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Opened 5 years ago
Closed 5 years ago
#4363 closed defect (can't reproduce)
glDrawBuffer: invalid operation
| Reported by: | 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: Linux-3.10.0-1160.6.1.el7.x86_64-x86_64-with-centos-7.9.2009-Core
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
> open chimera_sesion_best_pose_rigid-dock_surface.cxs
Log from Sat Mar 13 11:17:48 2021UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
> open chimera_sesion_best_pose_rigid-dock.cxs
Log from Sat Mar 13 11:12:28 2021UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
> open chimera_sesion_best_pose_rigid-dock.cxs
Log from Sat Mar 13 11:11:00 2021UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "chimera_sesion_best_pose_rigid -dock.cxs"
Log from Sat Mar 13 11:04:18 2021UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "chimera_sesion_best_pose_rigid -dock.cxs"
Log from Sat Mar 13 11:02:04 2021UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "chimera_sesion_best_pose_rigid -dock.cxs"
Log from Sat Mar 13 10:59:59 2021UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
> open
> "/c7/home/lchecaru/CnP/PRDX6-MALARIA/Docking_darapladib/Smina/pocket1-ChB/chimera_sesion_best_pose_rigid
> -dock.cxs" format session
Log from Fri Mar 12 18:29:34 2021UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "chimera_sesion_best_pose_rigid -dock.cxs"
Log from Fri Mar 12 17:36:23 2021UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "chimera_sesion_best_pose_rigid -dock.cxs"
Log from Thu Mar 11 18:19:10 2021UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
> open
> "/c7/home/lchecaru/CnP/PRDX6-MALARIA/Docking_darapladib/Smina/pocket1-ChB/chimera_sesion_best_pose_rigid
> -dock.cxs" format session
Log from Thu Mar 11 18:12:19 2021UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
> open
> "/c7/home/lchecaru/CnP/PRDX6-MALARIA/Docking_darapladib/Smina/pocket1-ChB/chimera_sesion_best_pose_rigid
> -dock.cxs" format session
Log from Thu Mar 11 18:04:20 2021UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
> open
> "/c7/home/lchecaru/CnP/PRDX6-MALARIA/Docking_darapladib/Smina/pocket1-ChB/chimera_sesion_best_pose_rigid
> -dock.cxs" format session
Log from Thu Mar 11 17:57:27 2021 Startup Errors
---
error | Bundle 'ChimeraX-Registration' custom initialization failed
warning | Traceback (most recent call last):
File
"/c7/shared/chimerax/release/1.1-1.el7.x86_64/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/registration/nag.py", line 266, in _strptime
month = _months.index(month_name)
ValueError: tuple.index(x): x not in tuple
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/c7/shared/chimerax/release/1.1-1.el7.x86_64/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 342, in initialize
api._api_caller.initialize(api, session, self)
File
"/c7/shared/chimerax/release/1.1-1.el7.x86_64/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/toolshed/__init__.py", line 1265, in initialize
return cls._get_func(api, "initialize")(session, bi)
File
"/c7/shared/chimerax/release/1.1-1.el7.x86_64/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/registration/__init__.py", line 41, in initialize
nag(session)
File
"/c7/shared/chimerax/release/1.1-1.el7.x86_64/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/registration/nag.py", line 38, in nag
_check_usage(session)
File
"/c7/shared/chimerax/release/1.1-1.el7.x86_64/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/registration/nag.py", line 192, in _check_usage
usage = _get_usage()
File
"/c7/shared/chimerax/release/1.1-1.el7.x86_64/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/registration/nag.py", line 228, in _get_usage
usage["dates"].append(_strptime(value))
File
"/c7/shared/chimerax/release/1.1-1.el7.x86_64/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/registration/nag.py", line 275, in _strptime
raise ValueError("time data does not match format")
ValueError: time data does not match format
UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /c7/home/lchecaru/CnP/PRDX6-MALARIA/Docking_darapladib/Smina/pocket1-ChB/results/out.pdbqt
> format pdbqt
Summary of feedback from opening
/c7/home/lchecaru/CnP/PRDX6-MALARIA/Docking_darapladib/Smina/pocket1-ChB/results/out.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK minimizedAffinity -8.24957561
Ignored bad PDB record found on line 3
REMARK minimizedRMSD -1
Ignored bad PDB record found on line 5
REMARK status: ('A' for Active; 'I' for Inactive)
Ignored bad PDB record found on line 6
REMARK 1 A between atoms: S_1 and C_19
Ignored bad PDB record found on line 7
REMARK 2 A between atoms: S_1 and C_27
475 messages similar to the above omitted
Opened out.pdbqt containing 10 structures (480 atoms, 520 bonds)
> hide #1.1 models
> hide #1.2 models
> hide #1.3 models
> hide #1.4 models
> hide #1.5-8 target m
> hide #1.5-10 target m
> show #1.1 models
> open /c7/home/lchecaru/CnP/PRDX6-MALARIA/5b6m_chainA-B.pdb
Chain information for 5b6m_chainA-B.pdb #2
---
Chain | Description
A B | No description available
> select #1
480 atoms, 520 bonds, 10 residues, 11 models selected
> coulombic sel & #1.1
Don't know how to assign charges to the following residue types: LIG
> select clear
> coulombic #2#1.1
Don't know how to assign charges to the following residue types: LIG
> select #2
3494 atoms, 3578 bonds, 442 residues, 1 model selected
> coulombic sel
> hide sel surfaces
> select clear
> show #1.1#!2 atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> ui mousemode right label
> label #2/B:31
> ui mousemode right label
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> ui mousemode right label
> label #2/B:27
> label #2/B:27
> label #2/B:67
> label color black
> select #2
3494 atoms, 3578 bonds, 442 residues, 2 models selected
> coulombic sel
> hide sel surfaces
> save
> "/c7/home/lchecaru/CnP/PRDX6-MALARIA/Docking_darapladib/Smina/pocket1-ChB/chimera_sesion_best_pose_rigid
> -dock.cxs"
> select clear
> ui tool show "Side View"
> select #1.1/d:1@C
36 atoms, 32 bonds, 1 residue, 1 model selected
> select up
48 atoms, 52 bonds, 1 residue, 1 model selected
> view sel
> ui mousemode right zone
> zone #1.1/d:1
> zone #1.1/d:1
> ui mousemode right "next docked"
> select sel :< 5
634 atoms, 674 bonds, 30 residues, 11 models selected
> select ~sel
3340 atoms, 3424 bonds, 422 residues, 3 models selected
> hide sel atoms
> select clear
> select #2/B:30
4 atoms, 3 bonds, 1 residue, 1 model selected
> select up
18 atoms, 17 bonds, 3 residues, 2 models selected
> select down
4 atoms, 3 bonds, 1 residue, 2 models selected
> show sel atoms
> show sel atoms
> select sel :< 6
1939 atoms, 299 bonds, 225 residues, 5 models selected
> select clear
> select #2/B:30
4 atoms, 3 bonds, 1 residue, 1 model selected
> hide sel atoms
> show sel atoms
> hide sel cartoons
> hide sel atoms
> show sel atoms
> hide sel atoms
> show sel cartoons
> select #2/B:32
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> select /B:26,140
18 atoms, 17 bonds, 2 residues, 1 model selected
> show sel atoms
> select /B:26,140,32
24 atoms, 22 bonds, 3 residues, 1 model selected
> color (#!2 & sel) orange red
> color (#!2 & sel) hot pink
> color sel byhetero
