Opened 4 years ago

Closed 4 years ago

#5941 closed defect (can't reproduce)

Crash checking if clip planes changed after 'select' command

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

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.19044
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Windows fatal exception: code 0x8001010e

Thread 0x00001354 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 1122 in _browse_parse
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 1194 in parse
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2447 in _parse_arg
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2588 in _process_positional_arguments
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2812 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\run.py", line 36 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\tool.py", line 528 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 2515 in _show_context_menu
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 2383 in show_context_menu
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 2264 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00001354 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 1122 in _browse_parse
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 1194 in parse
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2447 in _parse_arg
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2588 in _process_positional_arguments
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2812 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\run.py", line 36 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\tool.py", line 528 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 2515 in _show_context_menu
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 2383 in show_context_menu
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 2264 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00001354 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 1122 in _browse_parse
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 1194 in parse
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2447 in _parse_arg
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2588 in _process_positional_arguments
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2812 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\run.py", line 36 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\tool.py", line 528 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 2515 in _show_context_menu
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 2383 in show_context_menu
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 2264 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00001354 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 1122 in _browse_parse
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 1194 in parse
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2447 in _parse_arg
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2588 in _process_positional_arguments
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2812 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\run.py", line 36 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\tool.py", line 528 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 2515 in _show_context_menu
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 2383 in show_context_menu
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 2264 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00001354 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 1122 in _browse_parse
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 1194 in parse
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2447 in _parse_arg
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2588 in _process_positional_arguments
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2812 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\run.py", line 36 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\tool.py", line 528 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 2515 in _show_context_menu
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 2383 in show_context_menu
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 2264 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00001354 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 1122 in _browse_parse
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 1194 in parse
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2447 in _parse_arg
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2588 in _process_positional_arguments
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2812 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\run.py", line 36 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\seq-view\tool.py", line 528 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 2515 in _show_context_menu
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 2383 in show_context_menu
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 2264 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00001354 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\graphics\clipping.py", line 42 in 
Windows fatal exception: access violation

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

===== Log before crash start =====
> ui windowfill toggle

> open D:\RawData\BDC\processed_models\PCC_mutation_mapped_v0.1.cxs format
> session

opened ChimeraX session  

> close

> open D:\RawData\BDC\models\PYC-coot-8.pdb format pdb

Summary of feedback from opening D:\RawData\BDC\models\PYC-coot-8.pdb  
---  
warnings | Ignored bad PDB record found on line 20  
  
  
Ignored bad PDB record found on line 21  
GEOMETRY RESTRAINTS LIBRARY: CDL v1.2  
  
Ignored bad PDB record found on line 22  
DEVIATIONS FROM IDEAL VALUES.  
  
Ignored bad PDB record found on line 23  
BOND : 0.006 0.063 21524  
  
Ignored bad PDB record found on line 24  
ANGLE : 0.886 10.505 29172  
  
18 messages similar to the above omitted  
  
Chain information for PYC-coot-8.pdb #1  
---  
Chain | Description  
A B C D | No description available  
  

> show target m

> interfaces ~solvent

6 buried areas: A B 2132, C D 2128, B D 1323, A C 1322, B C 348, A D 348  

> hide cartoons

> show cartoons

> hide atoms

> color bypolymer

> color bychain

> select ::name="LIG"

60 atoms, 64 bonds, 4 residues, 1 model selected  

> show sel atoms

> color sel byhetero

> select clear

> show sel cartoons

> hide sel cartoons

> show sel cartoons

> select ::name="LIG"

60 atoms, 64 bonds, 4 residues, 1 model selected  

> show sel atoms

> select clear

> hide sel atoms

> select clear

> select ::34

Expected an objects specifier or a keyword  

> select :34

Nothing selected  

> open 6ybp

Summary of feedback from opening 6ybp fetched from pdb  
---  
notes | Fetching compressed mmCIF 6ybp from
http://files.rcsb.org/download/6ybp.cif  
Fetching CCD BTI from http://ligand-expo.rcsb.org/reports/B/BTI/BTI.cif  
  
6ybp title:  
Propionyl-CoA carboxylase of Methylorubrum extorquens with bound CoA [more
info...]  
  
Chain information for 6ybp #2  
---  
Chain | Description | UniProt  
A B C D E F | Propionyl-CoA carboxylase β chain | C5AP75_METEA  
G H I J K L | Propionyl-CoA carboxylase α subunit | C5AWU5_METEA  
  
Non-standard residues in 6ybp #2  
---  
BTI — 5-(hexahydro-2-oxo-1H-thieno[3,4-D]imidazol-6-yl)pentanal  
COA — coenzyme A  
  

> undo

> close #2

> open 2qf7

2qf7 title:  
Crystal structure of a complete multifunctional pyruvate carboxylase from
Rhizobium etli [more info...]  
  
Chain information for 2qf7 #2  
---  
Chain | Description | UniProt  
A B | Pyruvate carboxylase protein | Q2K340_RHIEC  
  
Non-standard residues in 2qf7 #2  
---  
AGS — phosphothiophosphoric acid-adenylate ester (atp-γ-S; adenosine
5'-(3-thiotriphosphate); adenosine 5'-(γ-thiotriphosphate);
adenosine-5'-diphosphate monothiophosphate)  
CL — chloride ion  
COA — coenzyme A  
FMT — formic acid  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
MG — magnesium ion  
ZN — zinc ion  
  
2qf7 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  

> interfaces ~solvent

7 buried areas: #2/A #2/B 2265, #1/A #1/B 2132, #1/C #1/D 2128, #1/B #1/D
1323, #1/A #1/C 1322, #1/B #1/C 348, #1/A #1/D 348  

> undo

> select clear

> show sel cartoons

> select clear

> hide sel cartoons

> hide sel atoms

> hide sel surfaces

> select ::name="HOH"

