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#3073 closed enhancement (not a bug)
empty surfaces slow things down
| Reported by: | Tristan Croll | Owned by: | Tom Goddard |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Surface | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-3.10.0-1062.9.1.el7.x86_64-x86_64-with-centos-7.7.1908-Core
ChimeraX Version: 0.93 (2020-04-03)
Description
If I do "surface selAtoms" followed by "~surface", the empty surface object hangs around and continues to run callbacks, making coordinate changes *really* slow.
Log:
UCSF ChimeraX version: 0.93 (2020-04-03)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open Atval.pdb
Chain information for Atval.pdb #1
---
Chain | Description
D E H I L M P Q | No description available
F J N R | No description available
G K O S | No description available
> toolshed show Shell
/opt/UCSF/ChimeraX/lib/python3.7/site-packages/IPython/core/history.py:226:
UserWarning: IPython History requires SQLite, your history will not be saved
warn("IPython History requires SQLite, your history will not be saved")
> select ~protein
704 atoms, 752 bonds, 1 model selected
> style sel stick
Changed 704 atom styles
> show sel cartoons
> hide sel atoms
> select clear
> show cartoons
> hide atoms
> style stick
Changed 46072 atom styles
> show cartoons
> dssp
> show ~protein
> select ~protein
704 atoms, 752 bonds, 1 model selected
> select zone sel 3
Selected 216 atoms
> show sel
> select up
1068 atoms, 980 bonds, 1 model selected
> show sel
> select clear
> view sel
> color byhetero
> select clear
> view sel
> select clear
> view sel
> select clear
> view sel
> select clear
> view sel
Expected an objects specifier or a keyword
> select ~protein
704 atoms, 752 bonds, 1 model selected
> hide sel cartoons
> select clear
> hide cartoons
> show
> addh
Summary of feedback from adding hydrogens to Atval.pdb #1
---
warnings | Not adding hydrogens to /H LYS 390 CB because it is missing heavy-
atom bond partners
Not adding hydrogens to /H GLU 431 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /H LYS 434 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /H LYS 450 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /I LYS 390 CB because it is missing heavy-atom bond
partners
27 messages similar to the above omitted
notes | No usable SEQRES records for Atval.pdb (#1) chain D; guessing termini
instead
No usable SEQRES records for Atval.pdb (#1) chain E; guessing termini instead
No usable SEQRES records for Atval.pdb (#1) chain F; guessing termini instead
No usable SEQRES records for Atval.pdb (#1) chain G; guessing termini instead
No usable SEQRES records for Atval.pdb (#1) chain H; guessing termini instead
11 messages similar to the above omitted
Chain-initial residues that are actual N termini: /D THR 86, /E THR 86, /F HIS
87, /G LEU 317, /H THR 86, /I THR 86, /J HIS 87, /K LEU 317, /L THR 86, /M THR
86, /N HIS 87, /O LEU 317, /P THR 86, /Q THR 86, /R HIS 87, /S LEU 317
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini: /D ARG 667, /E ARG 667, /F
MET 241, /G SER 475, /H ARG 667, /I ARG 667, /J MET 241, /K SER 475, /L ARG
667, /M ARG 667, /N MET 241, /O SER 475, /P ARG 667, /Q ARG 667, /R MET 241,
/S SER 475
3580 hydrogen bonds
/D ARG 667 is not terminus, removing H atom from 'C'
/E ARG 667 is not terminus, removing H atom from 'C'
/F MET 241 is not terminus, removing H atom from 'C'
/G SER 475 is not terminus, removing H atom from 'C'
/H ARG 667 is not terminus, removing H atom from 'C'
11 messages similar to the above omitted
46152 hydrogens added
> select /I:416@CA
1 atom, 1 model selected
> select /I:416@CA
1 atom, 1 model selected
> select up
22 atoms, 21 bonds, 1 model selected
> select clear
> select /B:729@C47
1 atom, 1 model selected
> select up
85 atoms, 90 bonds, 1 model selected
> select ~protein
1176 atoms, 1224 bonds, 1 model selected
> select clear
> view sel
> hide H
> select clear
Expected an objects specifier or a view name or a keyword
> view sel
> close
> open2
> /run/media/tic20/storage/structure_dump/aus/brisbane/guddat/ahas/RealSpaceRefine_12/working_noh_ligand_atoms_renamed_real_space_refined.pdb
Chain information for working_noh_ligand_atoms_renamed_real_space_refined.pdb
#1
---
Chain | Description
D E H I L M P Q | No description available
F J N R | No description available
G K O S | No description available
V | No description available
> isolde start
> set selectionWidth 4
Chain information for working_noh_ligand_atoms_renamed_real_space_refined.pdb
---
Chain | Description
1.2/D 1.2/E 1.2/H 1.2/I 1.2/L 1.2/M 1.2/P 1.2/Q | No description available
1.2/F 1.2/J 1.2/N 1.2/R | No description available
1.2/G 1.2/K 1.2/O 1.2/S | No description available
1.2/V | No description available
Done loading forcefield
> hide #!1 models
> open2
> /run/media/tic20/storage/structure_dump/aus/brisbane/guddat/ahas/RealSpaceRefine_12/working_noh_ligand_atoms_renamed_real_space_refined.pdb
