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Opened 5 years ago
Last modified 5 years ago
#3492 assigned enhancement
Try to continue on past session-restore error
| Reported by: | Tristan Croll | Owned by: | Greg Couch |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sessions | Version: | |
| Keywords: | Cc: | chimera-programmers | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-3.10.0-1127.13.1.el7.x86_64-x86_64-with-centos-7.8.2003-Core
ChimeraX Version: 1.0 (2020-06-04 23:15:07 UTC)
Description
If a class raises an error while restoring a session, would it be technically feasible for the restore to attempt to continue on without that object or anything that depends on it? I ran into that the other day (clearly a bug in my own code, and I think I know the source: if I create a distance restraint between two atoms and then later create a bond between them, the distance restraint will not be deleted - so gets saved with the session - but will refuse to re-create itself leading to a mismatch between the number of restraints and their saved parameters). I'll fix that - but perhaps it would be friendlier to the user in such cases for ChimeraX to still load what it can so they can salvage the model.
Log:
UCSF ChimeraX version: 1.0 (2020-06-04)
© 2016-2020 Regents of the University of California. All rights reserved.
> open working.cxs
restore_snapshot for "RotamerRestraintMgr" returned None
registering illegal selector name "3nd"
Log from Wed Jul 8 20:37:32 2020UCSF ChimeraX version: 1.0 (2020-06-04)
© 2016-2020 Regents of the University of California. All rights reserved.
> open ready_all_maps_masked.cxs
restore_snapshot for "RotamerRestraintMgr" returned None
registering illegal selector name "3nd"
Log from Wed Jul 8 11:32:30 2020UCSF ChimeraX version: 1.0 (2020-06-04)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> N_module_from_3NDsubunits_from_Qsite_from_CIVknee_from_CIV_butt_from_CIII_coot_edited_7July20_.cif
Summary of feedback from opening
N_module_from_3NDsubunits_from_Qsite_from_CIVknee_from_CIV_butt_from_CIII_coot_edited_7July20_.cif
---
warnings | Unknown polymer entity '1' near line 334
Unknown polymer entity '2' near line 2534
Unknown polymer entity '3' near line 5212
Unknown polymer entity '4' near line 8363
Unknown polymer entity '5' near line 15002
25 messages similar to the above omitted
Atom H1 is not in the residue template for MET /A:1
Atom H1 is not in the residue template for LEU /B:14
Atom H3 is not in the residue template for ALA /C:4
Atom H3 is not in the residue template for ASP /D:2
Atom HH11 is not in the residue template for 2MR /D:65
Atom H1 is not in the residue template for MET /E:1
Atom H3 is not in the residue template for GLN /E:9
Atom H3 is not in the residue template for ALA /G:2
Atom H1 is not in the residue template for ALA /H:2
Atom H4 is not in the residue template for P5S /H:1003
Atom H1 is not in the residue template for ALA /I:2
Atom H1 is not in the residue template for MET /J:1
Atom H1 is not in the residue template for MET /K:1
Atom H1 is not in the residue template for MET /M:1
Atom H363 is not in the residue template for 3PH /M:2007
Atom H3 is not in the residue template for ALA /P:3
Atom H1 is not in the residue template for MET /Q:1
Atom H1 is not in the residue template for THR /Z:2
Atom H4 is not in the residue template for P5S /a:1017
Atom H1 is not in the residue template for ALA /b:212
Atom H1 is not in the residue template for ALA /e:212
Atom H1 is not in the residue template for GLN /h:30
Atom H1 is not in the residue template for ALA /i:2
Atom H3 is not in the residue template for THR /j:8
Atom H1 is not in the residue template for GLN /l:30
Atom H1 is not in the residue template for ALA /m:2
Atom H1 is not in the residue template for THR /n:8
Atom H3 is not in the residue template for PHE /o:2
Atom H1 is not in the residue template for PHE /p:2
Atom H1 is not in the residue template for MET /q:1
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Chain information for
N_module_from_3NDsubunits_from_Qsite_from_CIVknee_from_CIV_butt_from_CIII_coot_edited_7July20_.cif
#1
---
Chain | Description
A | ?
B | ?
