![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 5 months ago
Last modified 5 months ago
#17827 closed defect
ChimeraX bug report submission — at Initial Version
| Reported by: | Owned by: | ||
|---|---|---|---|
| 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-10-10.0.22631
ChimeraX Version: 1.10rc202505210000 (2025-05-21 00:00:04 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Windows fatal exception: access violation
Current thread 0x000044e4 (most recent call first):
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\chimerax\graphics\opengl.py", line 1287 in flush
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\chimerax\graphics\drawing.py", line 1685 in draw_xor_rectangle
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\chimerax\graphics\view.py", line 336 in draw_xor_rectangle
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\chimerax\mouse_modes\std_modes.py", line 146 in _undraw_drag_rectangle
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\chimerax\mouse_modes\std_modes.py", line 55 in mouse_drag
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\chimerax\mouse_modes\mousemodes.py", line 556 in _dispatch_mouse_event
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\chimerax\mouse_modes\mousemodes.py", line 655 in
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\chimerax\ui\graphics.py", line 61 in event
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\chimerax\ui\gui.py", line 368 in event_loop
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\chimerax\core\__main__.py", line 1057 in init
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\chimerax\core\__main__.py", line 1220 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Windows fatal exception: access violation
Current thread 0x000044e4 (most recent call first):
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\chimerax\graphics\opengl.py", line 1287 in flush
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\chimerax\graphics\drawing.py", line 1685 in draw_xor_rectangle
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\chimerax\graphics\view.py", line 336 in draw_xor_rectangle
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\chimerax\mouse_modes\std_modes.py", line 146 in _undraw_drag_rectangle
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\chimerax\mouse_modes\std_modes.py", line 55 in mouse_drag
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\chimerax\mouse_modes\mousemodes.py", line 556 in _dispatch_mouse_event
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\chimerax\mouse_modes\mousemodes.py", line 655 in
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\chimerax\ui\graphics.py", line 61 in event
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\chimerax\ui\gui.py", line 368 in event_loop
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\chimerax\core\__main__.py", line 1057 in init
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\chimerax\core\__main__.py", line 1220 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Windows fatal exception: access violation
Current thread 0x000044e4 (most recent call first):
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\chimerax\graphics\opengl.py", line 1287 in flush
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\chimerax\graphics\drawing.py", line 1685 in draw_xor_rectangle
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\chimerax\graphics\view.py", line 336 in draw_xor_rectangle
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\chimerax\mouse_modes\std_modes.py", line 146 in _undraw_drag_rectangle
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\chimerax\mouse_modes\std_modes.py", line 55 in mouse_drag
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\chimerax\mouse_modes\mousemodes.py", line 556 in _dispatch_mouse_event
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\chimerax\mouse_modes\mousemodes.py", line 655 in
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\chimerax\ui\graphics.py", line 61 in event
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\chimerax\ui\gui.py", line 368 in event_loop
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\chimerax\core\__main__.py", line 1057 in init
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\chimerax\core\__main__.py", line 1220 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Windows fatal exception: access violation
Current thread 0x000044e4 (most recent call first):
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\chimerax\graphics\opengl.py", line 1287 in flush
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\chimerax\graphics\drawing.py", line 1685 in draw_xor_rectangle
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\chimerax\graphics\view.py", line 336 in draw_xor_rectangle
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\chimerax\mouse_modes\std_modes.py", line 146 in _undraw_drag_rectangle
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\chimerax\mouse_modes\std_modes.py", line 55 in mouse_drag
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\chimerax\mouse_modes\mousemodes.py", line 556 in _dispatch_mouse_event
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\chimerax\mouse_modes\mousemodes.py", line 655 in
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\chimerax\ui\graphics.py", line 61 in event
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\chimerax\ui\gui.py", line 368 in event_loop
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\chimerax\core\__main__.py", line 1057 in init
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\chimerax\core\__main__.py", line 1220 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Windows fatal exception: access violation
Current thread 0x000044e4 (most recent call first):
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\chimerax\graphics\opengl.py", line 1287 in flush
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\chimerax\graphics\drawing.py", line 1685 in draw_xor_rectangle
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\chimerax\graphics\view.py", line 336 in draw_xor_rectangle
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\chimerax\mouse_modes\std_modes.py", line 146 in _undraw_drag_rectangle
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\chimerax\mouse_modes\std_modes.py", line 59 in mouse_up
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\chimerax\mouse_modes\mousemodes.py", line 556 in _dispatch_mouse_event
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\chimerax\mouse_modes\mousemodes.py", line 656 in
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\chimerax\ui\graphics.py", line 61 in event
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\chimerax\ui\gui.py", line 368 in event_loop
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\chimerax\core\__main__.py", line 1057 in init
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\chimerax\core\__main__.py", line 1220 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Windows fatal exception: access violation
Current thread 0x000044e4 (most recent call first):
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\OpenGL\platform\baseplatform.py", line 186 in constructFunction
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\OpenGL\platform\win32.py", line 144 in constructFunction
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\OpenGL\platform\baseplatform.py", line 256 in createBaseFunction
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\OpenGL\raw\GLU\__init__.py", line 84 in
File "", line 241 in _call_with_frames_removed
File "", line 940 in exec_module
File "", line 690 in _load_unlocked
File "", line 1147 in _find_and_load_unlocked
File "", line 1176 in _find_and_load
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\OpenGL\GLU\__init__.py", line 4 in
File "", line 241 in _call_with_frames_removed
File "", line 940 in exec_module
File "", line 690 in _load_unlocked
File "", line 1147 in _find_and_load_unlocked
File "", line 1176 in _find_and_load
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\OpenGL\error.py", line 121 in format_description
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\OpenGL\error.py", line 98 in __str__
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\chimerax\core\updateloop.py", line 99 in draw_new_frame
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\chimerax\core\updateloop.py", line 150 in _redraw_timer_callback
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\chimerax\ui\gui.py", line 368 in event_loop
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\chimerax\core\__main__.py", line 1057 in init
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\chimerax\core\__main__.py", line 1220 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Windows fatal exception: access violation
Current thread 0x000044e4 (most recent call first):
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\OpenGL\platform\baseplatform.py", line 186 in constructFunction
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\OpenGL\platform\win32.py", line 144 in constructFunction
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\OpenGL\platform\baseplatform.py", line 256 in createBaseFunction
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\OpenGL\raw\GLU\__init__.py", line 84 in
File "", line 241 in _call_with_frames_removed
File "", line 940 in exec_module
File "", line 690 in _load_unlocked
File "", line 1147 in _find_and_load_unlocked
File "", line 1176 in _find_and_load
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\OpenGL\GLU\__init__.py", line 4 in
File "", line 241 in _call_with_frames_removed
File "", line 940 in exec_module
File "", line 690 in _load_unlocked
File "", line 1147 in _find_and_load_unlocked
File "", line 1176 in _find_and_load
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\OpenGL\error.py", line 121 in format_description
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\OpenGL\error.py", line 98 in __str__
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\traceback.py", line 175 in _safe_string
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\traceback.py", line 699 in __init__
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\traceback.py", line 139 in format_exception
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\traceback.py", line 187 in format_exc
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\chimerax\core\updateloop.py", line 99 in draw_new_frame
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\chimerax\core\updateloop.py", line 150 in _redraw_timer_callback
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\chimerax\ui\gui.py", line 368 in event_loop
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\chimerax\core\__main__.py", line 1057 in init
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\chimerax\core\__main__.py", line 1220 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Windows fatal exception: access violation
Current thread 0x000044e4 (most recent call first):
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\chimerax\graphics\opengl.py", line 122 in make_current
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\chimerax\graphics\opengl.py", line 555 in make_current
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\chimerax\ui\statusbar.py", line 157 in status
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\chimerax\ui\gui.py", line 1085 in status
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\chimerax\core\logger.py", line 220 in status
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\chimerax\core\logger.py", line 522 in status
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\chimerax\cmd_line\tool.py", line 303 in execute
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\chimerax\cmd_line\tool.py", line 146 in keyPressEvent
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\chimerax\ui\gui.py", line 368 in event_loop
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\chimerax\core\__main__.py", line 1057 in init
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-packages\chimerax\core\__main__.py", line 1220 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
===== Log before crash start =====
> open E:\Individual-Research\2024-Co-QueG\queg-co\5d0b.pdb format pdb
5d0b.pdb title:
Crystal structure of epoxyqueuosine reductase with A TRNA-tyr epoxyqueuosine-
modified TRNA stem loop [more info...]