Chain information for working_noh_ligand_atoms_renamed_real_space_refined.pdb
#2
---
Chain | Description
D E H I L M P Q | No description available
F J N R | No description available
G K O S | No description available
V | No description available
> hide #2&~/V
> cartoon #2
> ~cartoon #2&~/V
> select #2
46216 atoms, 47135 bonds, 45 pseudobonds, 2 models selected
> style sel sphere
Changed 46216 atom styles
> select clear
> toolshed show Shell
> close #2
> show #!1 models
> select /V
64 atoms, 63 bonds, 1 model selected
> select clear
> ~cartoon /V
> addh
Summary of feedback from adding hydrogens to
working_noh_ligand_atoms_renamed_real_space_refined.pdb #1.2
---
warnings | Not adding hydrogens to /D LYS 390 CB because it is missing heavy-
atom bond partners
Not adding hydrogens to /D GLU 431 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /D LYS 434 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /D LYS 450 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /E LYS 390 CB because it is missing heavy-atom bond
partners
27 messages similar to the above omitted
notes | No usable SEQRES records for
working_noh_ligand_atoms_renamed_real_space_refined.pdb (#1.2) chain D;
guessing termini instead
No usable SEQRES records for
working_noh_ligand_atoms_renamed_real_space_refined.pdb (#1.2) chain E;
guessing termini instead
No usable SEQRES records for
working_noh_ligand_atoms_renamed_real_space_refined.pdb (#1.2) chain F;
guessing termini instead
No usable SEQRES records for
working_noh_ligand_atoms_renamed_real_space_refined.pdb (#1.2) chain G;
guessing termini instead
No usable SEQRES records for
working_noh_ligand_atoms_renamed_real_space_refined.pdb (#1.2) chain H;
guessing termini instead
12 messages similar to the above omitted
Chain-initial residues that are actual N termini: /D THR 86, /E THR 86, /F LYS
83, /G LEU 317, /H THR 86, /I THR 86, /J LYS 83, /K LEU 317, /L THR 86, /M THR
86, /N LYS 83, /O LEU 317, /P THR 86, /Q THR 86, /R LYS 83, /S LEU 317, /V VAL
106
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: /V VAL 113
Chain-final residues that are not actual C termini: /D ARG 667, /E ARG 667, /F
MET 241, /G SER 475, /H ARG 667, /I ARG 667, /J MET 241, /K SER 475, /L ARG
667, /M ARG 667, /N MET 241, /O SER 475, /P ARG 667, /Q ARG 667, /R MET 241,
/S SER 475
5468 hydrogen bonds
/D ARG 667 is not terminus, removing H atom from 'C'
/E ARG 667 is not terminus, removing H atom from 'C'
/F MET 241 is not terminus, removing H atom from 'C'
/G SER 475 is not terminus, removing H atom from 'C'
/H ARG 667 is not terminus, removing H atom from 'C'
11 messages similar to the above omitted
46342 hydrogens added
> hide HC
> close #1.2.5
> select /V
152 atoms, 144 bonds, 1 model selected
> select /V
152 atoms, 144 bonds, 1 model selected
> open2
> /run/media/tic20/storage/structure_dump/aus/brisbane/guddat/ahas/AtAHAS_val.mrc
Opened AtAHAS_val.mrc, grid size 512,512,512, pixel 0.82, shown at level
0.128, step 2, values float32
> select /V
152 atoms, 144 bonds, 1 model selected
> select clear
> ~cartoon /V
> select clear
> ~cartoon /V
> ~cartoon /V
> ~cartoon
> cartoon
> select up
19 atoms, 18 bonds, 1 model selected
> select /V
152 atoms, 144 bonds, 1 model selected
> select clear
> view sel
> select up
19 atoms, 18 bonds, 1 model selected
> color sel bychain
> color sel byhetero
No template found for residue K1000 (VAL)
Doing nothing
Traceback (most recent call last):
File "/home/tic20/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2685, in _start_sim_or_toggle_pause
self.start_sim()
File "/home/tic20/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2705, in start_sim
self.params, self.sim_params, excluded_residues = self.ignored_residues)
File "/home/tic20/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 576, in __init__
self._prepare_validation_managers(mobile_atoms)
File "/home/tic20/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 746, in
_prepare_validation_managers
rota_a.restrict_to_selected_residues(mobile_res)
File "/home/tic20/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/rota_annotation.py", line 129, in
restrict_to_selected_residues
self.update_graphics()
File "/home/tic20/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/validation/rota_annotation.py", line 191, in
update_graphics
non_favored_only = self._hide_favored)
File "/home/tic20/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/molobject.py", line 1543, in
validate_scale_and_color_rotamers
non_favored_only, visible_only, pointer(rot_out), pointer(scale_out),
pointer(color_out))
IndexError: _Map_base::at
IndexError: _Map_base::at
File "/home/tic20/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/molobject.py", line 1543, in
validate_scale_and_color_rotamers
non_favored_only, visible_only, pointer(rot_out), pointer(scale_out),
pointer(color_out))
See log for complete Python traceback.