> ui mousemode right label
> label #2/B:26
> label #2/B:140
> label #2/B:32
> label #2/B:27
> label #2/B:67
> label #2/B:31
> label delete residues
> label #2/B:32
> label #2/B:26
> label delete residues
> label #2/B:140
> label #2/B:140
> label #2/B:140
> label delete residues
> label #2/B:32
> label #2/B:140
> label #2/B:26
> label #2/B:27
> label #2/B:31
> label #2/B:67
> ui mousemode right select
> ui mousemode right rotate
> ui mousemode right translate
> ui mousemode right rotate
> ui mousemode right label
> label #2/B:68
> select clear
> select #1.1/d:1@N
4 atoms, 1 residue, 1 model selected
> select up
48 atoms, 52 bonds, 1 residue, 1 model selected
> save
> "/c7/home/lchecaru/CnP/PRDX6-MALARIA/Docking_darapladib/Smina/pocket1-ChB/chimera_sesion_best_pose_rigid
> -dock.cxs"
> style sel sphere
Changed 48 atom styles
> label #1.1/d:1
> show sel atoms
> hide sel atoms
> show sel atoms
> style sel stick
Changed 48 atom styles
> style sel ball
Changed 48 atom styles
> mlp sel
mlp: no amino acids specified
> show sel surfaces
> style sel stick
Changed 48 atom styles
> hide sel surfaces
> hbonds sel
1 hydrogen bonds found
> select clear
> select #2/B:27
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> show (#!2 & sel) target ab
> hide (#!2 & sel-residues & (protein|nucleic)) target a
> cartoon hide (#!2 & sel-residues)
> show (#!2 & sel-residues & backbone) target ab
> show sel cartoons
> show sel atoms
> cartoon style (#!2 & sel) xsection oval modeHelix default
> select #1
480 atoms, 520 bonds, 10 residues, 11 models selected
> ~select #1
1 model selected
> select #3
1 pseudobond, 1 model selected
> ~select #3
Nothing selected
> select #2
3494 atoms, 3578 bonds, 442 residues, 2 models selected
> cartoon style (#!2 & sel) xsection oval modeHelix default
> cartoon style (#!2 & sel & coil) xsection oval
> cartoon style (#!2 & sel) xsection barbell modeHelix default
> select clear
> ui mousemode right distance
> distance #2/B:67@NZ #1.1/d:1@C
Expected exactly two atoms and/or measurable objects (e.g. axes, planes), got
37
> distance #1.1/d:1@C #2/B:67@NZ
Expected exactly two atoms and/or measurable objects (e.g. axes, planes), got
37
> ui mousemode right distance
> distance #1.1/d:1@C #2/B:67@NZ
Expected exactly two atoms and/or measurable objects (e.g. axes, planes), got
37
> ui mousemode right distance
> select #1.1/d:1@C
36 atoms, 32 bonds, 1 residue, 1 model selected
> select down
36 atoms, 32 bonds, 1 residue, 2 models selected
> select down
36 atoms, 32 bonds, 1 residue, 2 models selected
> select clear
> select #1.1/d:1@C
36 atoms, 32 bonds, 1 residue, 1 model selected
> select clear
> ui mousemode right distance
> distance #2/B:67@NZ #1.1/d:1@C
Expected exactly two atoms and/or measurable objects (e.g. axes, planes), got
37
> distance #2/B:67@NZ #1.1/d:1@N
Expected exactly two atoms and/or measurable objects (e.g. axes, planes), got
5
> select #3
1 pseudobond, 1 model selected
> ~select #3
Nothing selected
> select #2
3494 atoms, 3578 bonds, 442 residues, 2 models selected
> cartoon style (#!2 & sel) xsection oval modeHelix default
> select clear
> select #2/B:27
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel cartoons
> show sel cartoons
> hide sel cartoons
> show (#!2 & sel-residues & sidechain) target ab
> show sel cartoons
> show (#!2 & sel-residues & sidechain) target ab
> hide sel cartoons
> select #2/B:26
10 atoms, 10 bonds, 1 residue, 1 model selected
> select up
23 atoms, 23 bonds, 3 residues, 2 models selected
> select up
29 atoms, 30 bonds, 3 residues, 2 models selected
> show sel atoms
> hide sel cartoons
> ui mousemode right distance
> distance #2/B:27@O #1.1/d:1@N
Expected exactly two atoms and/or measurable objects (e.g. axes, planes), got
5
> show sel cartoons
> select clear
> select #3
1 pseudobond, 1 model selected
> ~select #3
Nothing selected
> select #2
3494 atoms, 3578 bonds, 442 residues, 2 models selected
> ui tool show "Color Actions"
> color sel byhetero
> select clear
> select #2
3494 atoms, 3578 bonds, 442 residues, 2 models selected
> show sel surfaces
> mlp sel
Map values for surface "5b6m_chainA-B.pdb_A SES surface": minimum -28.33, mean
-4.092, maximum 22.79
Map values for surface "5b6m_chainA-B.pdb_B SES surface": minimum -29.91, mean
-3.995, maximum 23.04
> hide sel surfaces
> coulombic sel
> label color black
> setattr s density 2.0
Must provide enough attribute-target characters to distinguish 'structures'
from 'surfaces'
> set subdivision 2
> set subdivision 5
> ui tool show "Show Volume Menu"
> hide sel surfaces
> show sel surfaces
> hide sel surfaces
> select #2/B:26@CG
1 atom, 1 residue, 1 model selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
10 atoms, 10 bonds, 1 residue, 2 models selected
> ui mousemode right label
> show sel surfaces
> select #2
3494 atoms, 3578 bonds, 442 residues, 5 models selected
> show sel surfaces
> select clear
> save
> "/c7/home/lchecaru/CnP/PRDX6-MALARIA/Docking_darapladib/Smina/pocket1-ChB/chimera_sesion_best_pose_rigid
> -dock.cxs"
opened ChimeraX session
> lighting soft
> ~hbonds
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.
Traceback (most recent call last):
File
"/c7/shared/chimerax/release/1.1-1.el7.x86_64/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 73, in draw_new_frame
view.draw(check_for_changes = False)
File
"/c7/shared/chimerax/release/1.1-1.el7.x86_64/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 165, in draw
self._draw_scene(camera, drawings)
File
"/c7/shared/chimerax/release/1.1-1.el7.x86_64/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 201, in _draw_scene
shadow, multishadow = self._compute_shadowmaps(opaque_drawings,
transparent_drawings, camera)
File
"/c7/shared/chimerax/release/1.1-1.el7.x86_64/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 581, in _compute_shadowmaps
multishadow_enabled = r.multishadow.use_multishadow_map(shadow_drawings)
File
"/c7/shared/chimerax/release/1.1-1.el7.x86_64/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/opengl.py", line 1499, in use_multishadow_map
self._start_rendering_multishadowmap(center, radius, size)
File
"/c7/shared/chimerax/release/1.1-1.el7.x86_64/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/opengl.py", line 1584, in
_start_rendering_multishadowmap
center, radius, size)
File
"/c7/shared/chimerax/release/1.1-1.el7.x86_64/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/opengl.py", line 1240, in start_depth_render
self.push_framebuffer(fb)
File
"/c7/shared/chimerax/release/1.1-1.el7.x86_64/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/opengl.py", line 642, in push_framebuffer
fb.activate()
File
"/c7/shared/chimerax/release/1.1-1.el7.x86_64/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/opengl.py", line 2182, in activate
GL.glDrawBuffer(self._draw_buffer)
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1282,
description = b'invalid operation',
baseOperation = glDrawBuffer,
cArguments = (GL_NONE,)
)
> save
> "/c7/home/lchecaru/CnP/PRDX6-MALARIA/Docking_darapladib/Smina/pocket1-ChB/chimera_sesion_best_pose_rigid
> -dock.cxs"
opened ChimeraX session
> lighting simple
> ui tool show "Side View"
> lighting soft
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.