Chain information for 5d0b.pdb #1
---
Chain | Description | UniProt
A B | queuosine biosynthesis protein QUEG | QUEG_BACSU 1-386
F | RNA (5'-D(*GP*CP*ap*GP*ap*CP*up*(56B) P*up*ap*ap*ap*up*CP*up*GP*C)-3') |
Non-standard residues in 5d0b.pdb #1
---
56B —
2-amino-5-({[(1S,4S,5R)-4,5-dihydroxycyclopent-2-en-1-yl]amino}methyl)-7-(5-O-phosphono-
β-D-ribofuranosyl)-3,7-dihydro-4H-pyrrolo[2,3-D]pyrimidin-4-one
B12 — cobalamin
GOL — glycerol (glycerin; propane-1,2,3-triol)
PO4 — phosphate ion
SF4 — iron/sulfur cluster
15 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> style stick
Changed 6571 atom styles
> style stick
Changed 6571 atom styles
> style sphere
Changed 6571 atom styles
> style ball
Changed 6571 atom styles
> nucleotides atoms
> style nucleic stick
Changed 368 atom styles
> style stick
Changed 6571 atom styles
> style stick
Changed 6571 atom styles
> style stick
Changed 6571 atom styles
> nucleotides atoms
> style nucleic stick
Changed 368 atom styles
> nucleotides fill
> style nucleic stick
Changed 368 atom styles
> nucleotides tube/slab shape box
> nucleotides ladder
> nucleotides atoms
> style nucleic stick
Changed 368 atom styles
> nucleotides tube/slab shape box
> color byhetero
> color bychain
> color bypolymer
> rainbow
> coulombic
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue 56B (net charge +0) with am1-bcc method
Running ANTECHAMBER command: D:/software/chimeraX/ChimeraX
1.10rc202505210000/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
C:\Users\ADMINI~1\AppData\Local\Temp\tmptrz71kzj\ante.in.mol2 -fi mol2 -o
C:\Users\ADMINI~1\AppData\Local\Temp\tmptrz71kzj\ante.out.mol2 -fo mol2 -c bcc
-nc -1 -j 5 -s 2 -dr n
(56B) ``
(56B) `Welcome to antechamber 20.0: molecular input file processor.`
(56B) ``
(56B) `Info: Finished reading file
(C:\Users\ADMINI~1\AppData\Local\Temp\tmptrz71kzj\ante.in.mol2); atoms read
(66), bonds read (69).`
(56B) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(56B) `Running: "D:/software/chimeraX/ChimeraX
1.10rc202505210000/bin/amber20/bin/bondtype" -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(56B) `bash.exe: warning: could not find /tmp, please create!`
(56B) ``
(56B) ``
(56B) `Running: "D:/software/chimeraX/ChimeraX
1.10rc202505210000/bin/amber20/bin/atomtype" -i ANTECHAMBER_AC.AC0 -o
ANTECHAMBER_AC.AC -p gaff`
(56B) `bash.exe: warning: could not find /tmp, please create!`
(56B) `Info: Total number of electrons: 304; net charge: -1`
(56B) ``
(56B) `Running: "D:/software/chimeraX/ChimeraX
1.10rc202505210000/bin/amber20/bin/sqm" -O -i sqm.in -o sqm.out`
(56B) `bash.exe: warning: could not find /tmp, please create!`
(56B) `/usr/bin/antechamber: Fatal Error!`
(56B) `Unable to find sqm charges in file (sqm.out).`
(56B) `Verify the filename and the file contents.`
Contents of sqm.out:
--------------------------------------------------------
AMBER SQM VERSION 19
By
Ross C. Walker, Michael F. Crowley, Scott Brozell,
Tim Giese, Andreas W. Goetz,
Tai-Sung Lee and David A. Case
--------------------------------------------------------
--------------------------------------------------------------------------------
QM CALCULATION INFO
--------------------------------------------------------------------------------
| QMMM: Citation for AMBER QMMM Run:
| QMMM: R.C. Walker, M.F. Crowley and D.A. Case, J. COMP. CHEM. 29:1019, 2008
QMMM: SINGLET STATE CALCULATION
QMMM: RHF CALCULATION, NO. OF DOUBLY OCCUPIED LEVELS =106
| QMMM: *** Selected Hamiltonian ***
| QMMM: AM1
| QMMM: *** Parameter sets in use ***
| QMMM: N : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: C : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: O : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: P : M.J.S.DEWAR et al. THEOCHEM, 187,1, (1989)
| QMMM: H : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: *** SCF convergence criteria ***
| QMMM: Energy change : 0.1D-07 kcal/mol
| QMMM: Error matrix |FP-PF| : 0.1D+00 au
| QMMM: Density matrix change : 0.5D-05
| QMMM: Maximum number of SCF cycles : 1000
| QMMM: *** Diagonalization Routine Information ***
| QMMM: Pseudo diagonalizations are allowed.
| QMMM: Auto diagonalization routine selection is in use.
| QMMM:
| QMMM: Timing diagonalization routines:
| QMMM: norbs = 180
| QMMM: diag iterations used for timing = 5
| QMMM:
| QMMM: Internal diag routine = 0.042079 seconds
| QMMM: Dspev diag routine = 0.039945 seconds
| QMMM: Dspevd diag routine = 0.030011 seconds
| QMMM: Dspevx diag routine = 0.135173 seconds
| QMMM: Dsyev diag routine = 0.043485 seconds
| QMMM: Dsyevd diag routine = 0.031687 seconds
| QMMM: Dsyevr diag routine = 0.035863 seconds
| QMMM:
| QMMM: Pseudo diag routine = 0.020319 seconds
| QMMM:
| QMMM: Using dspevd routine (diag_routine=3).