Traceback (most recent call last):
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/home/tic20/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 1060, in _selection_changed
self._enable_rebuild_residue_frame(r)
File "/home/tic20/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 1664, in
_enable_rebuild_residue_frame
self._update_selected_residue_info_live(None, None)
File "/home/tic20/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2217, in
_update_selected_residue_info_live
score = rot.score
File "/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/atomic/molc.py",
line 93, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
IndexError: _Map_base::at
Error processing trigger "selection changed":
IndexError: _Map_base::at
File "/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/atomic/molc.py",
line 93, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
See log for complete Python traceback.
> close #1.2.2
Traceback (most recent call last):
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/home/tic20/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 1027, in _update_model_list
self._update_sim_control_button_states()
File "/home/tic20/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 1127, in
_update_sim_control_button_states
self._selection_changed()
File "/home/tic20/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 1060, in _selection_changed
self._enable_rebuild_residue_frame(r)
File "/home/tic20/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 1664, in
_enable_rebuild_residue_frame
self._update_selected_residue_info_live(None, None)
File "/home/tic20/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2217, in
_update_selected_residue_info_live
score = rot.score
File "/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/atomic/molc.py",
line 93, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
IndexError: _Map_base::at
Error processing trigger "remove models":
IndexError: _Map_base::at
File "/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/atomic/molc.py",
line 93, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
See log for complete Python traceback.
> close #1.2.3
Traceback (most recent call last):
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/home/tic20/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 1027, in _update_model_list
self._update_sim_control_button_states()
File "/home/tic20/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 1127, in
_update_sim_control_button_states
self._selection_changed()
File "/home/tic20/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 1060, in _selection_changed
self._enable_rebuild_residue_frame(r)
File "/home/tic20/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 1664, in
_enable_rebuild_residue_frame
self._update_selected_residue_info_live(None, None)
File "/home/tic20/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2217, in
_update_selected_residue_info_live
score = rot.score
File "/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/atomic/molc.py",
line 93, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
IndexError: _Map_base::at
Error processing trigger "remove models":
IndexError: _Map_base::at
File "/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/atomic/molc.py",
line 93, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
See log for complete Python traceback.
> select clear
Traceback (most recent call last):
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/home/tic20/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 1060, in _selection_changed
self._enable_rebuild_residue_frame(r)
File "/home/tic20/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 1664, in
_enable_rebuild_residue_frame
self._update_selected_residue_info_live(None, None)
File "/home/tic20/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2217, in
_update_selected_residue_info_live
score = rot.score
File "/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/atomic/molc.py",
line 93, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
IndexError: _Map_base::at
Error processing trigger "selection changed":
IndexError: _Map_base::at
File "/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/atomic/molc.py",
line 93, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
See log for complete Python traceback.
Traceback (most recent call last):
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/home/tic20/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 1060, in _selection_changed
self._enable_rebuild_residue_frame(r)
File "/home/tic20/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 1664, in
_enable_rebuild_residue_frame
self._update_selected_residue_info_live(None, None)
File "/home/tic20/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2217, in
_update_selected_residue_info_live
score = rot.score
File "/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/atomic/molc.py",
line 93, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
IndexError: _Map_base::at
Error processing trigger "selection changed":
IndexError: _Map_base::at
File "/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/atomic/molc.py",
line 93, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
See log for complete Python traceback.
