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Opened 3 years ago
Closed 3 years ago
#8008 closed defect (fixed)
ISOLDE: dead Structure model
| Reported by: | Owned by: | Tristan Croll | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Third Party | Version: | |
| Keywords: | Cc: | Tom Goddard, Eric Pettersen | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-3.10.0-693.21.1.el7.x86_64-x86_64-with-centos-7.6.1810-Core
ChimeraX Version: 0.92 (2020-02-29)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 0.92 (2020-02-29)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
Downloading bundle ChimeraX_ISOLDE-1.0b4.dev2-cp37-cp37m-linux_x86_64.whl
Successfully installed ChimeraX-Clipper-0.11.1 ChimeraX-ISOLDE-1.0b4.dev2
Installed ChimeraX-Clipper (0.11.1)
Installed ChimeraX-ISOLDE (1.0b4.dev2)
'clip' is a prefix of an existing command 'clipper'
> open /home/YinGL/M_S/MS_modelbuilding_for_coot/Tekt1_1.mrc format mrc
Opened Tekt1_1.mrc, grid size 200,200,200, pixel 1.76, shown at level
5.94e-07, step 1, values float32
> toolshed show ISOLDE
> set selectionWidth 4
Cached rota8000-val data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-leu data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-ile data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-pro data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-phe data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-tyr data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-trp data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-ser data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-thr data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-cys data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-met data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-lys data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-his data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-arg data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-asp data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-asn data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-gln data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-glu data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
> volume #1 level 0.00414
Forcefield cache not found or out of date. Regenerating from ffXML files. This
is normal if running ISOLDE for the first time, or after upgrading OpenMM.
Done loading forcefield
> volume #1 level 0.004759
> set bgColor white
> open /home/YinGL/M_S/MS_modelbuilding_for_coot/Tekt1-1_RelTek1-1.pdb
Chain information for Tekt1-1_RelTek1-1.pdb #2
---
Chain | Description
a | No description available
b | No description available
c | No description available
Chain information for Tekt1-1_RelTek1-1.pdb
---
Chain | Description
2.1/a | No description available
2.1/b | No description available
2.1/c | No description available
Cached rama8000-cispro data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rama8000-transpro data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rama8000-gly-sym data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rama8000-prepro-noGP data not found. Regenerating from text file. This
is normal if running ISOLDE for the first time
Cached rama8000-ileval-nopreP data not found. Regenerating from text file.
This is normal if running ISOLDE for the first time
Cached rama8000-general-noGPIVpreP data not found. Regenerating from text
file. This is normal if running ISOLDE for the first time
> addh
Summary of feedback from adding hydrogens to Tekt1-1_RelTek1-1.pdb #2.1
---
warning | Skipped 5 atom(s) with bad connectivities; see log for details
notes | Termini for Tekt1-1_RelTek1-1.pdb (#2.1) chain a determined from
SEQRES records
Termini for Tekt1-1_RelTek1-1.pdb (#2.1) chain b determined from SEQRES
records
Termini for Tekt1-1_RelTek1-1.pdb (#2.1) chain c determined from SEQRES
records
Chain-initial residues that are actual N termini: /a ARG 1, /b PRO 1, /c PRO 1
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: /a ASP 351, /b ASP 396, /c LYS
263
Chain-final residues that are not actual C termini:
Skipping possible acceptor with bad geometry: /c VAL 116 OXT
Wrong number of grandchild atoms for phi/psi acceptor /c VAL 116 OXT
Skipping possible acceptor with bad geometry: /c VAL 116 O
Wrong number of grandchild atoms for phi/psi acceptor /c VAL 116 O
Skipping possible acceptor with bad geometry: /c VAL 116 OXT
Wrong number of grandchild atoms for phi/psi acceptor /c VAL 116 OXT
Skipping possible acceptor with bad geometry: /c VAL 116 O
Wrong number of grandchild atoms for phi/psi acceptor /c VAL 116 O
Skipping possible acceptor with bad geometry: /c VAL 116 OXT
Wrong number of grandchild atoms for phi/psi acceptor /c VAL 116 OXT
1096 hydrogen bonds
8357 hydrogens added
> hide HC
> select #2
16660 atoms, 16757 bonds, 8 models selected
> volume style mesh
> volume style image
> volume style image
> volume style mesh
> lighting shadows true
> graphics silhouettes true
> clipper isolate #2 maskRadius 16
> clipper isolate #2 maskRadius 16
> show ~HC
Missing or invalid "atoms" argument: invalid atoms specifier
Missing or invalid "atoms" argument: invalid atoms specifier
> isolde restrain distances "#2/a-c"
> usage isolde restrain
isolde restrain distances atoms [templateAtoms templateAtoms] [protein true or
false] [nucleic true or false] [customAtomNames customAtomNames] [perChain
true or false] [distanceCutoff a number] [alignmentCutoff a number]
[wellHalfWidth a number] [kappa a number] [tolerance a number] [fallOff a
number] [displayThreshold a number]
— Restrain interatomic distances to current values or a template.
atoms: some atoms specifiers
templateAtoms: some atoms specifiers
customAtomNames: some text strings
isolde restrain ligands models [distanceCutoff a number] [maxHeavyAtoms an
integer] [springConstant a number] [bondToCarbon true or false]
— Restrain small ligands to their surroundings and/or current positions. If
less than four distance restraints can be made for a given residue, they will
be supplemented with position restraints.
isolde restrain single distance atoms minDist maxDist [strength a number]
[wellHalfWidth a number] [confidence a number]
— Create a single adaptive distance restraint
minDist: a number
maxDist: a number
isolde restrain torsions residues [templateResidues a residues specifier]
[backbone true or false] [sidechains true or false] [angleRange a number]
[springConstant a number] [identicalSidechainsOnly true or false]
— Restrain amino acid backbone and/or sidechain torsions to their current
values or to those of a template model of identical or homologous sequence.
> select #2
16660 atoms, 16757 bonds, 9 models selected
> isolde sim start sel
QWidget::repaint: Recursive repaint detected
Traceback (most recent call last):
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/home/YinGL/.local/share/ChimeraX/0.92/site-
packages/chimerax/isolde/delayed_reaction.py", line 65, in callback
self.ff(*self.ff_args)
File "/home/YinGL/.local/share/ChimeraX/0.92/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1641, in
_update_coordinates_and_repeat
self.atoms.coords = th.coords
File "/home/YinGL/.local/share/ChimeraX/0.92/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 301, in coords
f(self._c_pointer, n, pointer(coords))
RuntimeError: Release Object
Error processing trigger "new frame":
RuntimeError: Release Object
File "/home/YinGL/.local/share/ChimeraX/0.92/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 301, in coords
f(self._c_pointer, n, pointer(coords))
See log for complete Python traceback.
> select #2
16660 atoms, 16757 bonds, 14 models selected
> isolde sim start sel
Simulation already running!
> select #2
16660 atoms, 16757 bonds, 14 models selected
> isolde sim start sel
Simulation already running!
> select #2
16660 atoms, 16757 bonds, 14 models selected
> isolde sim start sel
Simulation already running!
> select #2
16660 atoms, 16757 bonds, 14 models selected
> isolde sim start sel
Simulation already running!
