 toPosition
> -8.721,-86.37,146.3 color yellow radius 0.7463 label 2.077 labelHeight 1.493
> labelColor yellow

> view matrix models
> #2,0.78773,-0.5731,-0.22597,84.898,0.14345,0.52737,-0.83745,127.23,0.59909,0.62725,0.49763,136.14

Socket error The remote host closed the connection  
Disconnected from 68.84.133.89:50439  
Connection accepted from 68.84.133.89 port 50495  

> hide #!102 models

> show #!102 models

> hide #!102 models

> show #!102 models

> hide #!103 models

> hide #!102 models

> show #!103 models

> view matrix models
> #1,0.94608,-0.29831,-0.12627,55.925,0.30469,0.95184,0.034192,42.702,0.10999,-0.070821,0.99141,9.1431

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX-Oct-16-2020\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 614, in _data_available  
msg = self._read_message()  
File "C:\Program Files\ChimeraX-Oct-16-2020\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 633, in _read_message  
self._check_for_null_bytes(rbytes) # Debug code. Ticket #3784  
File "C:\Program Files\ChimeraX-Oct-16-2020\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 640, in _check_for_null_bytes  
last_block = self._bytes_list[-1]  
IndexError: list index out of range  
  
IndexError: list index out of range  
  
File "C:\Program Files\ChimeraX-Oct-16-2020\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 640, in _check_for_null_bytes  
last_block = self._bytes_list[-1]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX-Oct-16-2020\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 614, in _data_available  
msg = self._read_message()  
File "C:\Program Files\ChimeraX-Oct-16-2020\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 633, in _read_message  
self._check_for_null_bytes(rbytes) # Debug code. Ticket #3784  
File "C:\Program Files\ChimeraX-Oct-16-2020\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 640, in _check_for_null_bytes  
last_block = self._bytes_list[-1]  
IndexError: list index out of range  
  
IndexError: list index out of range  
  
File "C:\Program Files\ChimeraX-Oct-16-2020\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 640, in _check_for_null_bytes  
last_block = self._bytes_list[-1]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX-Oct-16-2020\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 614, in _data_available  
msg = self._read_message()  
File "C:\Program Files\ChimeraX-Oct-16-2020\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 633, in _read_message  
self._check_for_null_bytes(rbytes) # Debug code. Ticket #3784  
File "C:\Program Files\ChimeraX-Oct-16-2020\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 640, in _check_for_null_bytes  
last_block = self._bytes_list[-1]  
IndexError: list index out of range  
  
IndexError: list index out of range  
  
File "C:\Program Files\ChimeraX-Oct-16-2020\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 640, in _check_for_null_bytes  
last_block = self._bytes_list[-1]  
  
See log for complete Python traceback.  
  

> view matrix models
> #1,0.93848,-0.33728,-0.074178,167.42,0.33844,0.94099,0.0031649,61.488,0.068733,-0.028073,0.99724,16.197

> hide #2 models

> show #!3 models

> view matrix models
> #1,0.8847,0.42617,-0.18888,82.412,-0.43756,0.89894,-0.021172,-7.8268,0.16078,0.10138,0.98177,1.1626

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX-Oct-16-2020\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 614, in _data_available  
msg = self._read_message()  
File "C:\Program Files\ChimeraX-Oct-16-2020\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 633, in _read_message  
self._check_for_null_bytes(rbytes) # Debug code. Ticket #3784  
File "C:\Program Files\ChimeraX-Oct-16-2020\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 640, in _check_for_null_bytes  
last_block = self._bytes_list[-1]  
IndexError: list index out of range  
  
IndexError: list index out of range  
  
File "C:\Program Files\ChimeraX-Oct-16-2020\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 640, in _check_for_null_bytes  
last_block = self._bytes_list[-1]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX-Oct-16-2020\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 614, in _data_available  
msg = self._read_message()  
File "C:\Program Files\ChimeraX-Oct-16-2020\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 633, in _read_message  
self._check_for_null_bytes(rbytes) # Debug code. Ticket #3784  
File "C:\Program Files\ChimeraX-Oct-16-2020\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 640, in _check_for_null_bytes  
last_block = self._bytes_list[-1]  
IndexError: list index out of range  
  
IndexError: list index out of range  
  
File "C:\Program Files\ChimeraX-Oct-16-2020\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 640, in _check_for_null_bytes  
last_block = self._bytes_list[-1]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX-Oct-16-2020\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 614, in _data_available  
msg = self._read_message()  
File "C:\Program Files\ChimeraX-Oct-16-2020\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 633, in _read_message  
self._check_for_null_bytes(rbytes) # Debug code. Ticket #3784  
File "C:\Program Files\ChimeraX-Oct-16-2020\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 640, in _check_for_null_bytes  
last_block = self._bytes_list[-1]  
IndexError: list index out of range  
  
IndexError: list index out of range  
  
File "C:\Program Files\ChimeraX-Oct-16-2020\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 640, in _check_for_null_bytes  
last_block = self._bytes_list[-1]  
  
See log for complete Python traceback.  
  