1318 atoms, 1318 residues, 1 model selected  

> hide sel atoms

> hide sel cartoons

> ui mousemode right "translate selected models"

> view matrix models #1,1,0,0,-0.53715,0,1,0,3.2851,0,0,1,16.211

> view matrix models #1,1,0,0,7.3056,0,1,0,4.4588,0,0,1,20.393

> ui mousemode right "rotate selected models"

> view matrix models
> #1,-0.41627,0.16295,0.89452,74.815,0.071441,-0.97491,0.21084,242.09,0.90643,0.15167,0.39418,-54.184

> view matrix models
> #1,-0.55986,-0.10197,0.82229,139.65,0.70393,0.46497,0.53693,-82.044,-0.43709,0.87943,-0.18854,99.328

> view matrix models
> #1,-0.87372,-0.32961,0.35774,269,-0.14405,0.87776,0.45693,-12.617,-0.46462,0.3477,-0.81439,250.12

> select #2

17218 atoms, 16211 bonds, 52 pseudobonds, 3429 residues, 3 models selected  

> view matrix models
> #2,-0.52914,0.26396,-0.80644,198.85,-0.31461,-0.94368,-0.10245,246.5,-0.78806,0.1995,0.58238,95.949

> view matrix models
> #2,-0.2746,-0.57438,-0.77116,249.47,0.60023,-0.72894,0.3292,89.808,-0.75122,-0.37247,0.54492,150.55

> ~select #2

Nothing selected  

> ui mousemode right "translate selected models"

> select #1

21044 atoms, 21524 bonds, 2736 residues, 1 model selected  

> view matrix models
> #1,-0.87372,-0.32961,0.35774,265.06,-0.14405,0.87776,0.45693,-27.335,-0.46462,0.3477,-0.81439,238.12

> ui mousemode right "rotate selected models"

> view matrix models
> #1,-0.83135,-0.36119,0.42238,255.96,0.040194,0.71894,0.69391,-58.74,-0.5543,0.59386,-0.58317,189.32

> view matrix models
> #1,-0.66165,-0.60148,0.44771,262.71,0.70068,-0.28338,0.65479,-7.0059,-0.26697,0.74694,0.60894,-11.748

> view matrix models
> #1,-0.63836,-0.71318,0.28962,293.51,0.73772,-0.67424,-0.034258,122.9,0.2197,0.19179,0.95653,-43.23

> view matrix models
> #1,-0.69872,-0.53067,0.47977,254.28,0.56886,-0.0054734,0.82241,-46.882,-0.4338,0.84756,0.3057,33.082

> view matrix models
> #1,-0.19867,-0.93593,0.29079,263.46,-0.65247,0.3477,0.67333,90.38,-0.73131,-0.055962,-0.67975,314.7

> view matrix models
> #1,-0.10678,-0.92809,0.35672,241.94,-0.24843,0.3723,0.89425,5.2681,-0.96275,0.0068645,-0.27032,289.75

> ui mousemode right "translate selected models"

> view matrix models
> #1,-0.10678,-0.92809,0.35672,235.48,-0.24843,0.3723,0.89425,-9.9339,-0.96275,0.0068645,-0.27032,195.86

> hide sel cartoons

> view matrix models
> #1,-0.10678,-0.92809,0.35672,263.26,-0.24843,0.3723,0.89425,-1.3379,-0.96275,0.0068645,-0.27032,185.74

> view matrix models
> #1,-0.10678,-0.92809,0.35672,260.14,-0.24843,0.3723,0.89425,-10.37,-0.96275,0.0068645,-0.27032,191.11

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.14264,-0.79326,0.59194,172.89,-0.28195,0.54072,0.79255,-18.63,-0.94877,-0.27995,-0.14654,217.65

> view matrix models
> #1,0.11385,-0.71688,0.68784,154.65,-0.28635,0.63928,0.71367,-23.516,-0.95134,-0.27821,-0.13249,216.14

> view matrix models
> #1,0.39486,-0.57205,0.71892,84.427,-0.12476,0.74187,0.65884,-57.708,-0.91023,-0.34984,0.22156,178.78

> view matrix models
> #1,-0.11202,-0.99331,0.028108,308.74,0.12433,0.014054,0.99214,-26.279,-0.9859,0.11464,0.12192,132.38

> view matrix models
> #1,-0.11296,-0.99204,0.055637,305.45,0.12846,0.040944,0.99087,-30.847,-0.98526,0.11908,0.12281,131.51

> ui mousemode right "translate selected models"

> view matrix models
> #1,-0.11296,-0.99204,0.055637,301.14,0.12846,0.040944,0.99087,-47.442,-0.98526,0.11908,0.12281,130.8

> view matrix models
> #1,-0.11296,-0.99204,0.055637,317.72,0.12846,0.040944,0.99087,-56.543,-0.98526,0.11908,0.12281,130.83

> view matrix models
> #1,-0.11296,-0.99204,0.055637,321.2,0.12846,0.040944,0.99087,-50.817,-0.98526,0.11908,0.12281,131.13

> view matrix models
> #1,-0.11296,-0.99204,0.055637,321.33,0.12846,0.040944,0.99087,-50.909,-0.98526,0.11908,0.12281,131.42

> view matrix models
> #1,-0.11296,-0.99204,0.055637,320.07,0.12846,0.040944,0.99087,-52.927,-0.98526,0.11908,0.12281,130.88

> show sel cartoons

> select clear

> hide sel cartoons

Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 2 atomic models, 0 maps.  