Traceback (most recent call last):
File
"/c7/shared/chimerax/release/1.1-1.el7.x86_64/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 73, in draw_new_frame
view.draw(check_for_changes = False)
File
"/c7/shared/chimerax/release/1.1-1.el7.x86_64/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 165, in draw
self._draw_scene(camera, drawings)
File
"/c7/shared/chimerax/release/1.1-1.el7.x86_64/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 201, in _draw_scene
shadow, multishadow = self._compute_shadowmaps(opaque_drawings,
transparent_drawings, camera)
File
"/c7/shared/chimerax/release/1.1-1.el7.x86_64/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 581, in _compute_shadowmaps
multishadow_enabled = r.multishadow.use_multishadow_map(shadow_drawings)
File
"/c7/shared/chimerax/release/1.1-1.el7.x86_64/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/opengl.py", line 1499, in use_multishadow_map
self._start_rendering_multishadowmap(center, radius, size)
File
"/c7/shared/chimerax/release/1.1-1.el7.x86_64/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/opengl.py", line 1584, in
_start_rendering_multishadowmap
center, radius, size)
File
"/c7/shared/chimerax/release/1.1-1.el7.x86_64/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/opengl.py", line 1240, in start_depth_render
self.push_framebuffer(fb)
File
"/c7/shared/chimerax/release/1.1-1.el7.x86_64/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/opengl.py", line 642, in push_framebuffer
fb.activate()
File
"/c7/shared/chimerax/release/1.1-1.el7.x86_64/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/opengl.py", line 2182, in activate
GL.glDrawBuffer(self._draw_buffer)
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1282,
description = b'invalid operation',
baseOperation = glDrawBuffer,
cArguments = (GL_NONE,)
)
> lighting simple
> save
> "/c7/home/lchecaru/CnP/PRDX6-MALARIA/Docking_darapladib/Smina/pocket1-ChB/chimera_sesion_best_pose_rigid
> -dock.cxs"
opened ChimeraX session
> hide #!2#!1.1 surfaces
> ui mousemode right label
> label #2/B:67
> label color black
> coulombic #!2#!1.1
Don't know how to assign charges to the following residue types: LIG
> select #2
3494 atoms, 3578 bonds, 442 residues, 4 models selected
> coulombic sel
> select clear
> lighting soft
> save pocket1_chB_smina_best_pose_elec-surface.png pixelSize 0.02 supersample
> 3 transparentBackground true
> save
> "/c7/home/lchecaru/CnP/PRDX6-MALARIA/Docking_darapladib/Smina/pocket1-ChB/chimera_sesion_best_pose_rigid
> -dock.cxs"
opened ChimeraX session
> show #1.2 models
> hide #!1.1 models
> hide #1.2#!2 surfaces
> hbonds #1.2#!2
454 hydrogen bonds found
> ~hbonds
> select #1.2/d:1@N
4 atoms, 1 residue, 1 model selected
> select up
48 atoms, 52 bonds, 1 residue, 1 model selected
> hbonds sel
3 hydrogen bonds found
> show #!1.1 models
> select #2/B:66
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
51 atoms, 50 bonds, 7 residues, 2 models selected
> cartoon sel suppressBackboneDisplay false
> select clear
> select #2/B:65
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/B:64
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select #2
3494 atoms, 3578 bonds, 442 residues, 4 models selected
> coulombic sel
> select clear
> lighting full
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting simple
> lighting soft
> lighting full
> lighting shadows false
> graphics silhouettes false
> lighting soft
> hide #!1.1 models
> select #1.2
48 atoms, 52 bonds, 1 residue, 1 model selected
> color sel byhetero
> style sel sphere
Changed 48 atom styles
> style sel stick
Changed 48 atom styles
> select #1
480 atoms, 520 bonds, 10 residues, 11 models selected
> select #2
3494 atoms, 3578 bonds, 442 residues, 4 models selected
> mlp sel
Map values for surface "5b6m_chainA-B.pdb_A SES surface": minimum -28.33, mean
-4.092, maximum 22.79
Map values for surface "5b6m_chainA-B.pdb_B SES surface": minimum -29.91, mean
-3.995, maximum 23.04
> open
> /c7/home/lchecaru/CnP/PRDX6-MALARIA/Docking_darapladib/Smina/pocket1_ChA/results/chainA/out.pdbqt
Summary of feedback from opening
/c7/home/lchecaru/CnP/PRDX6-MALARIA/Docking_darapladib/Smina/pocket1_ChA/results/chainA/out.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK minimizedAffinity -8.01210594
Ignored bad PDB record found on line 3
REMARK minimizedRMSD -1
Ignored bad PDB record found on line 5
REMARK status: ('A' for Active; 'I' for Inactive)
Ignored bad PDB record found on line 6
REMARK 1 A between atoms: S_1 and C_19
Ignored bad PDB record found on line 7
REMARK 2 A between atoms: S_1 and C_27
475 messages similar to the above omitted
Opened out.pdbqt containing 10 structures (480 atoms, 520 bonds)
> select clear
> hide #4.2 models
> hide #4.3 models
> hide #4.4 models
> hide #4.10 models
> hide #4.9 models
> hide #4.8 models
> hide #4.7 models
> hide #4.6 models
> hide #4.5 models
> show #4.4 models
> hide #4.4 models
> show #4.2 models
> show #4.3 models
> hide #4.3 models
> hide #4.2 models
> hide #4.1 models
> show #4.1 models
> hide #1.2#4.1#!2 surfaces
> coulombic #1.2#4.1#!2
Don't know how to assign charges to the following residue types: LIG
> select #2
3494 atoms, 3578 bonds, 442 residues, 4 models selected
> coulombic sel
> show #4.2 models
> hide #4.1 models
> show #4.3 models
> hide #4.2 models
> hide #4.3 models
> select clear
> hide #1.2#!2 surfaces
> select #2/B:62
5 atoms, 4 bonds, 1 residue, 1 model selected
> cartoon sel suppressBackboneDisplay false
> select #2/B:61
11 atoms, 11 bonds, 1 residue, 1 model selected
> cartoon sel suppressBackboneDisplay false
> select clear
> open 5b6n
Summary of feedback from opening 5b6n fetched from pdb
---
notes | Fetching compressed mmCIF 5b6n from
http://files.rcsb.org/download/5b6n.cif
Fetching CCD CSD from http://ligand-expo.rcsb.org/reports/C/CSD/CSD.cif
5b6n title:
Crystal structures of human peroxiredoxin 6 in sulfinic acid state [more
info...]