> select #2
16660 atoms, 16757 bonds, 14 models selected
> isolde sim start sel
> hide #!2.1 models
> show #!2.1 models
> select #2.1
16660 atoms, 16757 bonds, 11 models selected
> select #2.1
16660 atoms, 16757 bonds, 11 models selected
> select #2.1
16660 atoms, 16757 bonds, 11 models selected
> select #2
16660 atoms, 16757 bonds, 14 models selected
> select #2
16660 atoms, 16757 bonds, 14 models selected
> select #2
16660 atoms, 16757 bonds, 14 models selected
> select up
16660 atoms, 16757 bonds, 14 models selected
> select up
16660 atoms, 16757 bonds, 16 models selected
> hide HC
> save tekt1-1.pdb format pdb models #2 relModel #1 selectedOnly true
Unable to open file 'tekt1-1.pdb' for writing
> save /home/YinGL/M_S/tekt1-1.pdb format pdb models #2 relModel #1
> selectedOnly true
> close #2.2-3#1-2#2.1
> open /home/YinGL/M_S/tekt1-1.pdb format PDB
Chain information for tekt1-1.pdb #1
---
Chain | Description
a | No description available
b | No description available
c | No description available
Chain information for tekt1-1.pdb
---
Chain | Description
1.1/a | No description available
1.1/b | No description available
1.1/c | No description available
> open /home/YinGL/M_S/MS_modelbuilding_for_coot/Tekt1-1_RelTek1-1.pdb
Chain information for Tekt1-1_RelTek1-1.pdb #2
---
Chain | Description
a | No description available
b | No description available
c | No description available
> close #2#1.2-3#1#1.1
> open /home/YinGL/M_S/tekt1-1.pdb format PDB
Chain information for tekt1-1.pdb #1
---
Chain | Description
a | No description available
b | No description available
c | No description available
Chain information for tekt1-1.pdb
---
Chain | Description
1.1/a | No description available
1.1/b | No description available
1.1/c | No description available
> open /home/YinGL/M_S/MS_modelbuilding_for_coot/Tekt1_1.mrc
Opened Tekt1_1.mrc, grid size 200,200,200, pixel 1.76, shown at level
5.94e-07, step 1, values float32
> volume #2 level 0.004955
> select up
Nothing selected
> select down
Traceback (most recent call last):
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 287, in forward_keystroke
run(self.session, 'select down')
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run
results = command.run(text, log=log)
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2845, in run
result = ci.function(session, **kw_args)
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/std_commands/select.py", line 162, in select_down
session.selection.demote(session)
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/selection.py", line 63, in demote
self._promotion.demote_selection()
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/selection.py", line 191, in demote_selection
p.demote()
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/selection.py", line 220, in demote
m.selected = False # This may clear child drawing selections.
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 243, in __setattr__
super(Drawing, self).__setattr__(key, value)
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1042, in _set_selected
Model.set_selected(self, sel, fire_trigger=fire_trigger)
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/models.py", line 198, in set_selected
self._selection_changed()
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/models.py", line 202, in _selection_changed
self.session.ui.thread_safe(self.session.triggers.activate_trigger,
AttributeError: 'NoneType' object has no attribute 'ui'
AttributeError: 'NoneType' object has no attribute 'ui'
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/models.py", line 202, in _selection_changed
self.session.ui.thread_safe(self.session.triggers.activate_trigger,
See log for complete Python traceback.
> volume style mesh
> lighting flat
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> graphics silhouettes false
> graphics silhouettes true
> addh
Summary of feedback from adding hydrogens to tekt1-1.pdb #1.1
---
warning | Skipped 9 atom(s) with bad connectivities; see log for details
notes | Termini for tekt1-1.pdb (#1.1) chain a determined from SEQRES records
Termini for tekt1-1.pdb (#1.1) chain b determined from SEQRES records
Termini for tekt1-1.pdb (#1.1) chain c determined from SEQRES records
Chain-initial residues that are actual N termini: /a ARG 1, /b PRO 1, /c PRO 1
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: /a ASP 351, /b ASP 396, /c LYS
263
Chain-final residues that are not actual C termini:
Skipping possible acceptor with bad geometry: /c VAL 116 OXT
Wrong number of grandchild atoms for phi/psi acceptor /c VAL 116 OXT
Skipping possible acceptor with bad geometry: /c VAL 116 OXT
Wrong number of grandchild atoms for phi/psi acceptor /c VAL 116 OXT
Skipping possible acceptor with bad geometry: /c VAL 116 O
Wrong number of grandchild atoms for phi/psi acceptor /c VAL 116 O
Skipping possible acceptor with bad geometry: /c VAL 116 OXT
Wrong number of grandchild atoms for phi/psi acceptor /c VAL 116 OXT
Skipping possible acceptor with bad geometry: /c VAL 116 O
Wrong number of grandchild atoms for phi/psi acceptor /c VAL 116 O
4 messages similar to the above omitted
1171 hydrogen bonds
0 hydrogens added
> hide HC
> select #1
16660 atoms, 16757 bonds, 8 models selected
> clipper isolate #1 maskRadius 16
> show ~HC
> isolde restrain distances "#1/a-c"
> usage isolde restrain
isolde restrain distances atoms [templateAtoms templateAtoms] [protein true or
false] [nucleic true or false] [customAtomNames customAtomNames] [perChain
true or false] [distanceCutoff a number] [alignmentCutoff a number]
[wellHalfWidth a number] [kappa a number] [tolerance a number] [fallOff a
number] [displayThreshold a number]
— Restrain interatomic distances to current values or a template.
atoms: some atoms specifiers
templateAtoms: some atoms specifiers
customAtomNames: some text strings
isolde restrain ligands models [distanceCutoff a number] [maxHeavyAtoms an
integer] [springConstant a number] [bondToCarbon true or false]
— Restrain small ligands to their surroundings and/or current positions. If
less than four distance restraints can be made for a given residue, they will
be supplemented with position restraints.
isolde restrain single distance atoms minDist maxDist [strength a number]
[wellHalfWidth a number] [confidence a number]
— Create a single adaptive distance restraint
minDist: a number
maxDist: a number
isolde restrain torsions residues [templateResidues a residues specifier]
[backbone true or false] [sidechains true or false] [angleRange a number]
[springConstant a number] [identicalSidechainsOnly true or false]
— Restrain amino acid backbone and/or sidechain torsions to their current
values or to those of a template model of identical or homologous sequence.