QMMM: QM Region Cartesian Coordinates (*=link atom)
QMMM: QM_NO. MM_NO. ATOM X Y Z
QMMM: 1 1 N -24.1620 -16.7370 -35.5630
QMMM: 2 2 C -26.2250 -17.6950 -34.4400
QMMM: 3 3 O -26.0700 -19.0930 -34.5590
QMMM: 4 4 P -28.6990 -12.9600 -32.5250
QMMM: 5 5 C -25.6100 -16.9530 -35.6250
QMMM: 6 6 N -19.5770 -16.0010 -34.4890
QMMM: 7 7 O -17.6230 -14.0330 -32.1540
QMMM: 8 8 C -23.4490 -16.2470 -34.4880
QMMM: 9 9 N -23.6290 -17.4370 -37.8180
QMMM: 10 10 O -15.6520 -13.5610 -34.0240
QMMM: 11 11 C -22.1080 -16.1430 -34.8030
QMMM: 12 12 N -22.7710 -17.9910 -39.8880
QMMM: 13 13 O -19.7290 -16.4890 -36.8590
QMMM: 14 14 C -20.9280 -15.6500 -33.9760
QMMM: 15 15 N -21.3050 -17.2230 -38.2880
QMMM: 16 16 O -26.2520 -15.6920 -35.6660
QMMM: 17 17 C -18.4950 -15.8420 -33.5050
QMMM: 18 18 O -28.5220 -14.4180 -33.1400
QMMM: 19 19 C -17.9610 -14.4070 -33.4890
QMMM: 20 20 O -27.9530 -11.9950 -33.3630
QMMM: 21 21 C -16.7060 -14.4490 -34.4030
QMMM: 22 22 C -16.2400 -15.8840 -34.3460
QMMM: 23 23 O -28.4420 -13.0230 -31.0700
QMMM: 24 24 C -17.2420 -16.6730 -33.8510
QMMM: 25 25 O -28.2630 -17.8700 -35.6570
QMMM: 26 26 C -22.0030 -16.6080 -36.1700
QMMM: 27 27 C -23.2970 -16.9640 -36.5980
QMMM: 28 28 C -22.5840 -17.5480 -38.6440
QMMM: 29 29 C -20.9170 -16.7400 -37.0540
QMMM: 30 30 C -27.4620 -15.7420 -34.8680
QMMM: 31 31 C -27.2760 -14.8410 -33.6740
QMMM: 32 32 C -27.6640 -17.2150 -34.5350
QMMM: 33 33 H -25.7770 -17.3480 -33.5090
QMMM: 34 34 H -25.8450 -17.4970 -36.5400
QMMM: 35 35 H -19.5930 -16.9660 -34.7880
QMMM: 36 36 H -19.3740 -15.4190 -35.2890
QMMM: 37 37 H -23.8790 -15.9820 -33.5340
QMMM: 38 38 H -20.9910 -14.5630 -33.9210
QMMM: 39 39 H -21.0260 -16.0500 -32.9670
QMMM: 40 40 H -20.5840 -17.3460 -38.9850
QMMM: 41 41 H -18.8550 -16.1130 -32.5130
QMMM: 42 42 H -18.7040 -13.7220 -33.8970
QMMM: 43 43 H -17.0080 -14.2190 -35.4250
QMMM: 44 44 H -15.2640 -16.2340 -34.6500
QMMM: 45 45 H -17.1660 -17.7420 -33.7190
QMMM: 46 46 H -28.3030 -15.3860 -35.4630
QMMM: 47 47 H -26.7050 -13.9640 -33.9780
QMMM: 48 48 H -26.7220 -15.3780 -32.9040
QMMM: 49 49 H -28.2210 -17.3660 -33.6110
QMMM: 50 50 H -23.6980 -18.2420 -40.2010
QMMM: 51 51 H -21.9860 -18.0750 -40.5170
QMMM: 52 52 H -26.2020 -19.3530 -35.4740
QMMM: 53 53 H -14.8060 -13.9990 -34.1430
QMMM: 54 54 H -18.4240 -13.9640 -31.6290
QMMM: 55 55 O -30.2620 -12.6740 -32.7380
QMMM: 56 56 C -30.7370 -12.2120 -33.9910
QMMM: 57 57 H -30.7400 -11.1120 -34.0000
QMMM: 58 58 H -30.0800 -12.5830 -34.7910
QMMM: 59 59 H -31.7590 -12.5830 -34.1550
QMMM: 60 60 P -29.8420 -17.7880 -35.9480
QMMM: 61 61 C -29.9180 -17.2430 -37.4410
QMMM: 62 62 H -29.9180 -16.1430 -37.4310
QMMM: 63 63 H -29.0470 -17.6050 -38.0080
QMMM: 64 64 H -30.8410 -17.6050 -37.9170
QMMM: 65 65 O -30.4430 -16.7790 -35.0400
QMMM: 66 66 O -30.3830 -19.1700 -35.9790
--------------------------------------------------------------------------------
RESULTS
--------------------------------------------------------------------------------
iter sqm energy rms gradient
---- ------------------- -----------------------
xmin 10 -526.9431 kcal/mol 3.0231 kcal/(mol*A)
Failure running ANTECHAMBER for residue 56B Check reply log for details
> coulombic
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue 56B (net charge +0) with am1-bcc method
Running ANTECHAMBER command: D:/software/chimeraX/ChimeraX
1.10rc202505210000/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
C:\Users\ADMINI~1\AppData\Local\Temp\tmpagsequ_x\ante.in.mol2 -fi mol2 -o
C:\Users\ADMINI~1\AppData\Local\Temp\tmpagsequ_x\ante.out.mol2 -fo mol2 -c bcc
-nc -1 -j 5 -s 2 -dr n
(56B) ``
(56B) `Welcome to antechamber 20.0: molecular input file processor.`
(56B) ``
(56B) `Info: Finished reading file
(C:\Users\ADMINI~1\AppData\Local\Temp\tmpagsequ_x\ante.in.mol2); atoms read
(66), bonds read (69).`
(56B) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(56B) `Running: "D:/software/chimeraX/ChimeraX
1.10rc202505210000/bin/amber20/bin/bondtype" -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(56B) `bash.exe: warning: could not find /tmp, please create!`
(56B) ``
(56B) ``
(56B) `Running: "D:/software/chimeraX/ChimeraX
1.10rc202505210000/bin/amber20/bin/atomtype" -i ANTECHAMBER_AC.AC0 -o
ANTECHAMBER_AC.AC -p gaff`
(56B) `bash.exe: warning: could not find /tmp, please create!`
(56B) `Info: Total number of electrons: 304; net charge: -1`
(56B) ``
(56B) `Running: "D:/software/chimeraX/ChimeraX
1.10rc202505210000/bin/amber20/bin/sqm" -O -i sqm.in -o sqm.out`
(56B) `bash.exe: warning: could not find /tmp, please create!`
(56B) `/usr/bin/antechamber: Fatal Error!`
(56B) `Unable to find sqm charges in file (sqm.out).`
(56B) `Verify the filename and the file contents.`
Contents of sqm.out:
--------------------------------------------------------
AMBER SQM VERSION 19
By
Ross C. Walker, Michael F. Crowley, Scott Brozell,
Tim Giese, Andreas W. Goetz,
Tai-Sung Lee and David A. Case
--------------------------------------------------------
--------------------------------------------------------------------------------
QM CALCULATION INFO
--------------------------------------------------------------------------------
| QMMM: Citation for AMBER QMMM Run:
| QMMM: R.C. Walker, M.F. Crowley and D.A. Case, J. COMP. CHEM. 29:1019, 2008
QMMM: SINGLET STATE CALCULATION
QMMM: RHF CALCULATION, NO. OF DOUBLY OCCUPIED LEVELS =106
| QMMM: *** Selected Hamiltonian ***
| QMMM: AM1
| QMMM: *** Parameter sets in use ***
| QMMM: N : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: C : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: O : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: P : M.J.S.DEWAR et al. THEOCHEM, 187,1, (1989)
| QMMM: H : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: *** SCF convergence criteria ***
| QMMM: Energy change : 0.1D-07 kcal/mol
| QMMM: Error matrix |FP-PF| : 0.1D+00 au
| QMMM: Density matrix change : 0.5D-05
| QMMM: Maximum number of SCF cycles : 1000
| QMMM: *** Diagonalization Routine Information ***
| QMMM: Pseudo diagonalizations are allowed.