Chain information for 5b6n #5
---
Chain | Description
A B C D E F | Peroxiredoxin-6
5b6n mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
3| author_and_software_defined_assembly
> show #1.2#!2,5 cartoons
> select #5
10576 atoms, 10669 bonds, 2 pseudobonds, 1472 residues, 2 models selected
> show sel cartoons
> style sel stick
Changed 10576 atom styles
> select clear
> select #5
10576 atoms, 10669 bonds, 2 pseudobonds, 1472 residues, 2 models selected
> color sel byhetero
> select clear
> ui tool show "Side View"
> select clear
> hide #!5 models
> ui mousemode right distance
> distance #2/B:32@OG #2/B:67@NZ
Distance between 5b6m_chainA-B.pdb #2/B SER 32 OG and LYS 67 NZ: 3.679Å
> distance #2/B:67@NZ #1.2/d:1@N
Expected exactly two atoms and/or measurable objects (e.g. axes, planes), got
5
> open
> /c7/home/lchecaru/CnP/PRDX6-MALARIA/Docking_darapladib/Smina/pocket1_ChA/results/chainA/out.sdf
> close #7
> close #4
> close #1
> open
> /c7/home/lchecaru/CnP/PRDX6-MALARIA/Docking_darapladib/Smina/pocket1-ChB/results/out.sdf
> hide #1.2 models
> hide #1.3 models
> hide #1.4 models
> hide #1.5 models
> hide #1.10 models
> hide #1.9 models
> hide #1.6-8 target m
> show #1.2 models
> ui mousemode right distance
> distance #1.2:1@O2 #2/B:67@NZ
Distance between out.pdbqt #1.2 UNL 1 O2 and 5b6m_chainA-B.pdb #2/B LYS 67 NZ:
3.057Å
> distance #1.2:1@N4 #2/B:67@NZ
Distance between out.pdbqt #1.2 UNL 1 N4 and 5b6m_chainA-B.pdb #2/B LYS 67 NZ:
2.830Å
> ui mousemode right "move label"
> ui tool show Distances
> distance style dashes 8
> distance style dashes 8
> distance style dashes 7
> distance style dashes 7
> distance style decimalPlaces 2
> distance style decimalPlaces 2
> distance style decimalPlaces 1
> distance style decimalPlaces 1
> distance style radius 0.09
> distance style radius 0.09
> distance style radius 0.07
> distance style radius 0.07
> distance style dashes 8
> distance style dashes 8
> distance style dashes 9
> distance style dashes 9
> distance style radius 0.06
> distance style radius 0.06
> distance style radius 0.05
> distance style radius 0.05
> distance style radius 0.04
> distance style radius 0.04
> distance style radius 0.05
> distance style radius 0.05
> hide #1.1 models
> select #2
3494 atoms, 3578 bonds, 1 pseudobond, 442 residues, 5 models selected
> cartoon sel suppressBackboneDisplay true
> select clear
> select #2/B:99
7 atoms, 7 bonds, 1 residue, 1 model selected
> cartoon sel suppressBackboneDisplay false
> cartoon sel suppressBackboneDisplay true
> select #2/B:98
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
89 atoms, 92 bonds, 11 residues, 2 models selected
> select down
8 atoms, 7 bonds, 1 residue, 2 models selected
> select up
89 atoms, 92 bonds, 11 residues, 2 models selected
> select up
1747 atoms, 1789 bonds, 221 residues, 2 models selected
> select down
89 atoms, 92 bonds, 11 residues, 2 models selected
> select down
8 atoms, 7 bonds, 1 residue, 2 models selected
> cartoon sel suppressBackboneDisplay false
> select #1
480 atoms, 520 bonds, 10 residues, 11 models selected
> cofr sel
> select clear
> ui mousemode right distance
> distance #2/B:98@O #1.2:1@N2
Distance between 5b6m_chainA-B.pdb #2/B LEU 98 O and out.pdbqt #1.2 UNL 1 N2:
3.1Å
> select clear
> select #1
480 atoms, 520 bonds, 10 residues, 11 models selected
> select sel :< 5
970 atoms, 1004 bonds, 4 pseudobonds, 76 residues, 14 models selected
> show sel & #1.2#!2 atoms
> select clear
> select #1
480 atoms, 520 bonds, 10 residues, 11 models selected
> view sel
> select clear
> ui mousemode right label
> label #2/B:98
> ~select #3
Nothing selected
> select #2
3494 atoms, 3578 bonds, 1 pseudobond, 442 residues, 5 models selected
> coulombic sel
> mlp sel
Map values for surface "5b6m_chainA-B.pdb_A SES surface": minimum -28.33, mean
-4.092, maximum 22.79
Map values for surface "5b6m_chainA-B.pdb_B SES surface": minimum -29.91, mean
-3.995, maximum 23.04
> hide sel surfaces
> select clear
> select #2/B:55
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
125 atoms, 127 bonds, 17 residues, 2 models selected
> select up
1747 atoms, 1789 bonds, 221 residues, 2 models selected
> hide sel atoms
> select clear
> select #1
480 atoms, 520 bonds, 10 residues, 11 models selected
> select sel :< 5
970 atoms, 1004 bonds, 4 pseudobonds, 76 residues, 14 models selected
> show sel & #1.2#!2 atoms
> select clear
> select #2/B:140
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/B:26
10 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> ui mousemode right label
> label #2/B:140
> label #2/B:26
> label #2/B:58
> label #2/B:62
> ui mousemode right "move label"
> ui mousemode right label
> label color black
> ui mousemode right "move label"
> ui tool show Distances
> distance style radius 0.04
> distance style radius 0.04
> distance style radius 0.03
> distance style radius 0.03
> distance style radius 0.02
> distance style radius 0.02
> distance style radius 0.03
> distance style radius 0.03
> distance style radius 0.04
> distance style radius 0.04
> size font-size 30
Expected a keyword
> label font-size 30
Expected one of 'atoms', 'bonds', 'pseudobonds', or 'residues' or a keyword
> label height 30
> label height default
Invalid "height" argument: Expected 'fixed' or a number
> label height 20
> label height
Missing "height" keyword's argument
> select #2
3494 atoms, 3578 bonds, 1 pseudobond, 442 residues, 6 models selected
> mlp sel
Map values for surface "5b6m_chainA-B.pdb_A SES surface": minimum -28.33, mean
-4.092, maximum 22.79
Map values for surface "5b6m_chainA-B.pdb_B SES surface": minimum -29.91, mean
-3.995, maximum 23.04
> label height 10
> label height 1
> label height 0.5
> hide sel surfaces
> label height 0.6
> ui mousemode right "move label"
> label #6 height 0.9
> label #6 height 0.2
> label #6 height 0.5
> select clear
> save
> "/c7/home/lchecaru/CnP/PRDX6-MALARIA/Docking_darapladib/Smina/pocket1-ChB/chimera_sesion_best_pose_rigid
> -dock.cxs"
> save pose-2_smina_pocket1_chB_5b6m.png pixelSize 0.1 supersample 3
> transparentBackground true