> select #1
16660 atoms, 16757 bonds, 9 models selected
> isolde sim start sel
> select #1
16660 atoms, 16757 bonds, 14 models selected
> isolde sim start sel
> toolshed show "Fit in Map"
> toolshed show "Side View"
> volume #2 level 0.006454
> select up
16660 atoms, 16757 bonds, 1 model selected
> select up
16660 atoms, 16757 bonds, 3 models selected
> save tekt1-1.pdb format pdb models #1 relModel #2 selectedOnly true
Unable to open file 'tekt1-1.pdb' for writing
> save /home/YinGL/M_S/tekt1-1.pdb format pdb models #1 relModel #2
> selectedOnly true
> close #1.2-3#1-2#1.1
> open /home/YinGL/M_S/tekt1-1.pdb format PDB
Chain information for tekt1-1.pdb #1
---
Chain | Description
a | No description available
b | No description available
c | No description available
Chain information for tekt1-1.pdb
---
Chain | Description
1.1/a | No description available
1.1/b | No description available
1.1/c | No description available
> open /home/YinGL/M_S/MS_modelbuilding_for_coot/Tekt1-1_RelTek1-1.pdb
Chain information for Tekt1-1_RelTek1-1.pdb #2
---
Chain | Description
a | No description available
b | No description available
c | No description available
> close #2
> open /home/YinGL/M_S/MS_modelbuilding_for_coot/Tekt1_1.mrc
Opened Tekt1_1.mrc, grid size 200,200,200, pixel 1.76, shown at level
5.94e-07, step 1, values float32
> volume #2 level 0.00414
> open /home/YinGL/M_S/MS_modelbuilding_for_coot/Tekt1-1_RelTek1-1.pdb
Chain information for Tekt1-1_RelTek1-1.pdb #3
---
Chain | Description
a | No description available
b | No description available
c | No description available
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> close #2
> close #3#1.2-3#1#1.1
> open /home/YinGL/M_S/MS_modelbuilding_for_coot/Tekt1_1.mrc
Opened Tekt1_1.mrc, grid size 200,200,200, pixel 1.76, shown at level
5.94e-07, step 1, values float32
> volume #1 level 0.005378
> volume style mesh
> open /home/YinGL/M_S/MS_modelbuilding_for_coot/Tekt1-1_RelTek1-1.pdb
Chain information for Tekt1-1_RelTek1-1.pdb #2
---
Chain | Description
a | No description available
b | No description available
c | No description available
Chain information for Tekt1-1_RelTek1-1.pdb
---
Chain | Description
2.1/a | No description available
2.1/b | No description available
2.1/c | No description available
> select up
Nothing selected
> select up
Nothing selected
> addh
Summary of feedback from adding hydrogens to Tekt1-1_RelTek1-1.pdb #2.1
---
warning | Skipped 5 atom(s) with bad connectivities; see log for details
notes | Termini for Tekt1-1_RelTek1-1.pdb (#2.1) chain a determined from
SEQRES records
Termini for Tekt1-1_RelTek1-1.pdb (#2.1) chain b determined from SEQRES
records
Termini for Tekt1-1_RelTek1-1.pdb (#2.1) chain c determined from SEQRES
records
Chain-initial residues that are actual N termini: /a ARG 1, /b PRO 1, /c PRO 1
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: /a ASP 351, /b ASP 396, /c LYS
263
Chain-final residues that are not actual C termini:
Skipping possible acceptor with bad geometry: /c VAL 116 OXT
Wrong number of grandchild atoms for phi/psi acceptor /c VAL 116 OXT
Skipping possible acceptor with bad geometry: /c VAL 116 O
Wrong number of grandchild atoms for phi/psi acceptor /c VAL 116 O
Skipping possible acceptor with bad geometry: /c VAL 116 OXT
Wrong number of grandchild atoms for phi/psi acceptor /c VAL 116 OXT
Skipping possible acceptor with bad geometry: /c VAL 116 O
Wrong number of grandchild atoms for phi/psi acceptor /c VAL 116 O
Skipping possible acceptor with bad geometry: /c VAL 116 OXT
Wrong number of grandchild atoms for phi/psi acceptor /c VAL 116 OXT
1096 hydrogen bonds
8357 hydrogens added
> hide HC
> select #2
16660 atoms, 16757 bonds, 8 models selected
> clipper isolate #2 maskRadius 16
> show ~HC
> isolde restrain distances "#2/a-c"
> isolde restrain distances "#2"
> isolde restrain distances "#1"
No residues specified to restrain!
> isolde restrain distances "#1/a-c"
No residues specified to restrain!
> isolde restrain distances "#2/a-c"
> usage isolde restrain
isolde restrain distances atoms [templateAtoms templateAtoms] [protein true or
false] [nucleic true or false] [customAtomNames customAtomNames] [perChain
true or false] [distanceCutoff a number] [alignmentCutoff a number]
[wellHalfWidth a number] [kappa a number] [tolerance a number] [fallOff a
number] [displayThreshold a number]
— Restrain interatomic distances to current values or a template.
atoms: some atoms specifiers
templateAtoms: some atoms specifiers
customAtomNames: some text strings
isolde restrain ligands models [distanceCutoff a number] [maxHeavyAtoms an
integer] [springConstant a number] [bondToCarbon true or false]
— Restrain small ligands to their surroundings and/or current positions. If
less than four distance restraints can be made for a given residue, they will
be supplemented with position restraints.
isolde restrain single distance atoms minDist maxDist [strength a number]
[wellHalfWidth a number] [confidence a number]
— Create a single adaptive distance restraint
minDist: a number
maxDist: a number
isolde restrain torsions residues [templateResidues a residues specifier]
[backbone true or false] [sidechains true or false] [angleRange a number]
[springConstant a number] [identicalSidechainsOnly true or false]
— Restrain amino acid backbone and/or sidechain torsions to their current
values or to those of a template model of identical or homologous sequence.
> select #2
16660 atoms, 16757 bonds, 9 models selected
> isolde sim start sel
> close #2.2-3#1-2#2.1
> open /home/YinGL/M_S/MS_modelbuilding_for_coot/Tekt1_1.mrc
Opened Tekt1_1.mrc, grid size 200,200,200, pixel 1.76, shown at level
5.94e-07, step 1, values float32
> volume #1 level 0.005476
> open /home/YinGL/M_S/MS_modelbuilding_for_coot/Tekt1-1_RelTek1-1.pdb
Chain information for Tekt1-1_RelTek1-1.pdb #2
---
Chain | Description
a | No description available
b | No description available
c | No description available
Chain information for Tekt1-1_RelTek1-1.pdb
---
Chain | Description
2.1/a | No description available
2.1/b | No description available
2.1/c | No description available
Invalid "toModel" argument: Must specify 1 structure, got 0 for "#1"
Invalid "toModel" argument: Must specify 1 structure, got 0 for "#1"
> clipper associate #1 toModel #2
> set silhouettes false
> transparency 50
> volume style mesh
> transparency 50
> volume style mesh
> delete ~protein
> addh
Summary of feedback from adding hydrogens to Tekt1-1_RelTek1-1.pdb #2.1
---
warning | Skipped 5 atom(s) with bad connectivities; see log for details
notes | Termini for Tekt1-1_RelTek1-1.pdb (#2.1) chain a determined from
SEQRES records
Termini for Tekt1-1_RelTek1-1.pdb (#2.1) chain b determined from SEQRES
records
Termini for Tekt1-1_RelTek1-1.pdb (#2.1) chain c determined from SEQRES
records
Chain-initial residues that are actual N termini: /a ARG 1, /b PRO 1, /c PRO 1
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: /a ASP 351, /b ASP 396, /c LYS
263
Chain-final residues that are not actual C termini:
Skipping possible acceptor with bad geometry: /c VAL 116 OXT
Wrong number of grandchild atoms for phi/psi acceptor /c VAL 116 OXT
Skipping possible acceptor with bad geometry: /c VAL 116 O
Wrong number of grandchild atoms for phi/psi acceptor /c VAL 116 O
Skipping possible acceptor with bad geometry: /c VAL 116 OXT
Wrong number of grandchild atoms for phi/psi acceptor /c VAL 116 OXT
Skipping possible acceptor with bad geometry: /c VAL 116 O
Wrong number of grandchild atoms for phi/psi acceptor /c VAL 116 O
Skipping possible acceptor with bad geometry: /c VAL 116 OXT
Wrong number of grandchild atoms for phi/psi acceptor /c VAL 116 OXT
1096 hydrogen bonds
8357 hydrogens added
> hide HC
> select #2
16660 atoms, 16757 bonds, 12 models selected
> clipper isolate #2 maskRadius 16
> show ~HC
> isolde restrain distances "#2/a-c"
> usage isolde restrain
isolde restrain distances atoms [templateAtoms templateAtoms] [protein true or
false] [nucleic true or false] [customAtomNames customAtomNames] [perChain
true or false] [distanceCutoff a number] [alignmentCutoff a number]
[wellHalfWidth a number] [kappa a number] [tolerance a number] [fallOff a
number] [displayThreshold a number]
— Restrain interatomic distances to current values or a template.
atoms: some atoms specifiers
templateAtoms: some atoms specifiers
customAtomNames: some text strings
isolde restrain ligands models [distanceCutoff a number] [maxHeavyAtoms an
integer] [springConstant a number] [bondToCarbon true or false]
— Restrain small ligands to their surroundings and/or current positions. If
less than four distance restraints can be made for a given residue, they will
be supplemented with position restraints.
isolde restrain single distance atoms minDist maxDist [strength a number]
[wellHalfWidth a number] [confidence a number]
— Create a single adaptive distance restraint
minDist: a number
maxDist: a number
isolde restrain torsions residues [templateResidues a residues specifier]
[backbone true or false] [sidechains true or false] [angleRange a number]
[springConstant a number] [identicalSidechainsOnly true or false]
— Restrain amino acid backbone and/or sidechain torsions to their current
values or to those of a template model of identical or homologous sequence.