| QMMM: Auto diagonalization routine selection is in use.
| QMMM:
| QMMM: Timing diagonalization routines:
| QMMM: norbs = 180
| QMMM: diag iterations used for timing = 5
| QMMM:
| QMMM: Internal diag routine = 0.048882 seconds
| QMMM: Dspev diag routine = 0.042256 seconds
| QMMM: Dspevd diag routine = 0.029983 seconds
| QMMM: Dspevx diag routine = 0.141428 seconds
| QMMM: Dsyev diag routine = 0.043951 seconds
| QMMM: Dsyevd diag routine = 0.032264 seconds
| QMMM: Dsyevr diag routine = 0.036786 seconds
| QMMM:
| QMMM: Pseudo diag routine = 0.019519 seconds
| QMMM:
| QMMM: Using dspevd routine (diag_routine=3).
QMMM: QM Region Cartesian Coordinates (*=link atom)
QMMM: QM_NO. MM_NO. ATOM X Y Z
QMMM: 1 1 N -24.1620 -16.7370 -35.5630
QMMM: 2 2 C -26.2250 -17.6950 -34.4400
QMMM: 3 3 O -26.0700 -19.0930 -34.5590
QMMM: 4 4 P -28.6990 -12.9600 -32.5250
QMMM: 5 5 C -25.6100 -16.9530 -35.6250
QMMM: 6 6 N -19.5770 -16.0010 -34.4890
QMMM: 7 7 O -17.6230 -14.0330 -32.1540
QMMM: 8 8 C -23.4490 -16.2470 -34.4880
QMMM: 9 9 N -23.6290 -17.4370 -37.8180
QMMM: 10 10 O -15.6520 -13.5610 -34.0240
QMMM: 11 11 C -22.1080 -16.1430 -34.8030
QMMM: 12 12 N -22.7710 -17.9910 -39.8880
QMMM: 13 13 O -19.7290 -16.4890 -36.8590
QMMM: 14 14 C -20.9280 -15.6500 -33.9760
QMMM: 15 15 N -21.3050 -17.2230 -38.2880
QMMM: 16 16 O -26.2520 -15.6920 -35.6660
QMMM: 17 17 C -18.4950 -15.8420 -33.5050
QMMM: 18 18 O -28.5220 -14.4180 -33.1400
QMMM: 19 19 C -17.9610 -14.4070 -33.4890
QMMM: 20 20 O -27.9530 -11.9950 -33.3630
QMMM: 21 21 C -16.7060 -14.4490 -34.4030
QMMM: 22 22 C -16.2400 -15.8840 -34.3460
QMMM: 23 23 O -28.4420 -13.0230 -31.0700
QMMM: 24 24 C -17.2420 -16.6730 -33.8510
QMMM: 25 25 O -28.2630 -17.8700 -35.6570
QMMM: 26 26 C -22.0030 -16.6080 -36.1700
QMMM: 27 27 C -23.2970 -16.9640 -36.5980
QMMM: 28 28 C -22.5840 -17.5480 -38.6440
QMMM: 29 29 C -20.9170 -16.7400 -37.0540
QMMM: 30 30 C -27.4620 -15.7420 -34.8680
QMMM: 31 31 C -27.2760 -14.8410 -33.6740
QMMM: 32 32 C -27.6640 -17.2150 -34.5350
QMMM: 33 33 H -25.7770 -17.3480 -33.5090
QMMM: 34 34 H -25.8450 -17.4970 -36.5400
QMMM: 35 35 H -19.5930 -16.9660 -34.7880
QMMM: 36 36 H -19.3740 -15.4190 -35.2890
QMMM: 37 37 H -23.8790 -15.9820 -33.5340
QMMM: 38 38 H -20.9910 -14.5630 -33.9210
QMMM: 39 39 H -21.0260 -16.0500 -32.9670
QMMM: 40 40 H -20.5840 -17.3460 -38.9850
QMMM: 41 41 H -18.8550 -16.1130 -32.5130
QMMM: 42 42 H -18.7040 -13.7220 -33.8970
QMMM: 43 43 H -17.0080 -14.2190 -35.4250
QMMM: 44 44 H -15.2640 -16.2340 -34.6500
QMMM: 45 45 H -17.1660 -17.7420 -33.7190
QMMM: 46 46 H -28.3030 -15.3860 -35.4630
QMMM: 47 47 H -26.7050 -13.9640 -33.9780
QMMM: 48 48 H -26.7220 -15.3780 -32.9040
QMMM: 49 49 H -28.2210 -17.3660 -33.6110
QMMM: 50 50 H -23.6980 -18.2420 -40.2010
QMMM: 51 51 H -21.9860 -18.0750 -40.5170
QMMM: 52 52 H -26.2020 -19.3530 -35.4740
QMMM: 53 53 H -14.8060 -13.9990 -34.1430
QMMM: 54 54 H -18.4240 -13.9640 -31.6290
QMMM: 55 55 O -30.2620 -12.6740 -32.7380
QMMM: 56 56 C -30.7370 -12.2120 -33.9910
QMMM: 57 57 H -30.7400 -11.1120 -34.0000
QMMM: 58 58 H -30.0800 -12.5830 -34.7910
QMMM: 59 59 H -31.7590 -12.5830 -34.1550
QMMM: 60 60 P -29.8420 -17.7880 -35.9480
QMMM: 61 61 C -29.9180 -17.2430 -37.4410
QMMM: 62 62 H -29.9180 -16.1430 -37.4310
QMMM: 63 63 H -29.0470 -17.6050 -38.0080
QMMM: 64 64 H -30.8410 -17.6050 -37.9170
QMMM: 65 65 O -30.4430 -16.7790 -35.0400
QMMM: 66 66 O -30.3830 -19.1700 -35.9790
--------------------------------------------------------------------------------
RESULTS
--------------------------------------------------------------------------------
Failure running ANTECHAMBER for residue 56B Check reply log for details
> mlp
Map values for surface "5d0b.pdb_A SES surface": minimum -27.96, mean -4.72,
maximum 23.34
Map values for surface "5d0b.pdb_B SES surface": minimum -27.94, mean -4.733,
maximum 24.69
To also show corresponding color key, enter the above mlp command and add key
true
> hbonds reveal true
972 hydrogen bonds found
> ~hbonds
Alignment identifier is 1
Alignment identifier is 1/F
> interfaces ~solvent
2 buried areas: A F 874, A B 707
> color bychain
> color bypolymer
> color byhetero
> hbonds reveal true
972 hydrogen bonds found
> color byhetero
> style stick
Changed 6571 atom styles
> style sphere
Changed 6571 atom styles
> style stick
Changed 6571 atom styles
> style stick
Changed 6571 atom styles
> color byhetero
> hide #!1 models
> show #!1 models
> select add #1
6571 atoms, 6686 bonds, 997 pseudobonds, 847 residues, 5 models selected
> select subtract #1
2 models selected
> select add #1
6571 atoms, 6686 bonds, 997 pseudobonds, 847 residues, 5 models selected
> select subtract #1
2 models selected
> select add #1
6571 atoms, 6686 bonds, 997 pseudobonds, 847 residues, 5 models selected
> select subtract #1
2 models selected
> close #1
> open E:\Individual-Research\2024-Co-QueG\queg-co\5d0b.pdb format pdb
5d0b.pdb title:
Crystal structure of epoxyqueuosine reductase with A TRNA-tyr epoxyqueuosine-
modified TRNA stem loop [more info...]