> save pose-2_smina_pocket1_chB_5b6m.png pixelSize 0.05 supersample 3
> transparentBackground true
> save pose-2_smina_pocket1_chB_5b6m.png pixelSize 0.05 supersample 3
> transparentBackground true
> save pose-2_smina_pocket1_chB_5b6m.png pixelSize 0.02 supersample 3
> transparentBackground true
> coulombic #1.2#!2
Don't know how to assign charges to the following residue types: UNL
> select #2
3494 atoms, 3578 bonds, 1 pseudobond, 442 residues, 6 models selected
> coulombic sel
> hide #6.1 models
> show #6.1 models
> hide #6.1 models
> show #6.1 models
> hide #6.1 models
> hide #!6 models
> show #!6 models
> select clear
> show #6.1 models
> hide #1.2#!2 surfaces
> select #2/B:66
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/B:65
8 atoms, 7 bonds, 1 residue, 1 model selected
> cartoon sel suppressBackboneDisplay false
> select clear
> ui mousemode right distance
> distance #2/B:67@N #1.2:1@O2
Distance between 5b6m_chainA-B.pdb #2/B LYS 67 N and out.pdbqt #1.2 UNL 1 O2:
3.6Å
> distance #1.2:1@O2 #2/B:65@OD1
Distance between out.pdbqt #1.2 UNL 1 O2 and 5b6m_chainA-B.pdb #2/B ASN 65
OD1: 5.3Å
> select #2
3494 atoms, 3578 bonds, 1 pseudobond, 442 residues, 6 models selected
> mlp sel
Map values for surface "5b6m_chainA-B.pdb_A SES surface": minimum -28.33, mean
-4.092, maximum 22.79
Map values for surface "5b6m_chainA-B.pdb_B SES surface": minimum -29.91, mean
-3.995, maximum 23.04
> hide sel surfaces
> select clear
> select #2
3494 atoms, 3578 bonds, 1 pseudobond, 442 residues, 7 models selected
> mlp sel
Map values for surface "5b6m_chainA-B.pdb_A SES surface": minimum -28.33, mean
-4.092, maximum 22.79
Map values for surface "5b6m_chainA-B.pdb_B SES surface": minimum -29.91, mean
-3.995, maximum 23.04
> select clear
> select #1.2:1@C22
1 atom, 1 residue, 1 model selected
> select up
48 atoms, 52 bonds, 1 residue, 1 model selected
> style sel sphere
Changed 48 atom styles
> select clear
> select #2
3494 atoms, 3578 bonds, 1 pseudobond, 442 residues, 7 models selected
> ~select #2
2 models selected
> select #1
480 atoms, 520 bonds, 10 residues, 11 models selected
> style sel & #1.2 stick
Changed 48 atom styles
> select clear
> hide #1.2 models
> show #1.1 models
> coulombic #1.1#!2
Don't know how to assign charges to the following residue types: UNL
> select #2
3494 atoms, 3578 bonds, 1 pseudobond, 442 residues, 7 models selected
> coulombic sel
> hide sel surfaces
> show #1.2 models
> hide #1.2 models
> mlp sel
Map values for surface "5b6m_chainA-B.pdb_A SES surface": minimum -28.33, mean
-4.092, maximum 22.79
Map values for surface "5b6m_chainA-B.pdb_B SES surface": minimum -29.91, mean
-3.995, maximum 23.04
> show #1.2 models
> hide #1.1 models
> coulombic sel
> hide sel surfaces
> select clear
> select #2
3494 atoms, 3578 bonds, 1 pseudobond, 442 residues, 7 models selected
> mlp sel
Map values for surface "5b6m_chainA-B.pdb_A SES surface": minimum -28.33, mean
-4.092, maximum 22.79
Map values for surface "5b6m_chainA-B.pdb_B SES surface": minimum -29.91, mean
-3.995, maximum 23.04
> coulombic sel
> select clear
> hide #1.2#!2 surfaces
> select #2/B:100
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/B:101
7 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel cartoons
> show sel cartoons
> hide sel cartoons
> coulombic sel
> hide sel surfaces
> open
> /c7/home/lchecaru/CnP/PRDX6-MALARIA/Docking_darapladib/Smina/dry_potential_chB_5b6m.ccp4
Opened dry_potential_chB_5b6m.ccp4, grid size 87,72,60, pixel 0.3,0.3,0.3,
shown at level 0.000251, step 1, values float32
> volume #4 level 0
> volume #4 step 4
> volume #4 level 0
> volume #4 level 0
> open /c7/home/lchecaru/CnP/PRDX6-MALARIA/Docking_darapladib/Smina/test.grid
Unrecognized file suffix '.grid'
> open /c7/home/lchecaru/CnP/PRDX6-MALARIA/Docking_darapladib/Smina/test.cns
Opened test.cns, grid size 87,72,60, pixel 0.3,0.3,0.3, shown at level
0.000251, step 1, values float32
> volume #7 level 0.00024
> volume #7 level 100
> volume #7 level 0
> volume #7 level 5
> volume #7 level -1.9
> volume #4 level -1.9
> volume #4 step 1
> volume #4 step 2
> volume #4 style mesh
> volume #4 level -1.236
> volume #4 style surface style image colorMode opaque8 showOutlineBox True
> imageMode "box faces"
Repeated keyword argument "style"
> volume #4 colorMode auto8 imageMode "tilted slab" tiltedSlabAxis
> 0.6563,-0.02689,0.7541 tiltedSlabOffset -6.889 tiltedSlabSpacing 0.3
> tiltedSlabPlaneCount 6
> volume #4 imageMode "full region"
> volume #4 level -0.1824,0 level -0.1642,0.8 level 0,1
> volume #4 style mesh
> volume #4 style surface style image maximumIntensityProjection True
Repeated keyword argument "style"
> volume #4 region 0,0,28,86,71,28 step 1 maximumIntensityProjection false
> select clear
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> graphics silhouettes false
> graphics silhouettes true
> lighting soft
> lighting flat
> lighting full
> lighting soft
> graphics silhouettes false
> volume #4 region 0,0,0,86,71,59 step 2
> volume #4 style surface region 0,0,0,86,71,59 step 2
> volume #4 level -0.7733
> volume #4 level 0
> volume #4 style mesh
> volume #4 level -0.04367
> volume #4 level -2.044
> volume #4 level -1.817
> ui tool show "Volume Viewer"
> ui tool show "Measure and Color Blobs"
> ui tool show "Volume Viewer"
> ui tool show "Show Volume Menu"
> close #7
> open /c7/home/lchecaru/CnP/PRDX6-MALARIA/Docking_darapladib/Smina/test.ccp4
Opened test.ccp4, grid size 87,72,60, pixel 0.3,0.3,0.3, shown at level
0.000251, step 1, values float32
> volume #7 level 0
> volume #7 step 2
> volume #7 step 4
> volume #7 step 8
> volume #7 style image maximumIntensityProjection true
> volume #7 maximumIntensityProjection false showOutlineBox true imageMode
> "tilted slab" tiltedSlabAxis 0.01494,-0.6939,0.7199 tiltedSlabOffset -13.82
> tiltedSlabSpacing 0.3
> volume #7 style surface
> volume #7 style mesh
> volume #7 step 1
> close #4
> close #7
> save
> "/c7/home/lchecaru/CnP/PRDX6-MALARIA/Docking_darapladib/Smina/pocket1-ChB/chimera_sesion_best_pose_rigid
> -dock.cxs"
opened ChimeraX session
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.