> select #2
16660 atoms, 16757 bonds, 13 models selected
> isolde sim start sel
> select up
16660 atoms, 16757 bonds, 1 model selected
> select up
16660 atoms, 16757 bonds, 3 models selected
> select up
16660 atoms, 16757 bonds, 4 models selected
> select up
16660 atoms, 16757 bonds, 4 models selected
> select up
16660 atoms, 16757 bonds, 4 models selected
> select up
16660 atoms, 16757 bonds, 4 models selected
> select up
16660 atoms, 16757 bonds, 4 models selected
> select up
16660 atoms, 16757 bonds, 4 models selected
> select up
16660 atoms, 16757 bonds, 4 models selected
> select up
16660 atoms, 16757 bonds, 4 models selected
> select up
16660 atoms, 16757 bonds, 4 models selected
> select up
16660 atoms, 16757 bonds, 4 models selected
> select up
16660 atoms, 16757 bonds, 4 models selected
Invalid "relModel" argument: Must specify 1 model, got 0
Invalid "relModel" argument: Must specify 1 model, got 0
> save /home/YinGL/M_S/MS_modelbuilding_for_coot/tekt1-1.pdb format pdb models
> #2 relModel #2 selectedOnly true
> hide #!2.1 models
> show #!2.1 models
> hide #!2.1 models
> hide #!2.2 models
> show #!2.2 models
> show #!2.1 models
> hide #!2.2 models
> hide #2.3 models
> show #2.3 models
> hide #!2 models
> show #!2 models
> hide #!2.1 models
> show #!2.1 models
> save /home/YinGL/M_S/MS_modelbuilding_for_coot/tekt1-1.pdb format pdb models
> #2.1 relModel #2.2 selectedOnly true
> hide #!2 models
> open /home/YinGL/M_S/MS_modelbuilding_for_coot/tekt1-1.pdb
Chain information for tekt1-1.pdb #1
---
Chain | Description
a | No description available
b | No description available
c | No description available
> show #!2.2 models
> hide #!2.2 models
> show #!2.2 models
> hide #!2 models
> hide #!2.2 models
> show #!2.2 models
> hide #!2.1 models
> close #1
> show #!2.1 models
> show ~HC
> isolde restrain distances "#2/a-c"
> usage isolde restrain
isolde restrain distances atoms [templateAtoms templateAtoms] [protein true or
false] [nucleic true or false] [customAtomNames customAtomNames] [perChain
true or false] [distanceCutoff a number] [alignmentCutoff a number]
[wellHalfWidth a number] [kappa a number] [tolerance a number] [fallOff a
number] [displayThreshold a number]
— Restrain interatomic distances to current values or a template.
atoms: some atoms specifiers
templateAtoms: some atoms specifiers
customAtomNames: some text strings
isolde restrain ligands models [distanceCutoff a number] [maxHeavyAtoms an
integer] [springConstant a number] [bondToCarbon true or false]
— Restrain small ligands to their surroundings and/or current positions. If
less than four distance restraints can be made for a given residue, they will
be supplemented with position restraints.
isolde restrain single distance atoms minDist maxDist [strength a number]
[wellHalfWidth a number] [confidence a number]
— Create a single adaptive distance restraint
minDist: a number
maxDist: a number
isolde restrain torsions residues [templateResidues a residues specifier]
[backbone true or false] [sidechains true or false] [angleRange a number]
[springConstant a number] [identicalSidechainsOnly true or false]
— Restrain amino acid backbone and/or sidechain torsions to their current
values or to those of a template model of identical or homologous sequence.
> select #2
16660 atoms, 16757 bonds, 18 models selected
> isolde sim start sel
> select up
16660 atoms, 16757 bonds, 1 model selected
> select up
16660 atoms, 16757 bonds, 3 models selected
> select up
16660 atoms, 16757 bonds, 4 models selected
> select up
16660 atoms, 16757 bonds, 4 models selected
> select up
16660 atoms, 16757 bonds, 4 models selected
> select up
16660 atoms, 16757 bonds, 4 models selected
> select up
16660 atoms, 16757 bonds, 4 models selected
> select up
16660 atoms, 16757 bonds, 4 models selected
> select up
16660 atoms, 16757 bonds, 4 models selected
> select up
16660 atoms, 16757 bonds, 4 models selected
> select up
16660 atoms, 16757 bonds, 4 models selected
> select up
16660 atoms, 16757 bonds, 4 models selected
> save /home/YinGL/M_S/MS_modelbuilding_for_coot/tekt1-1.pdb format pdb models
> #2.1 relModel #2.2 selectedOnly true
> close #2.3#2#2.1-2
> open /home/YinGL/M_S/MS_modelbuilding_for_coot/Tekt2-1_RelTek2-1.pdb
Chain information for Tekt2-1_RelTek2-1.pdb #1
---
Chain | Description
T | No description available
U V | No description available
W | No description available
Chain information for Tekt2-1_RelTek2-1.pdb
---
Chain | Description
1.1/T | No description available
1.1/U 1.1/V | No description available
1.1/W | No description available
> open /home/YinGL/M_S/MS_modelbuilding_for_coot/Tekt2_1.mrc
Opened Tekt2_1.mrc, grid size 200,200,200, pixel 1.76, shown at level
5.94e-07, step 1, values float32
> volume #2 level 0.005574
> select up
Nothing selected
> select up
Nothing selected
> select up
Nothing selected
> select up
Nothing selected
> select up
Nothing selected
> select up
Nothing selected
Invalid "toModel" argument: Must specify 1 structure, got 0 for "#2"
> clipper associate #2 toModel #1
> set silhouettes false
> delete ~protein
> addh
Summary of feedback from adding hydrogens to Tekt2-1_RelTek2-1.pdb #1.1
---
notes | Termini for Tekt2-1_RelTek2-1.pdb (#1.1) chain T determined from
SEQRES records
Termini for Tekt2-1_RelTek2-1.pdb (#1.1) chain U determined from SEQRES
records
Termini for Tekt2-1_RelTek2-1.pdb (#1.1) chain V determined from SEQRES
records
Termini for Tekt2-1_RelTek2-1.pdb (#1.1) chain W determined from SEQRES
records
Chain-initial residues that are actual N termini: /T ARG 11, /U ARG 11, /V ARG
11, /W ARG 270
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: /T ILE 237, /U ALA 401, /V ALA
401, /W LEU 386
Chain-final residues that are not actual C termini:
1180 hydrogen bonds
8753 hydrogens added
> hide HC
> select #1
17470 atoms, 17564 bonds, 2 pseudobonds, 13 models selected
> clipper isolate #1 maskRadius 16
> show ~HC
> isolde restrain distances "#1/T-W"
> volume sel style mesh
> usage isolde restrain
isolde restrain distances atoms [templateAtoms templateAtoms] [protein true or
false] [nucleic true or false] [customAtomNames customAtomNames] [perChain
true or false] [distanceCutoff a number] [alignmentCutoff a number]
[wellHalfWidth a number] [kappa a number] [tolerance a number] [fallOff a
number] [displayThreshold a number]
— Restrain interatomic distances to current values or a template.