> hide #!3 models

> show #4 models

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX-Oct-16-2020\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 614, in _data_available  
msg = self._read_message()  
File "C:\Program Files\ChimeraX-Oct-16-2020\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 633, in _read_message  
self._check_for_null_bytes(rbytes) # Debug code. Ticket #3784  
File "C:\Program Files\ChimeraX-Oct-16-2020\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 640, in _check_for_null_bytes  
last_block = self._bytes_list[-1]  
IndexError: list index out of range  
  
IndexError: list index out of range  
  
File "C:\Program Files\ChimeraX-Oct-16-2020\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 640, in _check_for_null_bytes  
last_block = self._bytes_list[-1]  
  
See log for complete Python traceback.  
  

> view matrix models
> #1,0.97561,0.01776,-0.2188,58.939,-0.037443,0.99558,-0.08614,19.636,0.2163,0.092231,0.97196,5.2177

> view matrix models
> #1,0.89545,0.18185,-0.40631,-26.028,-0.17972,0.98274,0.043778,28.157,0.40726,0.033818,0.91269,-42.377

> view matrix models
> #1,0.98425,-0.089833,-0.1522,47.886,0.11901,0.97355,0.19503,-50.718,0.13066,-0.21007,0.96892,14.084

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX-Oct-16-2020\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 614, in _data_available  
msg = self._read_message()  
File "C:\Program Files\ChimeraX-Oct-16-2020\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 633, in _read_message  
self._check_for_null_bytes(rbytes) # Debug code. Ticket #3784  
File "C:\Program Files\ChimeraX-Oct-16-2020\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 640, in _check_for_null_bytes  
last_block = self._bytes_list[-1]  
IndexError: list index out of range  
  
IndexError: list index out of range  
  
File "C:\Program Files\ChimeraX-Oct-16-2020\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 640, in _check_for_null_bytes  
last_block = self._bytes_list[-1]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX-Oct-16-2020\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 614, in _data_available  
msg = self._read_message()  
File "C:\Program Files\ChimeraX-Oct-16-2020\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 633, in _read_message  
self._check_for_null_bytes(rbytes) # Debug code. Ticket #3784  
File "C:\Program Files\ChimeraX-Oct-16-2020\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 640, in _check_for_null_bytes  
last_block = self._bytes_list[-1]  
IndexError: list index out of range  
  
IndexError: list index out of range  
  
File "C:\Program Files\ChimeraX-Oct-16-2020\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 640, in _check_for_null_bytes  
last_block = self._bytes_list[-1]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX-Oct-16-2020\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 614, in _data_available  
msg = self._read_message()  
File "C:\Program Files\ChimeraX-Oct-16-2020\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 633, in _read_message  
self._check_for_null_bytes(rbytes) # Debug code. Ticket #3784  
File "C:\Program Files\ChimeraX-Oct-16-2020\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 640, in _check_for_null_bytes  
last_block = self._bytes_list[-1]  
IndexError: list index out of range  
  
IndexError: list index out of range  
  
File "C:\Program Files\ChimeraX-Oct-16-2020\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 640, in _check_for_null_bytes  
last_block = self._bytes_list[-1]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX-Oct-16-2020\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 614, in _data_available  
msg = self._read_message()  
File "C:\Program Files\ChimeraX-Oct-16-2020\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 633, in _read_message  
self._check_for_null_bytes(rbytes) # Debug code. Ticket #3784  
File "C:\Program Files\ChimeraX-Oct-16-2020\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 640, in _check_for_null_bytes  
last_block = self._bytes_list[-1]  
IndexError: list index out of range  
  
IndexError: list index out of range  
  
File "C:\Program Files\ChimeraX-Oct-16-2020\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 640, in _check_for_null_bytes  
last_block = self._bytes_list[-1]  
  
See log for complete Python traceback.  
  

> hide #4 models

> show #!5 models

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX-Oct-16-2020\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 614, in _data_available  
msg = self._read_message()  
File "C:\Program Files\ChimeraX-Oct-16-2020\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 633, in _read_message  
self._check_for_null_bytes(rbytes) # Debug code. Ticket #3784  
File "C:\Program Files\ChimeraX-Oct-16-2020\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 640, in _check_for_null_bytes  
last_block = self._bytes_list[-1]  
IndexError: list index out of range  
  
IndexError: list index out of range  
  
File "C:\Program Files\ChimeraX-Oct-16-2020\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 640, in _check_for_null_bytes  
last_block = self._bytes_list[-1]  
  
See log for complete Python traceback.  
  