> view matrix models
> #2,-0.2746,-0.57438,-0.77116,248.67,0.60023,-0.72894,0.3292,89.916,-0.75122,-0.37247,0.54492,150.03

> view matrix models
> #2,-0.2746,-0.57438,-0.77116,248.85,0.60023,-0.72894,0.3292,90.309,-0.75122,-0.37247,0.54492,150.02

> view matrix models
> #2,-0.2746,-0.57438,-0.77116,247.13,0.60023,-0.72894,0.3292,87.773,-0.75122,-0.37247,0.54492,149.89

> view matrix models
> #2,-0.2746,-0.57438,-0.77116,248.29,0.60023,-0.72894,0.3292,90.351,-0.75122,-0.37247,0.54492,150.08

> view matrix models
> #2,-0.2746,-0.57438,-0.77116,248.45,0.60023,-0.72894,0.3292,89.3,-0.75122,-0.37247,0.54492,150.1

> view matrix models
> #2,-0.2746,-0.57438,-0.77116,247.54,0.60023,-0.72894,0.3292,89.416,-0.75122,-0.37247,0.54492,150.02

> view matrix models
> #2,-0.2746,-0.57438,-0.77116,248.01,0.60023,-0.72894,0.3292,88.51,-0.75122,-0.37247,0.54492,150.01

> view matrix models
> #2,-0.2746,-0.57438,-0.77116,247.04,0.60023,-0.72894,0.3292,89.013,-0.75122,-0.37247,0.54492,151.21

> ui tool show Matchmaker

> matchmaker #!2 to #1

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 PYC-coot-8.pdb, chain A (#1) with 2qf7, chain A (#2), sequence
alignment score = 1834.1  
RMSD between 411 pruned atom pairs is 1.055 angstroms; (across all 673 pairs:
15.575)  
  

> show sel cartoons

> select clear

> hide sel cartoons

> hide sel atoms

> hide sel cartoons

> hide sel atoms

> select #1/A:1144

9 atoms, 8 bonds, 1 residue, 1 model selected  

> show sel atoms

> select clear

> select ::name="LIG"

60 atoms, 64 bonds, 4 residues, 1 model selected  

> select ::name="AGS"

62 atoms, 66 bonds, 2 residues, 1 model selected  

> hide sel atoms

> select clear

> show sel cartoons

> hide sel cartoons

> open 4qsl

Summary of feedback from opening 4qsl fetched from pdb  
---  
note | Fetching compressed mmCIF 4qsl from
http://files.rcsb.org/download/4qsl.cif  
  
4qsl title:  
Crystal Structure of Listeria Monocytogenes Pyruvate Carboxylase [more
info...]  
  
Chain information for 4qsl #3  
---  
Chain | Description | UniProt  
A B C D E F G H | Pyruvate carboxylase | W6G6F5_LISMN  
  
4qsl mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  

> interfaces select & ~solvent

Missing or invalid "atoms" argument: invalid atoms specifier  

> interfaces select & ~solvent

Missing or invalid "atoms" argument: invalid atoms specifier  

> select #3/A#3/B#3/C#3/D#3/E#3/F#3/G#3/H

60495 atoms, 61704 bonds, 18 pseudobonds, 8107 residues, 2 models selected  

> select #3/B:223@OD1

1 atom, 1 residue, 1 model selected  

> select #3/A#3/B#3/C#3/D#3/E#3/F#3/G#3/H

60495 atoms, 61704 bonds, 18 pseudobonds, 8107 residues, 2 models selected  

> select subtract #3/B:270@OD1

60494 atoms, 61704 bonds, 18 pseudobonds, 8107 residues, 2 models selected  

> select subtract #3/B:2@ND2

60493 atoms, 61704 bonds, 18 pseudobonds, 8107 residues, 2 models selected  

> select subtract #3/B:951@CG2

60492 atoms, 61704 bonds, 18 pseudobonds, 8107 residues, 2 models selected  
Drag select of 157 atoms  

> select clear

> select #3/A

7969 atoms, 8136 bonds, 1 pseudobond, 1052 residues, 2 models selected  

> select #3/B

7492 atoms, 7639 bonds, 4 pseudobonds, 1031 residues, 2 models selected  

> select #3/A,C,D,E,F,G

45122 atoms, 46023 bonds, 13 pseudobonds, 6047 residues, 2 models selected  

> hide sel atoms

> hide sel cartoons

> select #3/A,C,D,E,F,G,H

53003 atoms, 54065 bonds, 14 pseudobonds, 7076 residues, 2 models selected  

> hide sel cartoons

> hide sel atoms

> hide sel cartoons

> hide sel atoms

> select #3/B

7492 atoms, 7639 bonds, 4 pseudobonds, 1031 residues, 2 models selected  

> hide sel atoms

> show sel cartoons

> ui mousemode right "translate selected models"

> view matrix models #3,1,0,0,267.48,0,1,0,56.193,0,0,1,-17.252

> view matrix models #3,1,0,0,250.82,0,1,0,53.244,0,0,1,-14.201

> select clear

> select #3/B

7492 atoms, 7639 bonds, 4 pseudobonds, 1031 residues, 2 models selected  

> view matrix models #3,1,0,0,215.16,0,1,0,-12.612,0,0,1,-57.398

> view matrix models #3,1,0,0,279.56,0,1,0,113.22,0,0,1,9.4109

> view matrix models #3,1,0,0,278.78,0,1,0,112.15,0,0,1,7.8829

> ui tool show Matchmaker

> matchmaker #!2-3 to #1

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 PYC-coot-8.pdb, chain A (#1) with 2qf7, chain A (#2), sequence
alignment score = 1834.1  
RMSD between 411 pruned atom pairs is 1.055 angstroms; (across all 673 pairs:
15.575)  
  
Matchmaker PYC-coot-8.pdb, chain A (#1) with 4qsl, chain A (#3), sequence
alignment score = 1879.2  
RMSD between 467 pruned atom pairs is 0.893 angstroms; (across all 596 pairs:
2.247)  
  