atoms: some atoms specifiers
templateAtoms: some atoms specifiers
customAtomNames: some text strings
isolde restrain ligands models [distanceCutoff a number] [maxHeavyAtoms an
integer] [springConstant a number] [bondToCarbon true or false]
— Restrain small ligands to their surroundings and/or current positions. If
less than four distance restraints can be made for a given residue, they will
be supplemented with position restraints.
isolde restrain single distance atoms minDist maxDist [strength a number]
[wellHalfWidth a number] [confidence a number]
— Create a single adaptive distance restraint
minDist: a number
maxDist: a number
isolde restrain torsions residues [templateResidues a residues specifier]
[backbone true or false] [sidechains true or false] [angleRange a number]
[springConstant a number] [identicalSidechainsOnly true or false]
— Restrain amino acid backbone and/or sidechain torsions to their current
values or to those of a template model of identical or homologous sequence.
> select #1
17470 atoms, 17564 bonds, 2 pseudobonds, 14 models selected
> isolde sim start sel
> hide #!1.2 models
> show #!1.2 models
> hide #!1.1 models
> show #!1.1 models
> select up
17470 atoms, 17564 bonds, 1 model selected
> select up
17470 atoms, 17564 bonds, 3 models selected
> save /home/YinGL/M_S/MS_modelbuilding_for_coot/tekt2-1.pdb format pdb models
> #1.1 relModel #1.2 selectedOnly true
> close #1.3#1#1.1-2
> open /home/YinGL/M_S/MS_modelbuilding_for_coot/Tekt2-2_RelTek2-2.pdb
Chain information for Tekt2-2_RelTek2-2.pdb #1
---
Chain | Description
X | No description available
Y | No description available
Z | No description available
Chain information for Tekt2-2_RelTek2-2.pdb
---
Chain | Description
1.1/X | No description available
1.1/Y | No description available
1.1/Z | No description available
> open /home/YinGL/M_S/MS_modelbuilding_for_coot/Tekt2_1.mrc
Opened Tekt2_1.mrc, grid size 200,200,200, pixel 1.76, shown at level
5.94e-07, step 1, values float32
> close #2
> open /home/YinGL/M_S/MS_modelbuilding_for_coot/Tekt2_2.mrc
Opened Tekt2_2.mrc, grid size 200,200,200, pixel 1.76, shown at level
1.17e-08, step 1, values float32
> ui mousemode rightMode translate
> ui mousemode rightMode zoom
> volume #2 level 0.004521
> select up
Nothing selected
> clipper associate #2 toModel #1
> set silhouettes false
> delete ~protein
> addh
Summary of feedback from adding hydrogens to Tekt2-2_RelTek2-2.pdb #1.1
---
notes | Termini for Tekt2-2_RelTek2-2.pdb (#1.1) chain X determined from
SEQRES records
Termini for Tekt2-2_RelTek2-2.pdb (#1.1) chain Y determined from SEQRES
records
Termini for Tekt2-2_RelTek2-2.pdb (#1.1) chain Z determined from SEQRES
records
Chain-initial residues that are actual N termini: /X ILE 53, /Y ARG 11, /Z ARG
11
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: /X ALA 401, /Y ALA 401, /Z ALA
401
Chain-final residues that are not actual C termini:
1150 hydrogen bonds
8557 hydrogens added
> hide HC
> select #1
17045 atoms, 17133 bonds, 2 pseudobonds, 13 models selected
> clipper isolate #1 maskRadius 16
> show ~HC
> isolde restrain distances "#1/X-Z"
> usage isolde restrain
isolde restrain distances atoms [templateAtoms templateAtoms] [protein true or
false] [nucleic true or false] [customAtomNames customAtomNames] [perChain
true or false] [distanceCutoff a number] [alignmentCutoff a number]
[wellHalfWidth a number] [kappa a number] [tolerance a number] [fallOff a
number] [displayThreshold a number]
— Restrain interatomic distances to current values or a template.
atoms: some atoms specifiers
templateAtoms: some atoms specifiers
customAtomNames: some text strings
isolde restrain ligands models [distanceCutoff a number] [maxHeavyAtoms an
integer] [springConstant a number] [bondToCarbon true or false]
— Restrain small ligands to their surroundings and/or current positions. If
less than four distance restraints can be made for a given residue, they will
be supplemented with position restraints.
isolde restrain single distance atoms minDist maxDist [strength a number]
[wellHalfWidth a number] [confidence a number]
— Create a single adaptive distance restraint
minDist: a number
maxDist: a number
isolde restrain torsions residues [templateResidues a residues specifier]
[backbone true or false] [sidechains true or false] [angleRange a number]
[springConstant a number] [identicalSidechainsOnly true or false]
— Restrain amino acid backbone and/or sidechain torsions to their current
values or to those of a template model of identical or homologous sequence.
> select #1
17045 atoms, 17133 bonds, 2 pseudobonds, 14 models selected
> isolde sim start sel
> save /home/YinGL/M_S/MS_modelbuilding_for_coot/tekt2-2.pdb format pdb models
> #1.1 relModel #1.2 selectedOnly true
> close #1.3#1#1.1-2
> open /home/YinGL/M_S/MS_modelbuilding_for_coot/Tekt5A_RelTek5A.pdb
Chain information for Tekt5A_RelTek5A.pdb #1
---
Chain | Description
k | No description available
l | No description available
m | No description available
Chain information for Tekt5A_RelTek5A.pdb
---
Chain | Description
1.1/k | No description available
1.1/l | No description available
1.1/m | No description available
> open /home/YinGL/M_S/MS_modelbuilding_for_coot/Tekt5A.mrc
Opened Tekt5A.mrc, grid size 200,200,200, pixel 1.76, shown at level 6.96e-07,
step 1, values float32
> volume #2 level 0.004508
> select up
Nothing selected
> select up
Nothing selected
> select up
Nothing selected
> clipper associate #2 toModel #1
> set silhouettes false
> delete ~protein
> addh
Summary of feedback from adding hydrogens to Tekt5A_RelTek5A.pdb #1.1
---
notes | Termini for Tekt5A_RelTek5A.pdb (#1.1) chain k determined from SEQRES
records
Termini for Tekt5A_RelTek5A.pdb (#1.1) chain l determined from SEQRES records
Termini for Tekt5A_RelTek5A.pdb (#1.1) chain m determined from SEQRES records
Chain-initial residues that are actual N termini: /k THR 172, /l ARG 89, /m
ARG 89
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: /k PRO 477, /l PRO 477, /m PRO
477
Chain-final residues that are not actual C termini:
1124 hydrogen bonds
8257 hydrogens added
> hide HC
> select #1
16434 atoms, 16533 bonds, 4 pseudobonds, 13 models selected
> clipper isolate #1 maskRadius 16
> show ~HC
> isolde restrain distances "#1/k-m"
> usage isolde restrain
isolde restrain distances atoms [templateAtoms templateAtoms] [protein true or
false] [nucleic true or false] [customAtomNames customAtomNames] [perChain
true or false] [distanceCutoff a number] [alignmentCutoff a number]
[wellHalfWidth a number] [kappa a number] [tolerance a number] [fallOff a
number] [displayThreshold a number]
— Restrain interatomic distances to current values or a template.
atoms: some atoms specifiers
templateAtoms: some atoms specifiers
customAtomNames: some text strings
isolde restrain ligands models [distanceCutoff a number] [maxHeavyAtoms an
integer] [springConstant a number] [bondToCarbon true or false]
— Restrain small ligands to their surroundings and/or current positions. If
less than four distance restraints can be made for a given residue, they will
be supplemented with position restraints.
isolde restrain single distance atoms minDist maxDist [strength a number]
[wellHalfWidth a number] [confidence a number]
— Create a single adaptive distance restraint
minDist: a number
maxDist: a number
isolde restrain torsions residues [templateResidues a residues specifier]
[backbone true or false] [sidechains true or false] [angleRange a number]
[springConstant a number] [identicalSidechainsOnly true or false]
— Restrain amino acid backbone and/or sidechain torsions to their current
values or to those of a template model of identical or homologous sequence.