Chain information for 5d0b.pdb #1
---
Chain | Description | UniProt
A B | queuosine biosynthesis protein QUEG | QUEG_BACSU 1-386
F | RNA (5'-D(*GP*CP*ap*GP*ap*CP*up*(56B) P*up*ap*ap*ap*up*CP*up*GP*C)-3') |
Non-standard residues in 5d0b.pdb #1
---
56B —
2-amino-5-({[(1S,4S,5R)-4,5-dihydroxycyclopent-2-en-1-yl]amino}methyl)-7-(5-O-phosphono-
β-D-ribofuranosyl)-3,7-dihydro-4H-pyrrolo[2,3-D]pyrimidin-4-one
B12 — cobalamin
GOL — glycerol (glycerin; propane-1,2,3-triol)
PO4 — phosphate ion
SF4 — iron/sulfur cluster
15 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> show atoms
> hide atoms
> show atoms
> show cartoons
> show surfaces
> hide surfaces
> hide cartoons
> hide atoms
> show atoms
> style stick
Changed 6571 atom styles
> style stick
Changed 6571 atom styles
> style sphere
Changed 6571 atom styles
> style ball
Changed 6571 atom styles
> nucleotides tube/slab shape box
> show atoms
> hide atoms
> show atoms
> show cartoons
> hide cartoons
> show cartoons
> hide atoms
> show atoms
> hide cartoons
> show cartoons
> hide surfaces
> show surfaces
> hide surfaces
> nucleotides fill
> style nucleic stick
Changed 368 atom styles
> nucleotides tube/slab shape box
> nucleotides ladder
> nucleotides stubs
> nucleotides tube/slab shape muffler
> volume style surface
No volumes specified
> volume style mesh
No volumes specified
Color zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic
models, 0 maps.
Hide dust shortcut requires a displayed map surface
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 1 atomic models, 0 maps.
> hide surfaces
> show surfaces
> volume showOutlineBox true
No volumes specified
> volume appearance airways
No volumes specified
> ui mousemode right "mark maximum"
> ui mousemode right "mark plane"
> ui mousemode right "move markers"
> ui mousemode right select
> ui mousemode right translate
> movie record
> turn y 2 180
> wait 180
> movie encode C:\Users\Administrator/Desktop\movie1.mp4
Movie saved to C:\Users\Administrator/Desktop\movie1.mp4
> movie record
> turn y 2 180
> wait 180
> movie encode C:\Users\Administrator/Desktop\movie2.mp4
D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\ffmpeg.exe -r 25 -i
C:\Users\ADMINI~1\AppData\Local\Temp\chimovie_XP3B-%05d.ppm -vf
crop=floor(in_w/2)*2:floor(in_h/2)*2:0:0 -y -vcodec libx264 -f mp4 -pix_fmt
yuv420p -crf 20 C:\Users\Administrator/Desktop\movie2.mp4
stdout:
stderr:
ffmpeg version 3.2.4 Copyright (c) 2000-2017 the FFmpeg developers
built with gcc 6.3.0 (GCC)
configuration: --enable-gpl --enable-version3 --enable-d3d11va --enable-dxva2
--enable-libmfx --enable-nvenc --enable-avisynth --enable-bzlib --enable-
fontconfig --enable-frei0r --enable-gnutls --enable-iconv --enable-libass
--enable-libbluray --enable-libbs2b --enable-libcaca --enable-libfreetype
--enable-libgme --enable-libgsm --enable-libilbc --enable-libmodplug --enable-
libmp3lame --enable-libopencore-amrnb --enable-libopencore-amrwb --enable-
libopenh264 --enable-libopenjpeg --enable-libopus --enable-librtmp --enable-
libsnappy --enable-libsoxr --enable-libspeex --enable-libtheora --enable-
libtwolame --enable-libvidstab --enable-libvo-amrwbenc --enable-libvorbis
--enable-libvpx --enable-libwavpack --enable-libwebp --enable-libx264
--enable-libx265 --enable-libxavs --enable-libxvid --enable-libzimg --enable-
lzma --enable-zlib
libavutil 55. 34.101 / 55. 34.101
libavcodec 57. 64.101 / 57. 64.101
libavformat 57. 56.101 / 57. 56.101
libavdevice 57. 1.100 / 57. 1.100
libavfilter 6. 65.100 / 6. 65.100
libswscale 4. 2.100 / 4. 2.100
libswresample 2. 3.100 / 2. 3.100
libpostproc 54. 1.100 / 54. 1.100
Input #0, image2, from
'C:\Users\ADMINI~1\AppData\Local\Temp\chimovie_XP3B-%05d.ppm':
Duration: 00:00:07.20, start: 0.000000, bitrate: N/A
Stream #0:0: Video: ppm, rgb24, 1339x809, 25 tbr, 25 tbn, 25 tbc
[libx264 @ 00000000029354c0] using cpu capabilities: MMX2 SSE2Fast SSSE3
SSE4.2 AVX FMA3 AVX2 LZCNT BMI2
[libx264 @ 00000000029354c0] profile High, level 3.2
[libx264 @ 00000000029354c0] 264 - core 148 r2762 90a61ec - H.264/MPEG-4 AVC
codec - Copyleft 2003-2017 - http://www.videolan.org/x264.html - options:
cabac=1 ref=3 deblock=1:0:0 analyse=0x3:0x113 me=hex subme=7 psy=1
psy_rd=1.00:0.00 mixed_ref=1 me_range=16 chroma_me=1 trellis=1 8x8dct=1 cqm=0
deadzone=21,11 fast_pskip=1 chroma_qp_offset=-2 threads=12 lookahead_threads=2
sliced_threads=0 nr=0 decimate=1 interlaced=0 bluray_compat=0
constrained_intra=0 bframes=3 b_pyramid=2 b_adapt=1 b_bias=0 direct=1
weightb=1 open_gop=0 weightp=2 keyint=250 keyint_min=25 scenecut=40
intra_refresh=0 rc_lookahead=40 rc=crf mbtree=1 crf=20.0 qcomp=0.60 qpmin=0
qpmax=69 qpstep=4 ip_ratio=1.40 aq=1:1.00
Output #0, mp4, to 'C:\Users\Administrator/Desktop\movie2.mp4':
Metadata:
encoder : Lavf57.56.101
Stream #0:0: Video: h264 (libx264) ([33][0][0][0] / 0x0021), yuv420p,
1338x808, q=-1--1, 25 fps, 12800 tbn, 25 tbc
Metadata:
encoder : Lavc57.64.101 libx264
Side data:
cpb: bitrate max/min/avg: 0/0/0 buffer size: 0 vbv_delay: -1
Stream mapping:
Stream #0:0 -> #0:0 (ppm (native) -> h264 (libx264))
Press [q] to stop, [?] for help
frame= 47 fps=0.0 q=0.0 size= 0kB time=00:00:00.00 bitrate=N/A speed= 0x
frame= 84 fps= 49 q=-1.0 Lsize= 1508kB time=00:00:03.24 bitrate=3813.1kbits/s
speed=1.88x
video:1506kB audio:0kB subtitle:0kB other streams:0kB global headers:0kB
muxing overhead: 0.117016%
[libx264 @ 00000000029354c0] frame I:1 Avg QP:15.49 size: 69086
[libx264 @ 00000000029354c0] frame P:44 Avg QP:24.01 size: 25814
[libx264 @ 00000000029354c0] frame B:39 Avg QP:27.91 size: 8639