> select #3/A#3/B#3/C#3/D#3/E#3/F#3/G#3/H

60495 atoms, 61704 bonds, 18 pseudobonds, 8107 residues, 2 models selected  

> show sel cartoons

> select #3/B,C,D,E,F,G,H

52526 atoms, 53568 bonds, 17 pseudobonds, 7055 residues, 2 models selected  

> hide sel cartoons

> select #2/A

8858 atoms, 8332 bonds, 24 pseudobonds, 1772 residues, 3 models selected  

> select #3/A

7969 atoms, 8136 bonds, 1 pseudobond, 1052 residues, 2 models selected  

> color (#!3 & sel) magenta

> select clear

> select #3/A

7969 atoms, 8136 bonds, 1 pseudobond, 1052 residues, 2 models selected  

> color (#!3 & sel) hot pink

> select #2/A:448

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select clear

> select #3/A:1140

Nothing selected  

> open 3bg5

Summary of feedback from opening 3bg5 fetched from pdb  
---  
notes | Fetching compressed mmCIF 3bg5 from
http://files.rcsb.org/download/3bg5.cif  
Fetching CCD MN from http://ligand-expo.rcsb.org/reports/M/MN/MN.cif  
Fetching CCD PYR from http://ligand-expo.rcsb.org/reports/P/PYR/PYR.cif  
Fetching CCD ATP from http://ligand-expo.rcsb.org/reports/A/ATP/ATP.cif  
  
3bg5 title:  
Crystal Structure of Staphylococcus Aureus Pyruvate Carboxylase [more info...]  
  
Chain information for 3bg5 #4  
---  
Chain | Description | UniProt  
A B C D | Pyruvate carboxylase | Q99UY8_STAAM  
  
Non-standard residues in 3bg5 #4  
---  
ATP — adenosine-5'-triphosphate  
BTI — 5-(hexahydro-2-oxo-1H-thieno[3,4-D]imidazol-6-yl)pentanal  
MN — manganese (II) ion  
PYR — pyruvic acid  
  
3bg5 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| software_defined_assembly  
3| software_defined_assembly  
  

> ui tool show Matchmaker

> matchmaker #!2-4 to #1

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 PYC-coot-8.pdb, chain A (#1) with 2qf7, chain A (#2), sequence
alignment score = 1834.1  
RMSD between 411 pruned atom pairs is 1.055 angstroms; (across all 673 pairs:
15.575)  
  
Matchmaker PYC-coot-8.pdb, chain A (#1) with 4qsl, chain A (#3), sequence
alignment score = 1879.2  
RMSD between 467 pruned atom pairs is 0.893 angstroms; (across all 596 pairs:
2.247)  
  
Matchmaker PYC-coot-8.pdb, chain A (#1) with 3bg5, chain D (#4), sequence
alignment score = 1919.7  
RMSD between 438 pruned atom pairs is 0.986 angstroms; (across all 669 pairs:
4.966)  
  

> select #4/D

8435 atoms, 8593 bonds, 3 pseudobonds, 1070 residues, 3 models selected  

> select #4/A,B,C

26003 atoms, 26499 bonds, 4 pseudobonds, 3289 residues, 3 models selected  

> hide sel cartoons

> hide sel atoms

> select #2

17218 atoms, 16211 bonds, 52 pseudobonds, 3429 residues, 3 models selected  

> color (#!2 & sel) white

> select #3

60495 atoms, 61704 bonds, 18 pseudobonds, 8107 residues, 2 models selected  

> color (#!3 & sel) light gray

> color (#!3 & sel) gray

> select #4

34438 atoms, 35092 bonds, 7 pseudobonds, 4359 residues, 3 models selected  

> color (#!4 & sel) dim gray

> select clear

> select #4

34438 atoms, 35092 bonds, 7 pseudobonds, 4359 residues, 3 models selected  

> color (#!4 & sel) black

> select clear

> select #4

34438 atoms, 35092 bonds, 7 pseudobonds, 4359 residues, 3 models selected  

> ui tool show "Color Actions"

> color sel light slate gray

> select #1

21044 atoms, 21524 bonds, 2736 residues, 1 model selected  

> color sel hot pink

> select clear

> select #3

60495 atoms, 61704 bonds, 18 pseudobonds, 8107 residues, 2 models selected  

> color (#!3 & sel) dim gray

> select clear

> close #3

> select #2

17218 atoms, 16211 bonds, 52 pseudobonds, 3429 residues, 3 models selected  

> select #4

34438 atoms, 35092 bonds, 7 pseudobonds, 4359 residues, 3 models selected  

> color (#!4 & sel) gray

> select clear

> select #2

17218 atoms, 16211 bonds, 52 pseudobonds, 3429 residues, 3 models selected  

> color (#!2 & sel) cornflower blue

> select #4

34438 atoms, 35092 bonds, 7 pseudobonds, 4359 residues, 3 models selected  

> color (#!4 & sel) light sea green

> select clear

> select #4

34438 atoms, 35092 bonds, 7 pseudobonds, 4359 residues, 3 models selected  

> color (#!4 & sel) cyan

> select clear

> select #4

34438 atoms, 35092 bonds, 7 pseudobonds, 4359 residues, 3 models selected  

> color (#!4 & sel) light gray

> select clear

> select #43.