> view matrix models
> #5,0.87419,0.48138,0.063625,-45.32,0.47187,-0.81131,-0.34513,155.62,-0.11452,0.33173,-0.9364,318.81

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX-Oct-16-2020\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 614, in _data_available  
msg = self._read_message()  
File "C:\Program Files\ChimeraX-Oct-16-2020\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 633, in _read_message  
self._check_for_null_bytes(rbytes) # Debug code. Ticket #3784  
File "C:\Program Files\ChimeraX-Oct-16-2020\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 640, in _check_for_null_bytes  
last_block = self._bytes_list[-1]  
IndexError: list index out of range  
  
IndexError: list index out of range  
  
File "C:\Program Files\ChimeraX-Oct-16-2020\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 640, in _check_for_null_bytes  
last_block = self._bytes_list[-1]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX-Oct-16-2020\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 614, in _data_available  
msg = self._read_message()  
File "C:\Program Files\ChimeraX-Oct-16-2020\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 633, in _read_message  
self._check_for_null_bytes(rbytes) # Debug code. Ticket #3784  
File "C:\Program Files\ChimeraX-Oct-16-2020\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 640, in _check_for_null_bytes  
last_block = self._bytes_list[-1]  
IndexError: list index out of range  
  
IndexError: list index out of range  
  
File "C:\Program Files\ChimeraX-Oct-16-2020\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 640, in _check_for_null_bytes  
last_block = self._bytes_list[-1]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX-Oct-16-2020\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 614, in _data_available  
msg = self._read_message()  
File "C:\Program Files\ChimeraX-Oct-16-2020\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 633, in _read_message  
self._check_for_null_bytes(rbytes) # Debug code. Ticket #3784  
File "C:\Program Files\ChimeraX-Oct-16-2020\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 640, in _check_for_null_bytes  
last_block = self._bytes_list[-1]  
IndexError: list index out of range  
  
IndexError: list index out of range  
  
File "C:\Program Files\ChimeraX-Oct-16-2020\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 640, in _check_for_null_bytes  
last_block = self._bytes_list[-1]  
  
See log for complete Python traceback.  
  
Socket error Unable to write  
Disconnected from 73.128.52.221:60122  
Socket error The remote host closed the connection  
Disconnected from 68.84.133.89:50495  




OpenGL version: 3.3.0 NVIDIA 442.19
OpenGL renderer: GeForce GTX 1080 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Gigabyte Technology Co., Ltd.
Model: Z270X-Gaming K7
OS: Microsoft Windows 10 Home (Build 19041)
Memory: 17,129,693,184
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-7700K CPU @ 4.20GHz
OSLanguage: en-US
Locale: ('en_US', 'cp1252')
PyQt version: 5.15.1
Compiled Qt version: 5.15.1
Runtime Qt version: 5.15.1
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.8.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.6.20
    cftime: 1.2.1
    chardet: 3.0.4
    ChimeraX-AddH: 2.1.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.8.2
    ChimeraX-AtomicLibrary: 1.1
    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: 2.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.0
    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-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.dev202010160427
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.0.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-DataFormats: 1.0
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1
    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: 1.0
    ChimeraX-HKCage: 1.0
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.1
    ChimeraX-Log: 1.1.1
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Map: 1.0.1
    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: 1.1
    ChimeraX-MDcrds: 2.1
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.0
    ChimeraX-mmCIF: 2.2
    ChimeraX-MMTF: 2.0
    ChimeraX-Modeller: 1.0
    ChimeraX-ModelPanel: 1.0
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.0
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0
    ChimeraX-OpenCommand: 1.3
    ChimeraX-PDB: 2.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0
    ChimeraX-PubChem: 2.0.1
    ChimeraX-Read-Pbonds: 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: 1.2
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.2.1
    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: 1.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.0
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0
    ChimeraX-ToolshedUtils: 1.0
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.3.1
    ChimeraX-uniprot: 2.0
    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: 4.4.2
    distlib: 0.3.1
    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
    imagecodecs-lite: 2020.1.31
    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: 4.6.3
    kiwisolver: 1.2.0
    line-profiler: 2.1.2
    lxml: 4.5.2
    MarkupSafe: 1.1.1
    matplotlib: 3.3.2
    msgpack: 1.0.0
    netCDF4: 1.5.4
    netifaces: 0.10.9
    networkx: 2.5
    numexpr: 2.7.1
    numpy: 1.19.2
    numpydoc: 1.1.0
    openvr: 1.14.1501
    packaging: 20.4
    parso: 0.7.1
    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 20.2.3
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.8
    psutil: 5.7.2
    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: 5.15.1
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.1
    python-dateutil: 2.8.1
    pytz: 2020.1
    pywin32: 228
    pyzmq: 19.0.2
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    setuptools: 50.3.0
    sfftk-rw: 0.6.6.dev0
    six: 1.15.0
    snowballstemmer: 2.0.0
    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: 1.0.3
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.4
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.9.3
    tinyarray: 1.2.3
    tornado: 6.0.4
    traitlets: 5.0.5
    urllib3: 1.25.10
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.34.2
    WMI: 1.5.1

[Tom Goddard]

Fixed. Duplicate of #3841

This was a bug in my debugging code that was supposed to be checking for null bytes in VR meeting messages. Wasn't properly handling case when socket reads only first 4 bytes of a message which is the length.