> select #1
16434 atoms, 16533 bonds, 4 pseudobonds, 14 models selected
> isolde sim start sel
No template found for residue k236 (ILE)
Adding hydrogens
Summary of feedback from adding hydrogens to Tekt5A_RelTek5A.pdb #1.1
---
notes | Termini for Tekt5A_RelTek5A.pdb (#1.1) chain k determined from SEQRES
records
Termini for Tekt5A_RelTek5A.pdb (#1.1) chain l determined from SEQRES records
Termini for Tekt5A_RelTek5A.pdb (#1.1) chain m determined from SEQRES records
Chain-initial residues that are actual N termini: /k THR 172, /l ARG 89, /m
ARG 89
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: /k PRO 477, /l PRO 477, /m PRO
477
Chain-final residues that are not actual C termini:
1087 hydrogen bonds
0 hydrogens added
No template found for residue k236 (ILE)
Excluding residue
No template found for residue m401 (ARG)
Excluding residue
> close #1.3#1#1.1-2
> open /home/YinGL/M_S/MS_modelbuilding_for_coot/Tekt5A_RelTek5A.pdb
Chain information for Tekt5A_RelTek5A.pdb #1
---
Chain | Description
k | No description available
l | No description available
m | No description available
Chain information for Tekt5A_RelTek5A.pdb
---
Chain | Description
1.1/k | No description available
1.1/l | No description available
1.1/m | No description available
> open /home/YinGL/M_S/MS_modelbuilding_for_coot/Tekt5A.mrc
Opened Tekt5A.mrc, grid size 200,200,200, pixel 1.76, shown at level 6.96e-07,
step 1, values float32
> volume #2 level 0.003785
> hide #!1.1 models
> show #!1.1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #1.3 models
> close #1.2-3#1-2#1.1
> open /home/YinGL/M_S/MS_modelbuilding_for_coot/Tekt5A.mrc
Opened Tekt5A.mrc, grid size 200,200,200, pixel 1.76, shown at level 6.96e-07,
step 1, values float32
> close
> open /home/YinGL/M_S/MS_modelbuilding_for_coot/Tekt5A_RelTek5A.pdb
Chain information for Tekt5A_RelTek5A.pdb #1
---
Chain | Description
k | No description available
l | No description available
m | No description available
Chain information for Tekt5A_RelTek5A.pdb
---
Chain | Description
1.1/k | No description available
1.1/l | No description available
1.1/m | No description available
> open /home/YinGL/M_S/MS_modelbuilding_for_coot/Tekt5A.mrc
Opened Tekt5A.mrc, grid size 200,200,200, pixel 1.76, shown at level 6.96e-07,
step 1, values float32
> volume #2 level 0.00376
> select up
Nothing selected
> select down
Traceback (most recent call last):
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 287, in forward_keystroke
run(self.session, 'select down')
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run
results = command.run(text, log=log)
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2845, in run
result = ci.function(session, **kw_args)
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/std_commands/select.py", line 162, in select_down
session.selection.demote(session)
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/selection.py", line 63, in demote
self._promotion.demote_selection()
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/selection.py", line 191, in demote_selection
p.demote()
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/selection.py", line 220, in demote
m.selected = False # This may clear child drawing selections.
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 243, in __setattr__
super(Drawing, self).__setattr__(key, value)
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/models.py", line 198, in set_selected
self._selection_changed()
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/models.py", line 202, in _selection_changed
self.session.ui.thread_safe(self.session.triggers.activate_trigger,
AttributeError: 'NoneType' object has no attribute 'ui'
AttributeError: 'NoneType' object has no attribute 'ui'
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/models.py", line 202, in _selection_changed
self.session.ui.thread_safe(self.session.triggers.activate_trigger,
See log for complete Python traceback.
> select up
Nothing selected
> clipper associate #2 toModel #1
> set silhouettes false
> delete ~protein
> addh
Summary of feedback from adding hydrogens to Tekt5A_RelTek5A.pdb #1.1
---
notes | Termini for Tekt5A_RelTek5A.pdb (#1.1) chain k determined from SEQRES
records
Termini for Tekt5A_RelTek5A.pdb (#1.1) chain l determined from SEQRES records
Termini for Tekt5A_RelTek5A.pdb (#1.1) chain m determined from SEQRES records
Chain-initial residues that are actual N termini: /k THR 172, /l ARG 89, /m
ARG 89
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: /k PRO 477, /l PRO 477, /m PRO
477
Chain-final residues that are not actual C termini:
1124 hydrogen bonds
8257 hydrogens added
> hide HC
> select #1
16434 atoms, 16533 bonds, 4 pseudobonds, 13 models selected
> clipper isolate #1 maskRadius 16
> show ~HC
> isolde restrain distances "#1/k,l,m"
> usage isolde restrain
isolde restrain distances atoms [templateAtoms templateAtoms] [protein true or
false] [nucleic true or false] [customAtomNames customAtomNames] [perChain
true or false] [distanceCutoff a number] [alignmentCutoff a number]
[wellHalfWidth a number] [kappa a number] [tolerance a number] [fallOff a
number] [displayThreshold a number]
— Restrain interatomic distances to current values or a template.
atoms: some atoms specifiers
templateAtoms: some atoms specifiers
customAtomNames: some text strings
isolde restrain ligands models [distanceCutoff a number] [maxHeavyAtoms an
integer] [springConstant a number] [bondToCarbon true or false]
— Restrain small ligands to their surroundings and/or current positions. If
less than four distance restraints can be made for a given residue, they will
be supplemented with position restraints.
isolde restrain single distance atoms minDist maxDist [strength a number]
[wellHalfWidth a number] [confidence a number]
— Create a single adaptive distance restraint
minDist: a number
maxDist: a number
isolde restrain torsions residues [templateResidues a residues specifier]
[backbone true or false] [sidechains true or false] [angleRange a number]
[springConstant a number] [identicalSidechainsOnly true or false]
— Restrain amino acid backbone and/or sidechain torsions to their current
values or to those of a template model of identical or homologous sequence.