[libx264 @ 00000000029354c0] consecutive B-frames: 14.3% 69.0% 7.1% 9.5%
[libx264 @ 00000000029354c0] mb I I16..4: 41.8% 35.6% 22.6%
[libx264 @ 00000000029354c0] mb P I16..4: 0.8% 1.8% 1.2% P16..4: 11.6% 15.9%
11.3% 0.0% 0.0% skip:57.4%
[libx264 @ 00000000029354c0] mb B I16..4: 0.0% 0.1% 0.0% B16..8: 15.3% 6.8%
4.0% direct: 2.3% skip:71.4% L0:22.2% L1:42.9% BI:34.9%
[libx264 @ 00000000029354c0] 8x8 transform intra:42.9% inter:44.7%
[libx264 @ 00000000029354c0] coded y,uvDC,uvAC intra: 42.3% 44.7% 40.1% inter:
16.4% 10.9% 3.0%
[libx264 @ 00000000029354c0] i16 v,h,dc,p: 93% 4% 3% 0%
[libx264 @ 00000000029354c0] i8 v,h,dc,ddl,ddr,vr,hd,vl,hu: 12% 10% 55% 3% 3%
4% 3% 5% 5%
[libx264 @ 00000000029354c0] i4 v,h,dc,ddl,ddr,vr,hd,vl,hu: 18% 15% 10% 8% 10%
12% 10% 10% 8%
[libx264 @ 00000000029354c0] i8c dc,h,v,p: 70% 12% 12% 6%
[libx264 @ 00000000029354c0] Weighted P-Frames: Y:18.2% UV:4.5%
[libx264 @ 00000000029354c0] ref P L0: 53.8% 36.0% 8.0% 1.9% 0.3%
[libx264 @ 00000000029354c0] ref B L0: 95.2% 4.7% 0.2%
[libx264 @ 00000000029354c0] ref B L1: 99.8% 0.2%
[libx264 @ 00000000029354c0] kb/s:3671.02
Exiting normally, received signal 15.
An error occurred during encoding. See Reply Log for details.
Error during MPEG encoding:
\-----------------------------
Exit value: 3221225786
Error message:
stdout:
stderr:
ffmpeg version 3.2.4 Copyright (c) 2000-2017 the FFmpeg developers
built with gcc 6.3.0 (GCC)
configuration: --enable-gpl --enable-version3 --enable-d3d11va --enable-dxva2
--enable-libmfx --enable-nvenc --enable-avisynth --enable-bzlib --enable-
fontconfig --enable-frei0r --enable-gnutls --enable-iconv --enable-libass
--enable-libbluray --enable-libbs2b --enable-libcaca --enable-libfreetype
--enable-libgme --enable-libgsm --enable-libilbc --enable-libmodplug --enable-
libmp3lame --enable-libopencore-amrnb --enable-libopencore-amrwb --enable-
libopenh264 --enable-libopenjpeg --enable-libopus --enable-librtmp --enable-
libsnappy --enable-libsoxr --enable-libspeex --enable-libtheora --enable-
libtwolame --enable-libvidstab --enable-libvo-amrwbenc --enable-libvorbis
--enable-libvpx --enable-libwavpack --enable-libwebp --enable-libx264
--enable-libx265 --enable-libxavs --enable-libxvid --enable-libzimg --enable-
lzma --enable-zlib
libavutil 55. 34.101 / 55. 34.101
libavcodec 57. 64.101 / 57. 64.101
libavformat 57. 56.101 / 57. 56.101
libavdevice 57. 1.100 / 57. 1.100
libavfilter 6. 65.100 / 6. 65.100
libswscale 4. 2.100 / 4. 2.100
libswresample 2. 3.100 / 2. 3.100
libpostproc 54. 1.100 / 54. 1.100
Input #0, image2, from
'C:\Users\ADMINI~1\AppData\Local\Temp\chimovie_XP3B-%05d.ppm':
Duration: 00:00:07.20, start: 0.000000, bitrate: N/A
Stream #0:0: Video: ppm, rgb24, 1339x809, 25 tbr, 25 tbn, 25 tbc
[libx264 @ 00000000029354c0] using cpu capabilities: MMX2 SSE2Fast SSSE3
SSE4.2 AVX FMA3 AVX2 LZCNT BMI2
[libx264 @ 00000000029354c0] profile High, level 3.2
[libx264 @ 00000000029354c0] 264 - core 148 r2762 90a61ec - H.264/MPEG-4 AVC
codec - Copyleft 2003-2017 - http://www.videolan.org/x264.html - options:
cabac=1 ref=3 deblock=1:0:0 analyse=0x3:0x113 me=hex subme=7 psy=1
psy_rd=1.00:0.00 mixed_ref=1 me_range=16 chroma_me=1 trellis=1 8x8dct=1 cqm=0
deadzone=21,11 fast_pskip=1 chroma_qp_offset=-2 threads=12 lookahead_threads=2
sliced_threads=0 nr=0 decimate=1 interlaced=0 bluray_compat=0
constrained_intra=0 bframes=3 b_pyramid=2 b_adapt=1 b_bias=0 direct=1
weightb=1 open_gop=0 weightp=2 keyint=250 keyint_min=25 scenecut=40
intra_refresh=0 rc_lookahead=40 rc=crf mbtree=1 crf=20.0 qcomp=0.60 qpmin=0
qpmax=69 qpstep=4 ip_ratio=1.40 aq=1:1.00
Output #0, mp4, to 'C:\Users\Administrator/Desktop\movie2.mp4':
Metadata:
encoder : Lavf57.56.101
Stream #0:0: Video: h264 (libx264) ([33][0][0][0] / 0x0021), yuv420p,
1338x808, q=-1--1, 25 fps, 12800 tbn, 25 tbc
Metadata:
encoder : Lavc57.64.101 libx264
Side data:
cpb: bitrate max/min/avg: 0/0/0 buffer size: 0 vbv_delay: -1
Stream mapping:
Stream #0:0 -> #0:0 (ppm (native) -> h264 (libx264))
Press [q] to stop, [?] for help
frame= 47 fps=0.0 q=0.0 size= 0kB time=00:00:00.00 bitrate=N/A speed= 0x
frame= 84 fps= 49 q=-1.0 Lsize= 1508kB time=00:00:03.24 bitrate=3813.1kbits/s
speed=1.88x
video:1506kB audio:0kB subtitle:0kB other streams:0kB global headers:0kB
muxing overhead: 0.117016%
[libx264 @ 00000000029354c0] frame I:1 Avg QP:15.49 size: 69086
[libx264 @ 00000000029354c0] frame P:44 Avg QP:24.01 size: 25814
[libx264 @ 00000000029354c0] frame B:39 Avg QP:27.91 size: 8639
[libx264 @ 00000000029354c0] consecutive B-frames: 14.3% 69.0% 7.1% 9.5%
[libx264 @ 00000000029354c0] mb I I16..4: 41.8% 35.6% 22.6%
[libx264 @ 00000000029354c0] mb P I16..4: 0.8% 1.8% 1.2% P16..4: 11.6% 15.9%
11.3% 0.0% 0.0% skip:57.4%
[libx264 @ 00000000029354c0] mb B I16..4: 0.0% 0.1% 0.0% B16..8: 15.3% 6.8%
4.0% direct: 2.3% skip:71.4% L0:22.2% L1:42.9% BI:34.9%
[libx264 @ 00000000029354c0] 8x8 transform intra:42.9% inter:44.7%
[libx264 @ 00000000029354c0] coded y,uvDC,uvAC intra: 42.3% 44.7% 40.1% inter:
16.4% 10.9% 3.0%
[libx264 @ 00000000029354c0] i16 v,h,dc,p: 93% 4% 3% 0%
[libx264 @ 00000000029354c0] i8 v,h,dc,ddl,ddr,vr,hd,vl,hu: 12% 10% 55% 3% 3%
4% 3% 5% 5%
[libx264 @ 00000000029354c0] i4 v,h,dc,ddl,ddr,vr,hd,vl,hu: 18% 15% 10% 8% 10%
12% 10% 10% 8%
[libx264 @ 00000000029354c0] i8c dc,h,v,p: 70% 12% 12% 6%
[libx264 @ 00000000029354c0] Weighted P-Frames: Y:18.2% UV:4.5%
[libx264 @ 00000000029354c0] ref P L0: 53.8% 36.0% 8.0% 1.9% 0.3%
[libx264 @ 00000000029354c0] ref B L0: 95.2% 4.7% 0.2%
[libx264 @ 00000000029354c0] ref B L1: 99.8% 0.2%
[libx264 @ 00000000029354c0] kb/s:3671.02
Exiting normally, received signal 15.