Expected an objects specifier or a keyword  

> select #4

34438 atoms, 35092 bonds, 7 pseudobonds, 4359 residues, 3 models selected  

> hide sel atoms

> select ::name="BTI"

60 atoms, 64 bonds, 4 residues, 1 model selected  

> show sel atoms

> select #4/A,B,C

26003 atoms, 26499 bonds, 4 pseudobonds, 3289 residues, 3 models selected  

> hide sel atoms

> select #1,2,4

72700 atoms, 72827 bonds, 59 pseudobonds, 10524 residues, 7 models selected  

> color sel byhetero

> select clear

> select ::name="LIG"

60 atoms, 64 bonds, 4 residues, 1 model selected  

> select clear

> save D:/RawData/BDC/processed_models/PYC-2qf7-3bg5-align.tif width 1509
> height 859 supersample 3 transparentBackground true

> hide #!2 models

> hide #2.2 models

> hide #!4 models

> hide #2.1 models

> select #1

21044 atoms, 21524 bonds, 2736 residues, 1 model selected  

> show sel cartoons

> color sel bychain

> select #1/A

5261 atoms, 5381 bonds, 684 residues, 1 model selected  

> select #1/B

5261 atoms, 5381 bonds, 684 residues, 1 model selected  

> color sel hot pink

> select clear

> select ::name="LIG"

60 atoms, 64 bonds, 4 residues, 1 model selected  

> show sel atoms

> color sel byhetero

> select clear

> select #1:1144

36 atoms, 32 bonds, 4 residues, 1 model selected  

> show sel atoms

> select clear

> save D:/RawData/BDC/processed_models/PYC-overall.tif width 1509 height 859
> supersample 3 transparentBackground true

> select clear

> select ::name="LIG"

60 atoms, 64 bonds, 4 residues, 1 model selected  

> show sel atoms

> select #1:1144

36 atoms, 32 bonds, 4 residues, 1 model selected  

> show sel atoms

> color sel byhetero

> select clear

> hide sel cartoons

> hide sel atoms

> hide sel cartoons

> hide sel atoms

> show sel cartoons

> color sel byhetero

> select clear

> select #1/B:name="LIG"

Expected an objects specifier or a keyword  

> select #1/B::name="LIG"

15 atoms, 16 bonds, 1 residue, 1 model selected  

> color sel dim gray

> select clear

> select #1/B

5261 atoms, 5381 bonds, 684 residues, 1 model selected  

> color sel hot pink

> color sel byhetero

> select #1/B::name="LIG"

15 atoms, 16 bonds, 1 residue, 1 model selected  

> color sel dim gray

> select clear

> select #1/B::name="LIG"

15 atoms, 16 bonds, 1 residue, 1 model selected  

> color sel byhetero

> select clear

> select #1/B::name="LIG"

15 atoms, 16 bonds, 1 residue, 1 model selected  

> hbonds sel reveal true

The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: 2qf7 #2/A ARG 353 NE; 2qf7 #2/B ARG 469 NE; 2qf7 #2/B ARG 641
NE  

3 hydrogen bonds found  

> hbonds sel reveal true

The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: 2qf7 #2/A ARG 353 NE; 2qf7 #2/B ARG 469 NE; 2qf7 #2/B ARG 641
NE  

3 hydrogen bonds found  

> ui tool show H-Bonds

> hbonds sel reveal true

The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: 2qf7 #2/A ARG 353 NE; 2qf7 #2/B ARG 469 NE; 2qf7 #2/B ARG 641
NE  

3 hydrogen bonds found  

> select clear

> ui tool show "Side View"

> select clear

> ui tool show Contacts

> select #1/B::name="LIG"

15 atoms, 16 bonds, 1 residue, 1 model selected  

> contacts sel resSeparation 5

72 contacts  

> contacts sel resSeparation 5 showDist true

72 contacts  

> contacts sel showDist true

72 contacts  

> hide sel atoms

> hbonds sel reveal true

The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: 2qf7 #2/A ARG 353 NE; 2qf7 #2/B ARG 469 NE; 2qf7 #2/B ARG 641
NE  

2514 hydrogen bonds found  

> ~hbonds

> select clear

> hide sel atoms

> hide sel cartoons

> hide sel atoms

> select #1/B::name="LIG"

15 atoms, 16 bonds, 1 residue, 1 model selected  

> hbonds sel reveal true

The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: 2qf7 #2/A ARG 353 NE; 2qf7 #2/B ARG 469 NE; 2qf7 #2/B ARG 641
NE  