Traceback (most recent call last):
File
"/c7/shared/chimerax/release/1.1-1.el7.x86_64/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 73, in draw_new_frame
view.draw(check_for_changes = False)
File
"/c7/shared/chimerax/release/1.1-1.el7.x86_64/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 165, in draw
self._draw_scene(camera, drawings)
File
"/c7/shared/chimerax/release/1.1-1.el7.x86_64/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 201, in _draw_scene
shadow, multishadow = self._compute_shadowmaps(opaque_drawings,
transparent_drawings, camera)
File
"/c7/shared/chimerax/release/1.1-1.el7.x86_64/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 581, in _compute_shadowmaps
multishadow_enabled = r.multishadow.use_multishadow_map(shadow_drawings)
File
"/c7/shared/chimerax/release/1.1-1.el7.x86_64/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/opengl.py", line 1499, in use_multishadow_map
self._start_rendering_multishadowmap(center, radius, size)
File
"/c7/shared/chimerax/release/1.1-1.el7.x86_64/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/opengl.py", line 1584, in
_start_rendering_multishadowmap
center, radius, size)
File
"/c7/shared/chimerax/release/1.1-1.el7.x86_64/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/opengl.py", line 1240, in start_depth_render
self.push_framebuffer(fb)
File
"/c7/shared/chimerax/release/1.1-1.el7.x86_64/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/opengl.py", line 642, in push_framebuffer
fb.activate()
File
"/c7/shared/chimerax/release/1.1-1.el7.x86_64/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/opengl.py", line 2182, in activate
GL.glDrawBuffer(self._draw_buffer)
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1282,
description = b'invalid operation',
baseOperation = glDrawBuffer,
cArguments = (GL_NONE,)
)
> lighting simple
> graphics restart
> save
> "/c7/home/lchecaru/CnP/PRDX6-MALARIA/Docking_darapladib/Smina/pocket1-ChB/chimera_sesion_best_pose_rigid
> -dock.cxs"
opened ChimeraX session
> open /c7/home/lchecaru/CnP/PRDX6-MALARIA/Docking_darapladib/Smina/test1.mrc
Opened test1.mrc, grid size 87,72,60, pixel 0.3,0.3,0.3, shown at level 0.283,
step 1, values float32
> volume #4 level -2.089
> volume twoSidedLighting false
> volume #4 level -2.411
> volume flipNormals true
> volume #4 flipNormals true
> volume #4 twoSidedLighting true
> volume #4 flipNormals true
> volume #4 style mesh
> volume #4 meshLighting true
> volume #4 flipNormals true
> volume #4 flipNormals false
> volume #4 level 0.282
> volume #4 flipNormals true
> volume #4 flipNormals false
> volume #4 level -0.8894
> volume #4 flipNormals false
> volume #4 flipNormals true
> capFaces true
Unknown command: capFaces true
> help help:user
> capFaces true
Unknown command: capFaces true
> capFaces true
Unknown command: capFaces true
> capFaces
Unknown command: capFaces
> volume capFaces true
> volume #4 style surface
> volume capFaces true
> volume #4 flipNormals true
> close #4
> open /c7/home/lchecaru/CnP/PRDX6-MALARIA/Docking_darapladib/Smina/test.ccp4
Opened test.ccp4, grid size 87,72,60, pixel 0.3,0.3,0.3, shown at level
0.000251, step 1, values float32
> volume #4 level -0.7123
> volume twoSidedLighting false
> volume #4 flipNormals true
> volume capFaces true
> close #4
> open /c7/home/lchecaru/CnP/PRDX6-MALARIA/Docking_darapladib/Smina/test_2.mrc
Opened test_2.mrc, grid size 87,72,60, pixel 0.3,0.3,0.3, shown at level
0.000251, step 1, values float32
> volume #4 level 0
> ui tool show "Show Volume Menu"
> ui tool show "Volume Viewer"
> open
> /c7/home/lchecaru/CnP/PRDX6-MALARIA/Docking_darapladib/Smina/sesio_test.py
ChimeraX cannot open a regular Chimera session.
An exporter from Chimera to ChimeraX is being worked on but is not ready at
this time.
> volume #4 style mesh
> volume capFaces true
> close #4
> ui mousemode right distance
> ~distance #1.2:1@O2 #2/B:65@OD1
> ~distance #2/B:67@N #1.2:1@O2
> ui mousemode right label
> label #2/B:20
> label #2/B:23
> label #2/B:28
> label #2/B:24
> label color black
> label color black height 0.5
> select up
2 atoms, 1 bond, 2 residues, 1 model selected
> select up
18 atoms, 19 bonds, 2 residues, 2 models selected
> show sel cartoons
> select up
97 atoms, 99 bonds, 12 residues, 2 models selected
> show sel cartoons
> hide sel cartoons
> show sel cartoons
> select up
148 atoms, 150 bonds, 19 residues, 2 models selected
> select down
104 atoms, 99 bonds, 13 residues, 2 models selected
> cartoon sel suppressBackboneDisplay false
> cartoon sel suppressBackboneDisplay true
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
3 atoms, 2 bonds, 1 residue, 2 models selected
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> select up
17 atoms, 16 bonds, 2 residues, 2 models selected
> show sel cartoons
> cartoon sel suppressBackboneDisplay true
> cartoon sel suppressBackboneDisplay false
> select up
51 atoms, 50 bonds, 7 residues, 2 models selected
> select down
17 atoms, 16 bonds, 2 residues, 2 models selected
> cartoon sel suppressBackboneDisplay true
> select clear
> ui mousemode right "move label"
> save 2pose_pocket1_chB_5b6m_smina.png pixelSize 0.02 supersample 3
> transparentBackground true
> preset "molecular surfaces" "ghostly white"
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color white targ s trans 80
> preset "molecular surfaces" "atomic coloring (transparent)"
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color fromatoms targ s trans 70
> preset "overall look" publication
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
> hide #1.2#!2 surfaces
> ui mousemode right "move label"
> preset "overall look" interactive
Preset expands to these ChimeraX commands:
~set bg
graphics silhouettes f
> preset "overall look" publication
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
> save 2pose_pocket1_chB_5b6m_smina_2.png pixelSize 0.02 supersample 3
> transparentBackground true
> label color black height 0.5
> label color black height 0.5
> select #2/B:23
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
34 atoms, 33 bonds, 4 residues, 2 models selected
> select up
1747 atoms, 1789 bonds, 221 residues, 2 models selected
> label sel color black height 0.5
> undo
> ui mousemode right label
> ui mousemode right label
> label delete residues
> label #2/B:140
> label sel color black height 0.5
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> label sel color black height 0.5
> label delete residues
> label delete residues
> ui mousemode right label
> label #2/B:23
> label #2/B:24
> label #2/B:28
> label #2/B:67
> label #2/B:32
> label #2/B:140
> label #2/B:65
> label #2/B:61
> label #2/B:68
> label #2/B:58
> label #2/B:98
> label #2/B:26
> select clear
> label color black height 0.5
> ui mousemode right "move label"
> save 2pose_pocket1_chB_5b6m_smina_2.png pixelSize 0.02 supersample 3
> transparentBackground true
> save
> "/c7/home/lchecaru/CnP/PRDX6-MALARIA/Docking_darapladib/Smina/pocket1-ChB/chimera_sesion_best_pose_rigid
> -dock.cxs"
opened ChimeraX session
> lighting soft
> graphics silhouettes false
> preset "overall look" interactive
Preset expands to these ChimeraX commands:
~set bg
graphics silhouettes f
> lighting shadows true intensity 0.5
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.