> select clear
Traceback (most recent call last):
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/home/tic20/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 1060, in _selection_changed
self._enable_rebuild_residue_frame(r)
File "/home/tic20/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 1664, in
_enable_rebuild_residue_frame
self._update_selected_residue_info_live(None, None)
File "/home/tic20/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2217, in
_update_selected_residue_info_live
score = rot.score
File "/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/atomic/molc.py",
line 93, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
IndexError: _Map_base::at
Error processing trigger "selection changed":
IndexError: _Map_base::at
File "/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/atomic/molc.py",
line 93, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
See log for complete Python traceback.
> close #1.2.4
> select clear
Traceback (most recent call last):
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/home/tic20/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 1060, in _selection_changed
self._enable_rebuild_residue_frame(r)
File "/home/tic20/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 1664, in
_enable_rebuild_residue_frame
self._update_selected_residue_info_live(None, None)
File "/home/tic20/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2217, in
_update_selected_residue_info_live
score = rot.score
File "/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/atomic/molc.py",
line 93, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
IndexError: _Map_base::at
Error processing trigger "selection changed":
IndexError: _Map_base::at
File "/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/atomic/molc.py",
line 93, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
See log for complete Python traceback.
Traceback (most recent call last):
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/home/tic20/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 1060, in _selection_changed
self._enable_rebuild_residue_frame(r)
File "/home/tic20/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 1646, in
_enable_rebuild_residue_frame
rot_m = session_extensions.get_rotamer_mgr(self.session)
File "/home/tic20/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/molobject.py", line 209, in get_rotamer_mgr
if hasattr(session, 'rota_mgr') and not session.rota_mgr.deleted:
AttributeError: 'NoneType' object has no attribute 'deleted'
Error processing trigger "selection changed":
AttributeError: 'NoneType' object has no attribute 'deleted'
File "/home/tic20/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/molobject.py", line 209, in get_rotamer_mgr
if hasattr(session, 'rota_mgr') and not session.rota_mgr.deleted:
See log for complete Python traceback.
Traceback (most recent call last):
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/home/tic20/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 1060, in _selection_changed
self._enable_rebuild_residue_frame(r)
File "/home/tic20/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 1646, in
_enable_rebuild_residue_frame
rot_m = session_extensions.get_rotamer_mgr(self.session)
File "/home/tic20/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/molobject.py", line 209, in get_rotamer_mgr
if hasattr(session, 'rota_mgr') and not session.rota_mgr.deleted:
AttributeError: 'NoneType' object has no attribute 'deleted'
Error processing trigger "selection changed":
AttributeError: 'NoneType' object has no attribute 'deleted'
File "/home/tic20/.local/share/ChimeraX/0.93/site-
packages/chimerax/isolde/molobject.py", line 209, in get_rotamer_mgr
if hasattr(session, 'rota_mgr') and not session.rota_mgr.deleted:
See log for complete Python traceback.
> select clear
> view sel
> color sel bychain
> color sel byhetero
> view sel
> color sel bychain
> color sel byhetero
> view sel
> view /F:1000
> select up
19 atoms, 18 bonds, 1 model selected
> color sel bychain
> color sel byhetero
> select up
19 atoms, 18 bonds, 1 model selected
> color sel bychain
> color sel byhetero
> select up
19 atoms, 18 bonds, 1 model selected
> color sel bychain
> color sel byhetero
> view sel
> color sel bychain
> color sel byhetero
Unknown command: v.atview sel
> view sel
> color sel bychain
> color sel byhetero
> view sel
> color sel bychain
> color sel byhetero
> view sel
> color sel bychain
> color sel byhetero
> view sel
> color sel bychain
> color sel byhetero
> select :1000
152 atoms, 144 bonds, 1 model selected
> select clear
> view sel
> select clear
> view sel
> select clear
> view sel
> select clear
> select clear
> view sel
No template found for residue B732 (FAD)
Doing nothing
> delete :FAD@H1
> select clear
> view sel
> select clear
> select clear
> view sel
> select clear
> view sel
> select clear
> select clear
> view sel
> select clear
> select clear
> view sel
> view sel
> select clear
> select clear
> view sel
> select clear
> view sel
> select clear
> view sel
> select clear
> view sel
> select clear
> view sel
> select clear
> pwd