3 hydrogen bonds found  

> contacts sel showDist true

72 contacts  

> contacts sel intraModel false showDist true

49 contacts  

> select #1/A:877

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select subtract #1/A:942

1205 atoms, 151 residues, 1 model selected  

> select subtract #1/A:916

1197 atoms, 150 residues, 1 model selected  

> select subtract #1/A:941

1190 atoms, 149 residues, 1 model selected  

> select subtract #1/B:1147

1183 atoms, 148 residues, 1 model selected  

> select subtract #1/B:1146

1174 atoms, 147 residues, 1 model selected  

> select subtract #1/B:1145

1166 atoms, 146 residues, 1 model selected  

> select subtract #1/B:1144

1157 atoms, 145 residues, 1 model selected  

> select subtract #1/B:1143

1149 atoms, 144 residues, 1 model selected  

> select subtract #1/B:1142

1144 atoms, 143 residues, 1 model selected  

> select subtract #1/A:881

1136 atoms, 142 residues, 1 model selected  

> select subtract #1/A:880

1130 atoms, 141 residues, 1 model selected  

> select subtract #1/A:920

1119 atoms, 140 residues, 1 model selected  

> select subtract #1/B:1148

1112 atoms, 139 residues, 1 model selected  

> select subtract #1/B:1116

1104 atoms, 138 residues, 1 model selected  

> select subtract #1/B:1115

1097 atoms, 137 residues, 1 model selected  

> select subtract #1/B:1117

1090 atoms, 136 residues, 1 model selected  

> select subtract #1/A:924

1082 atoms, 135 residues, 1 model selected  

> select subtract #1/A:923

1073 atoms, 134 residues, 1 model selected  

> select subtract #1/A:939

1067 atoms, 133 residues, 1 model selected  

> select subtract #1/A:938

1059 atoms, 132 residues, 1 model selected  

> select subtract #1/A:937

1050 atoms, 131 residues, 1 model selected  

> select subtract #1/A:936

1041 atoms, 130 residues, 1 model selected  

> select subtract #1/A:969

1032 atoms, 129 residues, 1 model selected  

> select subtract #1/B:1134

1028 atoms, 128 residues, 1 model selected  

> select add #1/B:1135

1037 atoms, 8 bonds, 129 residues, 1 model selected  

> select subtract #1/B:1150

1030 atoms, 8 bonds, 128 residues, 1 model selected  

> select subtract #1/B:1135

1021 atoms, 127 residues, 1 model selected  

> select subtract #1/B:1133

1012 atoms, 126 residues, 1 model selected  

> select subtract #1/B:1152

1005 atoms, 125 residues, 1 model selected  

> select subtract #1/B:1171

997 atoms, 124 residues, 1 model selected  

> select subtract #1/A:617

986 atoms, 123 residues, 1 model selected  

> select subtract #1/B:1106

977 atoms, 122 residues, 1 model selected  

> select subtract #1/B:1063

969 atoms, 121 residues, 1 model selected  

> show sel atoms

> color sel byhetero

> select clear

> select #1/B:1146

9 atoms, 8 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select #1/B::name="LIG"

15 atoms, 16 bonds, 1 residue, 1 model selected  

> contacts sel intraModel false showDist true

49 contacts  

> contacts sel showDist true

72 contacts  

> select #1/A:877

9 atoms, 8 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select #1/A:651

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

> hide sel atoms

> select clear

> contacts makePseudobonds false

445143 contacts  

> contacts makePseudobonds false

445143 contacts  

> select #1/A:876

11 atoms, 11 bonds, 1 residue, 1 model selected  

> color sel byhetero

> select clear

> save D:/RawData/BDC/processed_models/PYC-biotin-pocket.tif width 1508 height
> 859 supersample 3 transparentBackground true

> ui tool show "Show Sequence Viewer"

> sequence chain #1/A #1/B #1/C #1/D

Alignment identifier is 1  

QWindowsWindow::setGeometry: Unable to set geometry 3840x2583+0+57 (frame:
3872x2671-16-15) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 3840x2268+0+56 (frame: 3872x2356-16-16) margins: 16, 72,
16, 16 minimum size: 477x861 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=1463,2671 maxtrack=0,0)  

> select
> #1/A-D:496-510,541-558,572-577,584-597,611-617,623-633,656-669,683-695,720-732,749-762,779-789,799-801,810-816,828-844,846-848,850-852,859-864,868-880,887-900,910-924,929-932,934-936,942-949,963-967,987-998,1004-1012,1014-1026,1030-1032,1035-1040

8884 atoms, 8948 bonds, 1120 residues, 1 model selected  

> select clear

> select #1/B::name="LIG"

15 atoms, 16 bonds, 1 residue, 1 model selected  

> contacts makePseudobonds false

445143 contacts  

> contacts

445143 contacts  

> contacts sel showDist true

72 contacts  

> select clear

> hide sel cartoons

> show sel cartoons

> hide sel atoms

> select #1::name="LIG"

60 atoms, 64 bonds, 4 residues, 1 model selected  

> show sel atoms

> color sel byhetero

> select #1:1144

36 atoms, 32 bonds, 4 residues, 1 model selected  

> show sel atoms

> color sel byhetero

> select clear

> select #1/A:870

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select clear

> ui tool show Distances

No distances to delete!  

> ui tool show Contacts

> contacts makePseudobonds false

445143 contacts  

QWindowsWindow::setGeometry: Unable to set geometry 1398x304+6788+1726 (frame:
1420x360+6777+1681) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY1". Resulting geometry: 1401x304+6788+1726 (frame:
1423x360+6777+1681) margins: 11, 45, 11, 11 minimum size: 467x90 maximum size:
524287x524287 MINMAXINFO maxSize=0,0 maxpos=0,0 mintrack=1423,326
maxtrack=1572883,1572917)  

QWindowsWindow::setGeometry: Unable to set geometry 1380x300+6786+1722 (frame:
1402x356+6775+1677) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY1". Resulting geometry: 1401x300+6786+1722 (frame:
1423x356+6775+1677) margins: 11, 45, 11, 11 minimum size: 467x90 maximum size:
524287x524287 MINMAXINFO maxSize=0,0 maxpos=0,0 mintrack=1423,326
maxtrack=1572883,1572917)  

QWindowsWindow::setGeometry: Unable to set geometry 1350x292+6784+1718 (frame:
1372x348+6773+1673) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY1". Resulting geometry: 1401x292+6784+1718 (frame:
1423x348+6773+1673) margins: 11, 45, 11, 11 minimum size: 467x90 maximum size:
524287x524287 MINMAXINFO maxSize=0,0 maxpos=0,0 mintrack=1423,326
maxtrack=1572883,1572917)  

QWindowsWindow::setGeometry: Unable to set geometry 1310x280+6780+1710 (frame:
1332x336+6769+1665) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY1". Resulting geometry: 1401x280+6780+1710 (frame:
1423x336+6769+1665) margins: 11, 45, 11, 11 minimum size: 467x90 maximum size:
524287x524287 MINMAXINFO maxSize=0,0 maxpos=0,0 mintrack=1423,326
maxtrack=1572883,1572917)  

QWindowsWindow::setGeometry: Unable to set geometry 1256x266+6776+1700 (frame:
1278x322+6765+1655) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY1". Resulting geometry: 1401x270+6776+1700 (frame:
1423x326+6765+1655) margins: 11, 45, 11, 11 minimum size: 467x90 maximum size:
524287x524287 MINMAXINFO maxSize=0,0 maxpos=0,0 mintrack=1423,326
maxtrack=1572883,1572917)  