Traceback (most recent call last):
File
"/c7/shared/chimerax/release/1.1-1.el7.x86_64/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 73, in draw_new_frame
view.draw(check_for_changes = False)
File
"/c7/shared/chimerax/release/1.1-1.el7.x86_64/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 165, in draw
self._draw_scene(camera, drawings)
File
"/c7/shared/chimerax/release/1.1-1.el7.x86_64/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 201, in _draw_scene
shadow, multishadow = self._compute_shadowmaps(opaque_drawings,
transparent_drawings, camera)
File
"/c7/shared/chimerax/release/1.1-1.el7.x86_64/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 578, in _compute_shadowmaps
shadow_enabled = r.shadow.use_shadow_map(camera, shadow_drawings)
File
"/c7/shared/chimerax/release/1.1-1.el7.x86_64/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/opengl.py", line 1342, in use_shadow_map
self._start_rendering_shadowmap(center, radius, size)
File
"/c7/shared/chimerax/release/1.1-1.el7.x86_64/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/opengl.py", line 1376, in
_start_rendering_shadowmap
center, radius, size)
File
"/c7/shared/chimerax/release/1.1-1.el7.x86_64/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/opengl.py", line 1227, in start_depth_render
if not fb.activate():
File
"/c7/shared/chimerax/release/1.1-1.el7.x86_64/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/opengl.py", line 2178, in activate
fbo = self.framebuffer_id
File
"/c7/shared/chimerax/release/1.1-1.el7.x86_64/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/opengl.py", line 2174, in framebuffer_id
self._fbo = fbo = self._create_framebuffer()
File
"/c7/shared/chimerax/release/1.1-1.el7.x86_64/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/opengl.py", line 2011, in _create_framebuffer
self.depth_texture or self._depth_rb)
File
"/c7/shared/chimerax/release/1.1-1.el7.x86_64/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/opengl.py", line 2038, in _create_fbo
GL.glDrawBuffer(GL.GL_NONE)
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1282,
description = b'invalid operation',
baseOperation = glDrawBuffer,
cArguments = (GL_NONE,)
)
Exception ignored in: <function Framebuffer.__del__ at 0x7f8d0cbc53b0>
Traceback (most recent call last):
File
"/c7/shared/chimerax/release/1.1-1.el7.x86_64/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/opengl.py", line 2088, in __del__
% self.name)
chimerax.graphics.opengl.OpenGLError: OpenGL framebuffer "depth map" was not
deleted before graphics.Framebuffer destroyed
Exception ignored in: <function Texture.__del__ at 0x7f8d0cbc9440>
Traceback (most recent call last):
File
"/c7/shared/chimerax/release/1.1-1.el7.x86_64/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/opengl.py", line 2931, in __del__
raise OpenGLError('OpenGL texture was not deleted before graphics.Texture
destroyed')
chimerax.graphics.opengl.OpenGLError: OpenGL texture was not deleted before
graphics.Texture destroyed
> lighting shadows false
> save
> "/c7/home/lchecaru/CnP/PRDX6-MALARIA/Docking_darapladib/Smina/pocket1-ChB/chimera_sesion_best_pose_rigid
> -dock.cxs"
opened ChimeraX session
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.
Traceback (most recent call last):
File
"/c7/shared/chimerax/release/1.1-1.el7.x86_64/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 73, in draw_new_frame
view.draw(check_for_changes = False)
File
"/c7/shared/chimerax/release/1.1-1.el7.x86_64/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 165, in draw
self._draw_scene(camera, drawings)
File
"/c7/shared/chimerax/release/1.1-1.el7.x86_64/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 201, in _draw_scene
shadow, multishadow = self._compute_shadowmaps(opaque_drawings,
transparent_drawings, camera)
File
"/c7/shared/chimerax/release/1.1-1.el7.x86_64/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 581, in _compute_shadowmaps
multishadow_enabled = r.multishadow.use_multishadow_map(shadow_drawings)
File
"/c7/shared/chimerax/release/1.1-1.el7.x86_64/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/opengl.py", line 1499, in use_multishadow_map
self._start_rendering_multishadowmap(center, radius, size)
File
"/c7/shared/chimerax/release/1.1-1.el7.x86_64/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/opengl.py", line 1584, in
_start_rendering_multishadowmap
center, radius, size)
File
"/c7/shared/chimerax/release/1.1-1.el7.x86_64/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/opengl.py", line 1240, in start_depth_render
self.push_framebuffer(fb)
File
"/c7/shared/chimerax/release/1.1-1.el7.x86_64/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/opengl.py", line 642, in push_framebuffer
fb.activate()
File
"/c7/shared/chimerax/release/1.1-1.el7.x86_64/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/opengl.py", line 2182, in activate
GL.glDrawBuffer(self._draw_buffer)
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1282,
description = b'invalid operation',
baseOperation = glDrawBuffer,
cArguments = (GL_NONE,)
)
> lighting shadows true
> save 2pose_pocket1_chB_5b6m_smina_3.png pixelSize 0.02 supersample 3
> transparentBackground true
> lighting soft
> graphics restart
> lighting simple
> lighting simple
> lighting simple
> lighting simple
> lighting simple
> lighting shadows true
> lighting shadows false
> save
> "/c7/home/lchecaru/CnP/PRDX6-MALARIA/Docking_darapladib/Smina/pocket1-ChB/chimera_sesion_best_pose_rigid
> -dock.cxs"
opened ChimeraX session
> ui mousemode right label
> label #2/B:140
> label #2/B:32
> label #2/B:26
> label #2/B:24
> label #2/B:98
> label #2/B:67
> label #2/B:61
> label #2/B:61
> label #2/B:28
> label #2/B:65
> label #2/B:23
> label color black height 0.5
> view
> undo
> ui mousemode right "move label"
> set bgColor white
> save
> /c7/home/lchecaru/CnP/PRDX6-MALARIA/Docking_darapladib/Smina/pocket1-ChB/chimera_sesion_best_pose_rigid-
> dock.cxs
> lighting soft
> save
> /c7/home/lchecaru/CnP/PRDX6-MALARIA/Docking_darapladib/Smina/pocket1-ChB/chimera_sesion_best_pose_rigid-
> dock.cxs
opened ChimeraX session
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.
Traceback (most recent call last):
File
"/c7/shared/chimerax/release/1.1-1.el7.x86_64/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 73, in draw_new_frame
view.draw(check_for_changes = False)
File
"/c7/shared/chimerax/release/1.1-1.el7.x86_64/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 165, in draw
self._draw_scene(camera, drawings)
File
"/c7/shared/chimerax/release/1.1-1.el7.x86_64/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 201, in _draw_scene
shadow, multishadow = self._compute_shadowmaps(opaque_drawings,
transparent_drawings, camera)
File
"/c7/shared/chimerax/release/1.1-1.el7.x86_64/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 581, in _compute_shadowmaps
multishadow_enabled = r.multishadow.use_multishadow_map(shadow_drawings)
File
"/c7/shared/chimerax/release/1.1-1.el7.x86_64/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/opengl.py", line 1499, in use_multishadow_map
self._start_rendering_multishadowmap(center, radius, size)
File
"/c7/shared/chimerax/release/1.1-1.el7.x86_64/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/opengl.py", line 1584, in
_start_rendering_multishadowmap
center, radius, size)
File
"/c7/shared/chimerax/release/1.1-1.el7.x86_64/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/opengl.py", line 1240, in start_depth_render
self.push_framebuffer(fb)
File
"/c7/shared/chimerax/release/1.1-1.el7.x86_64/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/opengl.py", line 642, in push_framebuffer
fb.activate()
File
"/c7/shared/chimerax/release/1.1-1.el7.x86_64/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/opengl.py", line 2182, in activate
GL.glDrawBuffer(self._draw_buffer)
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1282,
description = b'invalid operation',
baseOperation = glDrawBuffer,
cArguments = (GL_NONE,)
)
> graphics restart
> lighting simple
> lighting simple
> lighting simple
> save
> /c7/home/lchecaru/CnP/PRDX6-MALARIA/Docking_darapladib/Smina/pocket1-ChB/chimera_sesion_best_pose_rigid-
> dock.cxs
opened ChimeraX session
> lighting simple
> set bgColor black
> ui tool show "Side View"
> lighting soft
> save 2pose_pocket1_chB_5b6m_smina_3.png pixelSize 0.02 supersample 3
> transparentBackground true
> ui mousemode right "move label"
> save 2pose_pocket1_chB_5b6m_smina_3.png pixelSize 0.02 supersample 3
> transparentBackground true
> lighting simple
> select #2
3494 atoms, 3578 bonds, 1 pseudobond, 442 residues, 3 models selected
> coulombic sel
> select clear
> save
> /c7/home/lchecaru/CnP/PRDX6-MALARIA/Docking_darapladib/Smina/pocket1-ChB/chimera_sesion_best_pose_rigid-
> dock_surface.cxs
> ui mousemode right label
> label #2/B:27
> save
> /c7/home/lchecaru/CnP/PRDX6-MALARIA/Docking_darapladib/Smina/pocket1-ChB/chimera_sesion_best_pose_rigid-
> dock_surface.cxs
opened ChimeraX session
> ui tool show "Side View"
> lighting soft
> save 2pose_pocket1_chB_5b6m_smina_3_surface.png pixelSize 0.02 supersample 3
> transparentBackground true
> lighting simple
> lighting soft
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.