Current working directory is:
/run/media/tic20/storage/structure_dump/aus/brisbane/guddat/ahas
> view sel
> select up
19 atoms, 18 bonds, 1 model selected
> select up
35 atoms, 33 bonds, 1 model selected
> select up
55 atoms, 53 bonds, 1 model selected
> select up
74 atoms, 71 bonds, 1 model selected
> select up
91 atoms, 88 bonds, 1 model selected
> select up
107 atoms, 103 bonds, 1 model selected
> select up
126 atoms, 121 bonds, 1 model selected
> select up
136 atoms, 130 bonds, 1 model selected
> select sel&sidechain
104 atoms, 97 bonds, 1 model selected
> show sel surfaces
> mlp sel
Map values for surface
"working_noh_ligand_atoms_renamed_real_space_refined.pdb_N SES surface":
minimum -25.26, mean -2.375, maximum 24.48
Map values for surface
"working_noh_ligand_atoms_renamed_real_space_refined.pdb_O SES surface":
minimum -27.95, mean -2.516, maximum 25.46
> select clear
> hide #1.3 models
> hide HC
> hbonds
5287 hydrogen bonds found
> set bgColor white
> lighting soft
> lighting full
> hide #!1.1 models
> lighting soft
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> select up
19 atoms, 18 bonds, 1 model selected
> style sel ball
Changed 19 atom styles
> select clear
> select up
19 atoms, 18 bonds, 1 model selected
> color sel tan
> color sel byhetero
> hide sel
> select up
26 atoms, 25 bonds, 2 models selected
> select down
16 atoms, 2 models selected
> select up
11 atoms, 10 bonds, 2 models selected
> select up
11 atoms, 10 bonds, 2 models selected
> hide sel
> ui mousemode rightMode label
> label #1.2/N:95
> select clear
> label #1.2/O:346
> label #1.2/O:347
> label #1.2/N:98
> label #1.2/N:100
> lighting full
> lighting soft
> graphics silhouettes true
> label #1.2/N:100
> cofr showPivot false
> save val_N_chain_binding_pocket.jpg
> close #1.2.14
> show #1.3 models
> show #!1.1 models
Missing command
> hide surfaces
> select clear
> graphics silhouettes false
> lighting simple
> save working.cxs
> select up
19 atoms, 18 bonds, 1 model selected
> style sel stick
Changed 19 atom styles
> select clear
> close #1.2.15
> save working.cxs
> show ~H
> save working.cxs
> save working.pdb #1
> lighting simple
> close #1.2.12-13
> select up
21 atoms, 21 bonds, 1 model selected
> surface sel
> ~surface
> select clear
> select clear
> select up
21 atoms, 21 bonds, 2 models selected
> surface sel
> ~surface
OpenGL version: 3.3.0 NVIDIA 440.33.01
OpenGL renderer: TITAN Xp/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: Precision T5600
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
CPU: 32 Intel(R) Xeon(R) CPU E5-2687W 0 @ 3.10GHz
Cache Size: 20480 KB
Graphics:
03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP102 [TITAN Xp] [10de:1b02] (rev a1)
Subsystem: NVIDIA Corporation Device [10de:11df]
Kernel driver in use: nvidia
Change History (6)
comment:1 by , 6 years ago
| Component: | Unassigned → Surface |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → empty surfaces slow things down |
| Type: | defect → enhancement |
comment:2 by , 6 years ago
| Resolution: | → not a bug |
|---|---|
| Status: | assigned → closed |
follow-up: 3 comment:3 by , 6 years ago
I think that’ll be a bit counterintuitive to people working via the top ribbon buttons rather than commands. Does it have to be recalculated while hidden, or would it be reasonable to delay the recalculation until it’s re-displayed?
comment:4 by , 6 years ago
The code to delay surface updating is complex and error prone so I do not want to do that for such a rare problem as running MD with a hidden surface. I know your pain with this -- it is not obvious why the MD is running dead slow. Until recently (1 year ago) ChimeraX did not automatically update the molecular surface when atoms were moved. I prefer it that way. But Elaine and Eric hammered on me for a few years that this was bad so I made them automatically update.
One idea is that the toolbar surface hide should really close the surface. Usually that is what I want. But in a fair number of cases I would be pretty unhappy because I colored the surface with much effort and if it gets closed that coloring is lost. So I think hide should really be hide.
So how to solve your problem. I think the best I can think of is when you start a simulation switch all MolecularSurface children of that surface to not auto update and log an message if you turned off update on any surfaces "Turned off auto-updating of 4 molecular surfaces so it does not slow down simulation.". Currently the molecular surface code only allows setting the auto-update mode when it is created. I'll change that so surf.auto_update = False will do the job.
comment:6 by , 6 years ago
Ok. Set surf.auto_update = False on all MolecularSurface child models of the structure you are going to start a simulation on should do the trick. I just checked in the code that makes the auto_update attribute work.
Note:
See TracTickets
for help on using tickets.
~surface is an alias for "surface hide". (The command "alias ~surface" will reveal that, or the User Guide.) Command surface hide does not close a surface it simply hides the atom patches. To close a surface use command "surface close".