\-----------------------------
> save C:\Users\Administrator/Desktop\image1.png supersample 3
> show atoms
> open E:/Individual-Research/2024-Co-QueG/queg-co/5d0b.pdb
5d0b.pdb title:
Crystal structure of epoxyqueuosine reductase with A TRNA-tyr epoxyqueuosine-
modified TRNA stem loop [more info...]
Chain information for 5d0b.pdb #2
---
Chain | Description | UniProt
A B | queuosine biosynthesis protein QUEG | QUEG_BACSU 1-386
F | RNA (5'-D(*GP*CP*ap*GP*ap*CP*up*(56B) P*up*ap*ap*ap*up*CP*up*GP*C)-3') |
Non-standard residues in 5d0b.pdb #2
---
56B —
2-amino-5-({[(1S,4S,5R)-4,5-dihydroxycyclopent-2-en-1-yl]amino}methyl)-7-(5-O-phosphono-
β-D-ribofuranosyl)-3,7-dihydro-4H-pyrrolo[2,3-D]pyrimidin-4-one
B12 — cobalamin
GOL — glycerol (glycerin; propane-1,2,3-triol)
PO4 — phosphate ion
SF4 — iron/sulfur cluster
15 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> hide #!1 target m
> select add #1
6571 atoms, 6686 bonds, 25 pseudobonds, 847 residues, 4 models selected
> select subtract #1
3 models selected
> close #1
> hide cartoons
> show cartoons
> set sill t
Expected a keyword
> set bgColor white
> show inface
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show sil t
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show sf4 t
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show SF4 t
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show SF4
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> color modify ions bue +45
Missing or invalid "adjuster" argument: Should be one of 'blackness', 'blue',
'contrast', 'green', 'hue', 'lightness', 'red', 'saturation', or 'whiteness'
> color modify ions hue +45
> select ligand
228 atoms, 255 bonds, 9 residues, 1 model selected
> color sel gray
> ui mousemode right rotate
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
Traceback (most recent call last):
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 655, in
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 556, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 55, in mouse_drag
self._undraw_drag_rectangle()
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 146, in
_undraw_drag_rectangle
v.draw_xor_rectangle(dx, h-dy, x, h-y, self._xor_color)
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-
packages\chimerax\graphics\view.py", line 336, in draw_xor_rectangle
self._rectangle_drawing = draw_xor_rectangle(self._render, x1, y1, x2, y2,
color, d)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1685, in draw_xor_rectangle
r.flush()
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 1287, in flush
GL.glFlush()
OSError: exception: access violation reading 0x0000000000000118
OSError: exception: access violation reading 0x0000000000000118
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 1287, in flush
GL.glFlush()
See log for complete Python traceback.
Traceback (most recent call last):
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 655, in
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 556, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 55, in mouse_drag
self._undraw_drag_rectangle()
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 146, in
_undraw_drag_rectangle
v.draw_xor_rectangle(dx, h-dy, x, h-y, self._xor_color)
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-
packages\chimerax\graphics\view.py", line 336, in draw_xor_rectangle
self._rectangle_drawing = draw_xor_rectangle(self._render, x1, y1, x2, y2,
color, d)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1685, in draw_xor_rectangle
r.flush()
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 1287, in flush
GL.glFlush()
OSError: exception: access violation reading 0x0000000000000040
OSError: exception: access violation reading 0x0000000000000040
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 1287, in flush
GL.glFlush()
See log for complete Python traceback.
Traceback (most recent call last):
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 655, in
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 556, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 55, in mouse_drag
self._undraw_drag_rectangle()
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 146, in
_undraw_drag_rectangle
v.draw_xor_rectangle(dx, h-dy, x, h-y, self._xor_color)
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-
packages\chimerax\graphics\view.py", line 336, in draw_xor_rectangle
self._rectangle_drawing = draw_xor_rectangle(self._render, x1, y1, x2, y2,
color, d)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1685, in draw_xor_rectangle
r.flush()
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 1287, in flush
GL.glFlush()
OSError: exception: access violation reading 0xFFFFFFFF00000051
OSError: exception: access violation reading 0xFFFFFFFF00000051
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 1287, in flush
GL.glFlush()
See log for complete Python traceback.
Traceback (most recent call last):
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 655, in
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 556, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 55, in mouse_drag
self._undraw_drag_rectangle()
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 146, in
_undraw_drag_rectangle
v.draw_xor_rectangle(dx, h-dy, x, h-y, self._xor_color)
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-
packages\chimerax\graphics\view.py", line 336, in draw_xor_rectangle
self._rectangle_drawing = draw_xor_rectangle(self._render, x1, y1, x2, y2,
color, d)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1685, in draw_xor_rectangle
r.flush()
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 1287, in flush
GL.glFlush()
OSError: exception: access violation reading 0xFFFFFFFF00000051
OSError: exception: access violation reading 0xFFFFFFFF00000051
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 1287, in flush
GL.glFlush()
See log for complete Python traceback.