QWindowsWindow::setGeometry: Unable to set geometry 1190x250+6770+1688 (frame:
1212x306+6759+1643) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY1". Resulting geometry: 1401x270+6770+1688 (frame:
1423x326+6759+1643) margins: 11, 45, 11, 11 minimum size: 467x90 maximum size:
524287x524287 MINMAXINFO maxSize=0,0 maxpos=0,0 mintrack=1423,326
maxtrack=1572883,1572917)  

QWindowsWindow::setGeometry: Unable to set geometry 1120x228+6762+1676 (frame:
1142x284+6751+1631) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY1". Resulting geometry: 1401x270+6762+1676 (frame:
1423x326+6751+1631) margins: 11, 45, 11, 11 minimum size: 467x90 maximum size:
524287x524287 MINMAXINFO maxSize=0,0 maxpos=0,0 mintrack=1423,326
maxtrack=1572883,1572917)  

QWindowsWindow::setGeometry: Unable to set geometry 1060x214+6756+1664 (frame:
1082x270+6745+1619) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY1". Resulting geometry: 1401x270+6756+1664 (frame:
1423x326+6745+1619) margins: 11, 45, 11, 11 minimum size: 467x90 maximum size:
524287x524287 MINMAXINFO maxSize=0,0 maxpos=0,0 mintrack=1423,326
maxtrack=1572883,1572917)  

QWindowsWindow::setGeometry: Unable to set geometry 1010x202+6752+1654 (frame:
1032x258+6741+1609) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY1". Resulting geometry: 1401x270+6752+1654 (frame:
1423x326+6741+1609) margins: 11, 45, 11, 11 minimum size: 467x90 maximum size:
524287x524287 MINMAXINFO maxSize=0,0 maxpos=0,0 mintrack=1423,326
maxtrack=1572883,1572917)  

QWindowsWindow::setGeometry: Unable to set geometry 974x190+6748+1648 (frame:
996x246+6737+1603) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY1". Resulting geometry: 1401x270+6748+1648 (frame:
1423x326+6737+1603) margins: 11, 45, 11, 11 minimum size: 467x90 maximum size:
524287x524287 MINMAXINFO maxSize=0,0 maxpos=0,0 mintrack=1423,326
maxtrack=1572883,1572917)  

QWindowsWindow::setGeometry: Unable to set geometry 950x184+6746+1644 (frame:
972x240+6735+1599) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY1". Resulting geometry: 1401x270+6746+1644 (frame:
1423x326+6735+1599) margins: 11, 45, 11, 11 minimum size: 467x90 maximum size:
524287x524287 MINMAXINFO maxSize=0,0 maxpos=0,0 mintrack=1423,326
maxtrack=1572883,1572917)  

QWindowsWindow::setGeometry: Unable to set geometry 936x180+6746+1642 (frame:
958x236+6735+1597) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY1". Resulting geometry: 1401x270+6746+1642 (frame:
1423x326+6735+1597) margins: 11, 45, 11, 11 minimum size: 467x90 maximum size:
524287x524287 MINMAXINFO maxSize=0,0 maxpos=0,0 mintrack=1423,326
maxtrack=1572883,1572917)  

QWindowsWindow::setGeometry: Unable to set geometry 934x180+6746+1642 (frame:
956x236+6735+1597) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY1". Resulting geometry: 1401x270+6746+1642 (frame:
1423x326+6735+1597) margins: 11, 45, 11, 11 minimum size: 467x90 maximum size:
524287x524287 MINMAXINFO maxSize=0,0 maxpos=0,0 mintrack=1423,326
maxtrack=1572883,1572917)  

> select clear

> show sel atoms

> color sel byhetero

> select clear

Restriction atom specifier must not be blank  

> contacts sel restrict both makePseudobonds false

452 contacts  

> select clear

> select #1:495-523

876 atoms, 900 bonds, 116 residues, 1 model selected  

> select #1:495-523,1032-1092

2832 atoms, 2876 bonds, 360 residues, 1 model selected  

> select ~sel

69868 atoms, 69951 bonds, 63 pseudobonds, 10164 residues, 9 models selected  

> hide sel & #1 cartoons

> hide sel & #1 atoms

> select #1/A,B:495-523,1032-1092

1416 atoms, 1438 bonds, 180 residues, 1 model selected  

> select #1/D,B:495-523,1032-1092

1416 atoms, 1438 bonds, 180 residues, 1 model selected  

> select #1/D,C:495-523,1032-1092

1416 atoms, 1438 bonds, 180 residues, 1 model selected  

> select #1/D,A:495-523,1032-1092

1416 atoms, 1438 bonds, 180 residues, 1 model selected  

> hide sel cartoons

> save D:/RawData/BDC/processed_models/PYC-BT-top.tif width 1449 height 859
> supersample 3 transparentBackground true

> save D:/RawData/BDC/processed_models/PYC-BT-side.tif width 1449 height 859
> supersample 3 transparentBackground true

> select #1/B

5261 atoms, 5381 bonds, 684 residues, 1 model selected  

> select #1/C'