Traceback (most recent call last):
File
"/c7/shared/chimerax/release/1.1-1.el7.x86_64/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 73, in draw_new_frame
view.draw(check_for_changes = False)
File
"/c7/shared/chimerax/release/1.1-1.el7.x86_64/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 165, in draw
self._draw_scene(camera, drawings)
File
"/c7/shared/chimerax/release/1.1-1.el7.x86_64/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 201, in _draw_scene
shadow, multishadow = self._compute_shadowmaps(opaque_drawings,
transparent_drawings, camera)
File
"/c7/shared/chimerax/release/1.1-1.el7.x86_64/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/view.py", line 581, in _compute_shadowmaps
multishadow_enabled = r.multishadow.use_multishadow_map(shadow_drawings)
File
"/c7/shared/chimerax/release/1.1-1.el7.x86_64/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/opengl.py", line 1499, in use_multishadow_map
self._start_rendering_multishadowmap(center, radius, size)
File
"/c7/shared/chimerax/release/1.1-1.el7.x86_64/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/opengl.py", line 1584, in
_start_rendering_multishadowmap
center, radius, size)
File
"/c7/shared/chimerax/release/1.1-1.el7.x86_64/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/opengl.py", line 1240, in start_depth_render
self.push_framebuffer(fb)
File
"/c7/shared/chimerax/release/1.1-1.el7.x86_64/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/opengl.py", line 642, in push_framebuffer
fb.activate()
File
"/c7/shared/chimerax/release/1.1-1.el7.x86_64/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/graphics/opengl.py", line 2182, in activate
GL.glDrawBuffer(self._draw_buffer)
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1282,
description = b'invalid operation',
baseOperation = glDrawBuffer,
cArguments = (GL_NONE,)
)
OpenGL version: 3.3.0 NVIDIA 450.80.02
OpenGL renderer: Quadro RTX 6000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: Precision 7920 Tower
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
CPU: 24 Intel(R) Xeon(R) Silver 4214 CPU @ 2.20GHz
Cache Size: 16896 KB
Memory:
total used free shared buff/cache available
Mem: 125G 15G 14G 487M 95G 108G
Swap: 126G 2.8G 124G
Graphics:
d5:00.0 VGA compatible controller [0300]: NVIDIA Corporation TU102GL [Quadro RTX 6000/8000] [10de:1e30] (rev a1)
Subsystem: Dell Device [1028:12ba]
Kernel driver in use: nvidia
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.8.0
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2020.6.20
chardet: 3.0.4
ChimeraX-AddH: 2.1.3
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.1
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.6.1
ChimeraX-AtomSearch: 2.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 1.0.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.0
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.0
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.1
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.0
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-CommandLine: 1.1.3
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.1
ChimeraX-CoreFormats: 1.0
ChimeraX-coulombic: 1.0.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-DataFormats: 1.0
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.0
ChimeraX-Hbonds: 2.0
ChimeraX-Help: 1.0
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.0
ChimeraX-ImageFormats: 1.0
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0
ChimeraX-Label: 1.0
ChimeraX-LinuxSupport: 1.0
ChimeraX-ListInfo: 1.0
ChimeraX-Log: 1.1.1
ChimeraX-LookingGlass: 1.1
ChimeraX-Map: 1.0.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.0
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 1.1
ChimeraX-MDcrds: 2.0
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.0
ChimeraX-mmCIF: 2.2
ChimeraX-MMTF: 2.0
ChimeraX-Modeller: 1.0
ChimeraX-ModelPanel: 1.0
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.0
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0
ChimeraX-OpenCommand: 1.2.1
ChimeraX-PDB: 2.1
ChimeraX-PDBBio: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0
ChimeraX-PubChem: 2.0
ChimeraX-Read-Pbonds: 1.0
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.0
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.2
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SeqView: 2.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.0
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.0
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.0.4
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.0
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.0
ChimeraX-ToolshedUtils: 1.0
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.2.3
ChimeraX-uniprot: 2.0
ChimeraX-ViewDockX: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.3
comtypes: 1.1.7
cxservices: 1.0
cycler: 0.10.0
Cython: 0.29.20
decorator: 4.4.2
distlib: 0.3.1
distro: 1.5.0
docutils: 0.16
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 2.10.0
html2text: 2020.1.16
idna: 2.10
ihm: 0.16
imagecodecs: 2020.5.30
imagecodecs-lite: 2020.1.31
imagesize: 1.2.0
ipykernel: 5.3.0
ipython: 7.15.0
ipython-genutils: 0.2.0
jedi: 0.17.2
Jinja2: 2.11.2
jupyter-client: 6.1.3
jupyter-core: 4.6.3
kiwisolver: 1.2.0
line-profiler: 2.1.2
lxml: 4.5.1
MarkupSafe: 1.1.1
matplotlib: 3.2.1
msgpack: 1.0.0
netifaces: 0.10.9
networkx: 2.4
numexpr: 2.7.1
numpy: 1.18.5
numpydoc: 1.0.0
openvr: 1.12.501
packaging: 20.4
parso: 0.7.1
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 7.1.2
pip: 20.2.2
pkginfo: 1.5.0.1
prompt-toolkit: 3.0.7
psutil: 5.7.0
ptyprocess: 0.6.0
pycollada: 0.7.1
pydicom: 2.0.0
Pygments: 2.6.1
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 2.4.7
PyQt5-commercial: 5.12.3
PyQt5-sip: 4.19.19
PyQtWebEngine-commercial: 5.12.1
python-dateutil: 2.8.1
pytz: 2020.1
pyzmq: 19.0.2
qtconsole: 4.7.4
QtPy: 1.9.0
RandomWords: 0.3.0
requests: 2.24.0
scipy: 1.4.1
setuptools: 49.4.0
sfftk-rw: 0.6.6.dev0
six: 1.15.0
snowballstemmer: 2.0.0
sortedcontainers: 2.2.2
Sphinx: 3.1.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 1.0.3
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.4
suds-jurko: 0.6
tables: 3.6.1
tifffile: 2020.6.3
tinyarray: 1.2.2
tornado: 6.0.4
traitlets: 5.0.4
urllib3: 1.25.10
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.34.2
Change History (2)
comment:1 by , 5 years ago
| Component: | Unassigned → Graphics |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → glDrawBuffer: invalid operation |
comment:2 by , 5 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | assigned → closed |
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Appears that glDrawBuffer(GL_NONE) returns a GL_INVALID_OPERATION when "light soft" is used. The OpenGL docs list 3 ways glDrawBuffer(GL_NONE) can return this error and none of the apply. So it appears to be some graphics driver bug. Linux, Quadro RTX 6000.