> select #1
16434 atoms, 16533 bonds, 4 pseudobonds, 14 models selected
> isolde sim start sel
No template found for residue k236 (ILE)
Excluding residue
No template found for residue m401 (ARG)
Doing nothing
> select up
77 atoms, 75 bonds, 1 model selected
> select up
6280 atoms, 6320 bonds, 1 model selected
> select up
16434 atoms, 16533 bonds, 1 model selected
> select down
6280 atoms, 6320 bonds, 1 model selected
> select down
77 atoms, 75 bonds, 1 model selected
> select up
6280 atoms, 6320 bonds, 1 model selected
> select up
16434 atoms, 16533 bonds, 1 model selected
> select up
16434 atoms, 16533 bonds, 3 models selected
> select up
16434 atoms, 16533 bonds, 4 models selected
> select up
16434 atoms, 16533 bonds, 4 models selected
> select up
16434 atoms, 16533 bonds, 4 models selected
> select up
16434 atoms, 16533 bonds, 4 models selected
> select up
16434 atoms, 16533 bonds, 4 models selected
> select up
16434 atoms, 16533 bonds, 4 models selected
> select up
16434 atoms, 16533 bonds, 4 models selected
> select up
16434 atoms, 16533 bonds, 4 models selected
> select up
16434 atoms, 16533 bonds, 4 models selected
> select up
16434 atoms, 16533 bonds, 4 models selected
> select up
16434 atoms, 16533 bonds, 4 models selected
> select up
16434 atoms, 16533 bonds, 4 models selected
> select up
16434 atoms, 16533 bonds, 4 models selected
> select up
16434 atoms, 16533 bonds, 4 models selected
> select up
16434 atoms, 16533 bonds, 4 models selected
> select down
16434 atoms, 16533 bonds, 3 models selected
> select down
16434 atoms, 16533 bonds, 1 model selected
> select down
6280 atoms, 6320 bonds, 1 model selected
> select down
77 atoms, 75 bonds, 1 model selected
> select down
25 atoms, 24 bonds, 1 model selected
> select down
Traceback (most recent call last):
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 287, in forward_keystroke
run(self.session, 'select down')
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run
results = command.run(text, log=log)
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2845, in run
result = ci.function(session, **kw_args)
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/std_commands/select.py", line 162, in select_down
session.selection.demote(session)
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/selection.py", line 63, in demote
self._promotion.demote_selection()
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/selection.py", line 191, in demote_selection
p.demote()
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 2865, in demote
s.atoms.selected = self._prev_atom_sel_mask
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 43, in _getattr_
return base.__getattr__(self, attr_name, look_in_class=base)
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 65, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
AttributeError: Execution of 'Structure' object's 'atoms' property raised
AttributeError
AttributeError: Execution of 'Structure' object's 'atoms' property raised
AttributeError
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 65, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
> select up
77 atoms, 75 bonds, 1 model selected
> select up
6280 atoms, 6320 bonds, 1 model selected
> select up
16434 atoms, 16533 bonds, 1 model selected
> select up
16434 atoms, 16533 bonds, 3 models selected
> select up
16434 atoms, 16533 bonds, 4 models selected
> select up
16434 atoms, 16533 bonds, 4 models selected
> select up
16434 atoms, 16533 bonds, 4 models selected
> select up
16434 atoms, 16533 bonds, 4 models selected
> select up
16434 atoms, 16533 bonds, 4 models selected
> select up
16434 atoms, 16533 bonds, 4 models selected
> select up
16434 atoms, 16533 bonds, 4 models selected
> select up
16434 atoms, 16533 bonds, 4 models selected
> select up
16434 atoms, 16533 bonds, 4 models selected
> select up
16434 atoms, 16533 bonds, 4 models selected
> select up
16434 atoms, 16533 bonds, 4 models selected
> select up
16434 atoms, 16533 bonds, 4 models selected
> select up
16434 atoms, 16533 bonds, 4 models selected
> select #1
16434 atoms, 16533 bonds, 4 pseudobonds, 19 models selected
> isolde sim start sel
No template found for residue m401 (ARG)
Doing nothing
> select #1
16434 atoms, 16533 bonds, 4 pseudobonds, 19 models selected
> isolde sim start sel
No template found for residue m401 (ARG)
Adding hydrogens
Summary of feedback from adding hydrogens to Tekt5A_RelTek5A.pdb #1.1
---
notes | Termini for Tekt5A_RelTek5A.pdb (#1.1) chain k determined from SEQRES
records
Termini for Tekt5A_RelTek5A.pdb (#1.1) chain l determined from SEQRES records
Termini for Tekt5A_RelTek5A.pdb (#1.1) chain m determined from SEQRES records
Chain-initial residues that are actual N termini: /k THR 172, /l ARG 89, /m
ARG 89
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: /k PRO 477, /l PRO 477, /m PRO
477
Chain-final residues that are not actual C termini:
1087 hydrogen bonds
0 hydrogens added
No template found for residue m401 (ARG)
Adding hydrogens
Summary of feedback from adding hydrogens to Tekt5A_RelTek5A.pdb #1.1
---
notes | Termini for Tekt5A_RelTek5A.pdb (#1.1) chain k determined from SEQRES
records
Termini for Tekt5A_RelTek5A.pdb (#1.1) chain l determined from SEQRES records
Termini for Tekt5A_RelTek5A.pdb (#1.1) chain m determined from SEQRES records
Chain-initial residues that are actual N termini: /k THR 172, /l ARG 89, /m
ARG 89
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: /k PRO 477, /l PRO 477, /m PRO
477
Chain-final residues that are not actual C termini:
1087 hydrogen bonds
0 hydrogens added
No template found for residue m401 (ARG)
Excluding residue
> clipper associate #2 toModel #1
> set silhouettes false
> delete ~protein
> addh
Summary of feedback from adding hydrogens to Tekt5A_RelTek5A.pdb #1.1
---
notes | Termini for Tekt5A_RelTek5A.pdb (#1.1) chain k determined from SEQRES
records
Termini for Tekt5A_RelTek5A.pdb (#1.1) chain l determined from SEQRES records
Termini for Tekt5A_RelTek5A.pdb (#1.1) chain m determined from SEQRES records
Chain-initial residues that are actual N termini: /k THR 172, /l ARG 89, /m
ARG 89
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: /k PRO 477, /l PRO 477, /m PRO
477
Chain-final residues that are not actual C termini:
1087 hydrogen bonds
0 hydrogens added
> hide HC
> select #1
16434 atoms, 16533 bonds, 4 pseudobonds, 19 models selected
> clipper isolate #1 maskRadius 16
> show ~HC
> isolde restrain distances "#1/k,l,m"
> usage isolde restrain
isolde restrain distances atoms [templateAtoms templateAtoms] [protein true or
false] [nucleic true or false] [customAtomNames customAtomNames] [perChain
true or false] [distanceCutoff a number] [alignmentCutoff a number]
[wellHalfWidth a number] [kappa a number] [tolerance a number] [fallOff a
number] [displayThreshold a number]
— Restrain interatomic distances to current values or a template.
atoms: some atoms specifiers
templateAtoms: some atoms specifiers
customAtomNames: some text strings
isolde restrain ligands models [distanceCutoff a number] [maxHeavyAtoms an
integer] [springConstant a number] [bondToCarbon true or false]
— Restrain small ligands to their surroundings and/or current positions. If
less than four distance restraints can be made for a given residue, they will
be supplemented with position restraints.
isolde restrain single distance atoms minDist maxDist [strength a number]
[wellHalfWidth a number] [confidence a number]
— Create a single adaptive distance restraint
minDist: a number
maxDist: a number
isolde restrain torsions residues [templateResidues a residues specifier]
[backbone true or false] [sidechains true or false] [angleRange a number]
[springConstant a number] [identicalSidechainsOnly true or false]
— Restrain amino acid backbone and/or sidechain torsions to their current
values or to those of a template model of identical or homologous sequence.