Nothing selected  

> select #1/C

5261 atoms, 5381 bonds, 684 residues, 1 model selected  

> hide sel cartoons

> hide sel atoms

> select #1/B

5261 atoms, 5381 bonds, 684 residues, 1 model selected  

> hide sel atoms

> select clear

> movie record

> turn y 2 180

> wait 180

> movie encode C:\Users\Fayang\Desktop\movie1.mp4

Movie saved to \C:Users\\...\Desktop\movie1.mp4  
  

> movie record

> turn y 2 180

> wait 180

> movie encode C:\Users\Fayang\Desktop\movie2.mp4

Movie saved to \C:Users\\...\Desktop\movie2.mp4  
  

> undo

> select clear

> select #1/B

5261 atoms, 5381 bonds, 684 residues, 1 model selected  

> select #1/C

5261 atoms, 5381 bonds, 684 residues, 1 model selected  

> hide sel cartoons

> hide sel atoms

> select #1/B:1063

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/B:1064

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select add #1/B:1063

13 atoms, 11 bonds, 2 residues, 1 model selected  

> select add #1/B:1066

19 atoms, 16 bonds, 3 residues, 1 model selected  

> select add #1/B:1075

28 atoms, 24 bonds, 4 residues, 1 model selected  

> select add #1/B:1077

39 atoms, 35 bonds, 5 residues, 1 model selected  

> select add #1/B:1084

47 atoms, 42 bonds, 6 residues, 1 model selected  

> select add #1/B:1065

54 atoms, 48 bonds, 7 residues, 1 model selected  

> show sel atoms

> select #1/B:1065

7 atoms, 6 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select #1/B:1063

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select add #1/B:1064

13 atoms, 11 bonds, 2 residues, 1 model selected  

> select add #1/B:1066

19 atoms, 16 bonds, 3 residues, 1 model selected  

> select add #1/B:1075

28 atoms, 24 bonds, 4 residues, 1 model selected  

> select add #1/B:1077

39 atoms, 35 bonds, 5 residues, 1 model selected  

> select add #1/B:1084

47 atoms, 42 bonds, 6 residues, 1 model selected  

QWindowsWindow::setGeometry: Unable to set geometry 7102x906-3046+806 (frame:
7134x994-3062+734) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY1". Resulting geometry: 7684x1515-3041+833 (frame:
7716x1603-3057+761) margins: 16, 72, 16, 16 minimum size: 62x37 maximum size:
524287x524287 MINMAXINFO maxSize=0,0 maxpos=0,0 mintrack=218,199
maxtrack=1572893,1572949)  

> select #1/C

5261 atoms, 5381 bonds, 684 residues, 1 model selected  

> select
> #1/A-D:564-567,604-608,639-644,673-677,699-706,737-742,767-772,793-796,1048-1051,1057-1065,1073-1080,1083-1090,1111-1113,1139-1141,1146-1148,1173-1176

2816 atoms, 2804 bonds, 344 residues, 1 model selected  

> select #1/A-D:1031-1032

56 atoms, 52 bonds, 8 residues, 1 model selected  

> select #1/A-D:1031-1092

1988 atoms, 2008 bonds, 248 residues, 1 model selected  


===== Log before crash end =====

Log:
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

QWindowsWindow::setGeometry: Unable to set geometry 5760x934+2152+1118 (frame:
5782x990+2141+1073) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY2". Resulting geometry: 3453x557+2147+1091 (frame:
3475x613+2136+1046) margins: 11, 45, 11, 11 minimum size: 600x289 maximum
size: 524287x524287 MINMAXINFO maxSize=0,0 maxpos=0,0 mintrack=1222,634
maxtrack=1048596,1048630)  




OpenGL version: 3.3.0 NVIDIA 471.35
OpenGL renderer: NVIDIA GeForce RTX 2060 with Max-Q Design/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: XPS 17 9700
OS: Microsoft Windows 10 专业版 (Build 19044)
Memory: 68,451,766,272
MaxProcessMemory: 137,438,953,344
CPU: 16 Intel(R) Core(TM) i9-10885H CPU @ 2.40GHz
OSLanguage: zh-CN
Locale: ('zh_CN', 'cp936')
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: 2021.10.8
    cftime: 1.5.1.1
    charset-normalizer: 2.0.9
    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.31
    ChimeraX-AtomicLibrary: 4.2
    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: 2.6.1
    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: 2.2.2
    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
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    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: 2.1.2
    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: 2.0.4
    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: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    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: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    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: 2.4.6
    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: 1.6.1
    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: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.7
    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
    comtypes: 1.1.10
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    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: 4.9.1
    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: 2.8.0
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.3
    ParmEd: 3.2.0
    parso: 0.8.3
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.23
    psutil: 5.8.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.6
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pywin32: 228
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.3
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    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
    tables: 3.6.1
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0
    WMI: 1.5.1

Change History (3)

comment:1 by pett, 4 years ago

Component: Unassigned → Graphics
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Crash checking if clip planes changed after 'select' command

comment:2 by Tom Goddard, 4 years ago

This line in clipping.py is checking the Python "changed" attributes of clipping planes. Can't see how this could cause a crash.

Thread 0x00001354 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\graphics\clipping.py", line 42 in 
Windows fatal exception: access violation

Last command seems to have completed

> select #1/A-D:1031-1092
1988 atoms, 2008 bonds, 248 residues, 1 model selected

A few select commands before the crash there was a window geometry error from Qt. And there were many more of these earlier, and one when they restarted ChimeraX after the crash. All of them list either very large windows (e.g. 6000 pixels wide, or very big offsets e.g. -3000 pixels in x.

QWindowsWindow::setGeometry: Unable to set geometry 7102x906-3046+806 (frame:
7134x994-3062+734) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY1". Resulting geometry: 7684x1515-3041+833 (frame:
7716x1603-3057+761) margins: 16, 72, 16, 16 minimum size: 62x37 maximum size:
524287x524287 MINMAXINFO maxSize=0,0 maxpos=0,0 mintrack=218,199
maxtrack=1572893,1572949)


comment:3 by Tom Goddard, 4 years ago

Resolution: → can't reproduce
Status: assigned → closed

Maybe it is a graphics driver crash. On Windows the Python faulthandler output does not seem to give the Python traceback where the access violation happened so there is rarely enough info to understand the crash.

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