Traceback (most recent call last):
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 656, in
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 556, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 59, in mouse_up
self._undraw_drag_rectangle()
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 146, in
_undraw_drag_rectangle
v.draw_xor_rectangle(dx, h-dy, x, h-y, self._xor_color)
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-
packages\chimerax\graphics\view.py", line 336, in draw_xor_rectangle
self._rectangle_drawing = draw_xor_rectangle(self._render, x1, y1, x2, y2,
color, d)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1685, in draw_xor_rectangle
r.flush()
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 1287, in flush
GL.glFlush()
OSError: exception: access violation reading 0x0000000000000050
OSError: exception: access violation reading 0x0000000000000050
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 1287, in flush
GL.glFlush()
See log for complete Python traceback.
> ui mousemode right "translate selected atoms"
An error occurred in drawing the scene. Redrawing graphics is now stopped to
avoid a continuous stream of error messages. To restart graphics use the
command "graphics restart" after changing the settings that caused the error.
GLError(
err = 1285,
baseOperation = glBufferData,
pyArgs = (
34962,
57216,
array([[-0.24047764, 0.7187815 , 0.6523218 ],
[-0.24047764, 0.7187815 , 0.6523218 ],
[-0.24047764, ...,
GL_STATIC_DRAW,
),
cArgs = (
34962,
57216,
array([[-0.24047764, 0.7187815 , 0.6523218 ],
[-0.24047764, 0.7187815 , 0.6523218 ],
[-0.24047764, ...,
GL_STATIC_DRAW,
),
cArguments = (
34962,
57216,
array([[-0.24047764, 0.7187815 , 0.6523218 ],
[-0.24047764, 0.7187815 , 0.6523218 ],
[-0.24047764, ...,
GL_STATIC_DRAW,
)
)
Traceback (most recent call last):
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-
packages\chimerax\core\updateloop.py", line 84, in draw_new_frame
view.draw(check_for_changes = False)
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-
packages\chimerax\graphics\view.py", line 188, in draw
self._draw_scene(camera, drawings)
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-
packages\chimerax\graphics\view.py", line 259, in _draw_scene
draw_opaque(r, opaque_drawings)
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1559, in draw_opaque
_draw_multiple(drawings, renderer, Drawing.OPAQUE_DRAW_PASS)
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1572, in _draw_multiple
d.draw(renderer, draw_pass)
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 784, in draw
self.draw_self(renderer, draw_pass)
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 791, in draw_self
self._draw_geometry(renderer, opaque_only = any_transp)
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 818, in _draw_geometry
ds.activate_bindings(renderer)
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1929, in activate_bindings
self.update_buffers()
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1917, in update_buffers
b.update_buffer_data(data)
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 2829, in update_buffer_data
GL.glBufferData(btype, size, d, GL.GL_STATIC_DRAW)
File "src\\\latebind.pyx", line 52, in
OpenGL_accelerate.latebind.Curry.__call__
File "D:\software\chimeraX\ChimeraX 1.10rc202505210000\bin\Lib\site-
packages\OpenGL\GL\VERSION\GL_1_5.py", line 89, in glBufferData
return baseOperation( target, size, data, usage )
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "src\\\latebind.pyx", line 40, in
OpenGL_accelerate.latebind.LateBind.__call__
File "src\\\wrapper.pyx", line 319, in
OpenGL_accelerate.wrapper.Wrapper.__call__
File "src\\\wrapper.pyx", line 312, in
OpenGL_accelerate.wrapper.Wrapper.__call__
File "src\\\errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1285,
baseOperation = glBufferData,
pyArgs = (
34962,
57216,
array([[-0.24047764, 0.7187815 , 0.6523218 ],
[-0.24047764, 0.7187815 , 0.6523218 ],
[-0.24047764, ...,
GL_STATIC_DRAW,
),
cArgs = (
34962,
57216,
array([[-0.24047764, 0.7187815 , 0.6523218 ],
[-0.24047764, 0.7187815 , 0.6523218 ],
[-0.24047764, ...,
GL_STATIC_DRAW,
),
cArguments = (
34962,
57216,
array([[-0.24047764, 0.7187815 , 0.6523218 ],
[-0.24047764, 0.7187815 , 0.6523218 ],
[-0.24047764, ...,
GL_STATIC_DRAW,
)
)
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.10rc202505210000 (2025-05-21)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.2 (Core Profile) Mesa 23.1.1 (git-fae5b32981)
OpenGL renderer: D3D12 (AMD Radeon R5 430)
OpenGL vendor: Microsoft Corporation
Python: 3.11.4
Locale: zh_CN.cp936
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: windows
Manufacturer: Dell Inc.
Model: OptiPlex 7070
OS: Microsoft Windows 11 专业版 (Build 22631)
Memory: 16,951,214,080
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-9700 CPU @ 3.00GHz
OSLanguage: zh-CN
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
asttokens: 3.0.0
auditwheel: 6.3.0
babel: 2.17.0
beautifulsoup4: 4.13.3
blockdiag: 3.0.0
blosc2: 3.3.3
build: 1.2.2.post1
certifi: 2025.4.26
cftime: 1.6.4.post1
charset-normalizer: 3.4.2
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.7
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.20.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.1.3
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.6
ChimeraX-AtomicLibrary: 14.1.18
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.5.1
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.10rc202505210000
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5.1
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.6.2
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.2.1
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.10.1
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.19
ChimeraX-ModelPanel: 1.5.1
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14.1
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.10
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.3
ChimeraX-ProfileGrids: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.3
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.1
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.45.1
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.5
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
comtypes: 1.4.10
contourpy: 1.3.2
coverage: 7.8.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.12
debugpy: 1.8.14
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.0
filelock: 3.18.0
fonttools: 4.58.0
funcparserlib: 2.0.0a0
glfw: 2.9.0
grako: 3.16.5
h5py: 3.13.0
html2text: 2024.2.26
idna: 3.10
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.1.0
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.7
jedi: 0.19.1
Jinja2: 3.1.6
jupyter_client: 8.6.3
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.15
kiwisolver: 1.4.8
line_profiler: 4.2.0
lxml: 5.3.1
lz4: 4.4.4
MarkupSafe: 3.0.2
matplotlib: 3.10.1
matplotlib-inline: 0.1.7
msgpack: 1.1.0
ndindex: 1.10.0
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 24.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pickleshare: 0.7.5
pillow: 10.4.0
pip: 25.0.1
pkginfo: 1.11.1
platformdirs: 4.3.8
pluggy: 1.6.0
prompt_toolkit: 3.0.51
psutil: 7.0.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.32
Pygments: 2.18.0
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.9
PyOpenGL-accelerate: 3.1.9
pyopenxr: 1.1.4501
pyparsing: 3.2.3
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.8.1
PyQt6-Qt6: 6.8.2
PyQt6-WebEngine-commercial: 6.8.0
PyQt6-WebEngine-Qt6: 6.8.2
PyQt6_sip: 13.10.0
pytest: 8.3.5
pytest-cov: 6.1.1
python-dateutil: 2.9.0.post0
pytz: 2025.2
pywin32: 310
pyzmq: 26.4.0
qtconsole: 5.5.2
QtPy: 2.4.3
qtshim: 1.1
RandomWords: 0.4.0
requests: 2.32.3
roman-numerals-py: 3.1.0
scipy: 1.14.0
setuptools: 78.1.0
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.7
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.1.0
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.7.1
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.4
tornado: 6.5
traitlets: 5.14.3
typing_extensions: 4.13.2
tzdata: 2025.2
urllib3: 2.4.0
wcwidth: 0.2.13
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.14
WMI: 1.5.1
Note:
See TracTickets
for help on using tickets.