> isolde restrain distances "#1/k,l,m"
> usage isolde restrain
isolde restrain distances atoms [templateAtoms templateAtoms] [protein true or
false] [nucleic true or false] [customAtomNames customAtomNames] [perChain
true or false] [distanceCutoff a number] [alignmentCutoff a number]
[wellHalfWidth a number] [kappa a number] [tolerance a number] [fallOff a
number] [displayThreshold a number]
— Restrain interatomic distances to current values or a template.
atoms: some atoms specifiers
templateAtoms: some atoms specifiers
customAtomNames: some text strings
isolde restrain ligands models [distanceCutoff a number] [maxHeavyAtoms an
integer] [springConstant a number] [bondToCarbon true or false]
— Restrain small ligands to their surroundings and/or current positions. If
less than four distance restraints can be made for a given residue, they will
be supplemented with position restraints.
isolde restrain single distance atoms minDist maxDist [strength a number]
[wellHalfWidth a number] [confidence a number]
— Create a single adaptive distance restraint
minDist: a number
maxDist: a number
isolde restrain torsions residues [templateResidues a residues specifier]
[backbone true or false] [sidechains true or false] [angleRange a number]
[springConstant a number] [identicalSidechainsOnly true or false]
— Restrain amino acid backbone and/or sidechain torsions to their current
values or to those of a template model of identical or homologous sequence.
> select #1
16434 atoms, 16533 bonds, 4 pseudobonds, 19 models selected
> isolde sim start sel
Simulation already running!
> select #1
16434 atoms, 16533 bonds, 4 pseudobonds, 19 models selected
> isolde sim start sel
> close #1.3#1#1.1-2
> open /home/YinGL/M_S/MS_modelbuilding_for_coot/Tekt5B_RelTek5B.pdb
Chain information for Tekt5B_RelTek5B.pdb #1
---
Chain | Description
g | No description available
h i | No description available
j | No description available
Chain information for Tekt5B_RelTek5B.pdb
---
Chain | Description
1.1/g | No description available
1.1/h 1.1/i | No description available
1.1/j | No description available
> open /home/YinGL/M_S/MS_modelbuilding_for_coot/Tekt5B.mrc
Opened Tekt5B.mrc, grid size 200,200,200, pixel 1.76, shown at level 1.26e-06,
step 1, values float32
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode zoom
> volume #2 level 0.004387
> select up
Nothing selected
> select up
Nothing selected
> select up
Nothing selected
> select up
Nothing selected
> select up
Nothing selected
> clipper associate #2 toModel #1
> set silhouettes false
> delete ~protein
> addh
Summary of feedback from adding hydrogens to Tekt5B_RelTek5B.pdb #1.1
---
notes | No usable SEQRES records for Tekt5B_RelTek5B.pdb (#1.1) chain g;
guessing termini instead
No usable SEQRES records for Tekt5B_RelTek5B.pdb (#1.1) chain h; guessing
termini instead
No usable SEQRES records for Tekt5B_RelTek5B.pdb (#1.1) chain i; guessing
termini instead
No usable SEQRES records for Tekt5B_RelTek5B.pdb (#1.1) chain j; guessing
termini instead
Chain-initial residues that are actual N termini: /g ARG 1, /h ARG 1, /i ARG
1, /j PRO 1
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: /h PRO 389, /i PRO 389, /j PRO
178
Chain-final residues that are not actual C termini: /g ILE 160
1261 hydrogen bonds
/g ILE 160 is not terminus, removing H atom from 'C'
9164 hydrogens added
> hide HC
> select #1
18329 atoms, 18452 bonds, 12 models selected
> clipper isolate #1 maskRadius 16
> show ~HC
> isolde restrain distances "#1/g-j"
> usage isolde restrain
isolde restrain distances atoms [templateAtoms templateAtoms] [protein true or
false] [nucleic true or false] [customAtomNames customAtomNames] [perChain
true or false] [distanceCutoff a number] [alignmentCutoff a number]
[wellHalfWidth a number] [kappa a number] [tolerance a number] [fallOff a
number] [displayThreshold a number]
— Restrain interatomic distances to current values or a template.
atoms: some atoms specifiers
templateAtoms: some atoms specifiers
customAtomNames: some text strings
isolde restrain ligands models [distanceCutoff a number] [maxHeavyAtoms an
integer] [springConstant a number] [bondToCarbon true or false]
— Restrain small ligands to their surroundings and/or current positions. If
less than four distance restraints can be made for a given residue, they will
be supplemented with position restraints.
isolde restrain single distance atoms minDist maxDist [strength a number]
[wellHalfWidth a number] [confidence a number]
— Create a single adaptive distance restraint
minDist: a number
maxDist: a number
isolde restrain torsions residues [templateResidues a residues specifier]
[backbone true or false] [sidechains true or false] [angleRange a number]
[springConstant a number] [identicalSidechainsOnly true or false]
— Restrain amino acid backbone and/or sidechain torsions to their current
values or to those of a template model of identical or homologous sequence.
> select #1
18329 atoms, 18452 bonds, 13 models selected
> isolde sim start sel
> select #1
18329 atoms, 18452 bonds, 18 models selected
> isolde sim start sel
Simulation already running!
> select #1
18329 atoms, 18452 bonds, 18 models selected
> isolde sim start sel
> close #1.3#1#1.1-2
> open /home/YinGL/M_S/BTube7.jpg
Unrecognized file suffix '.jpg'
> open /home/YinGL/M_S/Relion_Btube_7A/run_class001.mrc
Opened run_class001.mrc, grid size 200,200,200, pixel 1.76, shown at level
0.295, step 1, values float32
Traceback (most recent call last):
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/home/YinGL/.local/share/ChimeraX/0.92/site-
packages/chimerax/isolde/isolde.py", line 1027, in _update_model_list
self._update_sim_control_button_states()
File "/home/YinGL/.local/share/ChimeraX/0.92/site-
packages/chimerax/isolde/isolde.py", line 1127, in
_update_sim_control_button_states
self._selection_changed()
File "/home/YinGL/.local/share/ChimeraX/0.92/site-
packages/chimerax/isolde/isolde.py", line 1062, in _selection_changed
self._clear_rotamer()
File "/home/YinGL/.local/share/ChimeraX/0.92/site-
packages/chimerax/isolde/isolde.py", line 2092, in _clear_rotamer
rrm = session_extensions.get_rotamer_restraint_mgr(self.selected_model)
File "/home/YinGL/.local/share/ChimeraX/0.92/site-
packages/chimerax/isolde/session_extensions.py", line 81, in
get_rotamer_restraint_mgr
return RotamerRestraintMgr(model)
File "/home/YinGL/.local/share/ChimeraX/0.92/site-
packages/chimerax/isolde/molobject.py", line 3939, in __init__
session=model.session
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 43, in _getattr_
return base.__getattr__(self, attr_name, look_in_class=base)
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
AttributeError: 'Structure' object has no attribute 'session'
Error processing trigger "add models":
AttributeError: 'Structure' object has no attribute 'session'
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
Exception ignored in: <function Drawing.__del__ at 0x7f260aaebcb0>
Traceback (most recent call last):
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1111, in __del__
if not self.was_deleted:
AttributeError: 'RotamerRestraintMgr' object has no attribute 'was_deleted'
OpenGL version: 3.3.0 NVIDIA 515.76
OpenGL renderer: NVIDIA GeForce GTX 1080/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Change History (2)
comment:1 by , 3 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Third Party |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → ISOLDE: dead Structure model |
comment:2 by , 3 years ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
... what. Why on earth would a user be installing ISOLDE into ChimeraX 0.92 today?? Anyway, I'm pretty sure all of this is long since dealt with.
Note:
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This was only the last error of several (first was a recursive repaint), so conceivably could be reassigned.