C | ?
D | ?
E | ?
F | ?
G | ?
H | ?
I | ?
J | ?
K | ?
L | ?
M | ?
N | ?
P | ?
Q | ?
R | ?
Z | ?
a | ?
b e | ?
c | ?
d | ?
f | ?
g k | ?
h l | ?
i m | ?
j n | ?
o | ?
p | ?
q | ?
> hide HC
> name nmodule /E,F,G,Q,R,X
> select nmodule
22840 atoms, 23089 bonds, 19 pseudobonds, 2 models selected
> select clear
> select clear
> open
> /run/media/tic20/storage/structure_dump/cimr/yaikhomba/mar_2020/N-module_job1637/375_Box_postprocess_Default_Bfactor_1_048pix_job1637.mrc
Opened 375_Box_postprocess_Default_Bfactor_1_048pix_job1637.mrc, grid size
375,375,375, pixel 1.05, shown at level 0.0138, step 2, values float32
> ui tool 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 nmodule
22840 atoms, 23089 bonds, 19 pseudobonds, 2 models selected
> usage volume zone
volume zone volumes nearAtoms an atoms specifier [range a number]
[bondPointSpacing a number] [minimalBounds true or false] [newMap true or
false] [invert true or false] [subregion map region] [step map step] [modelId
modelId]
— Zero map values beyond a distance range from atoms
modelId: a model id
> volume zone #2 nearAtoms nmodule range 12 minimalBounds true
> select clear
> name qmodule /A,B,C,D,H,I,J,K,P,Q,Z,q,X
> select qmodule
40981 atoms, 41451 bonds, 12 pseudobonds, 2 models selected
Opened 375_Box_postprocess_Default_Bfactor_1_048pix_job1605.mrc, grid size
375,375,375, pixel 1.05, shown at level 0.0172, step 2, values float32
> volume zone #2 nearAtoms nmodule range 12 minimalBounds true newMap true
> close #2
> hide #!4 models
> show #!4 models
> hide #!3 models
> hide #!4 models
> show #!4 models
> volume #3 level 0.02358
> open
> /run/media/tic20/storage/structure_dump/cimr/yaikhomba/mar_2020/Q_module_job1605/375_Box_postprocess_Default_Bfactor_1_048pix_job1605.mrc
Opened Q module, grid size 375,375,375, pixel 1.05, shown at level 0.0172,
step 2, values float32
> close #2-4
> open
> /run/media/tic20/storage/structure_dump/cimr/yaikhomba/mar_2020/N-module_job1637/375_Box_postprocess_Default_Bfactor_1_048pix_job1637.mrc
Opened 375_Box_postprocess_Default_Bfactor_1_048pix_job1637.mrc, grid size
375,375,375, pixel 1.05, shown at level 0.0138, step 2, values float32
> volume zone #2 nearAtoms nmodule range 12 minimalBounds true newMap true
> close #2
> select clear
> volume #3 level 0.02347
Opened 375_Box_postprocess_Default_Bfactor_1_048pix_job1605.mrc, grid size
375,375,375, pixel 1.05, shown at level 0.0172, step 2, values float32
> volume zone #2 nearAtoms qmodule range 12 minimalBounds true newMap true
> close #2
> hide #!4 models
> show #!4 models
> volume #4 level 0.02544
> usage volume zone
volume zone volumes nearAtoms an atoms specifier [range a number]
[bondPointSpacing a number] [minimalBounds true or false] [newMap true or
false] [invert true or false] [subregion map region] [step map step] [modelId
modelId]
— Zero map values beyond a distance range from atoms
modelId: a model id
> name 3nd /L,M,N
registering illegal selector name "3nd"
> name threend /L,M,N
Opened 375_Box_postprocess_Default_Bfactor_1_048pix_job1636.mrc, grid size
375,375,375, pixel 1.05, shown at level 0.0146, step 2, values float32
> volume zone #2 nearAtoms threend range 12 minimalBounds true newMap true
> close #2
> volume #5 level 0.02051
> name ciiic /a,b,c,d,e,f,o,p,y,z
Opened 375_box_Default_Bfactor_1048pix_postprocess_job1613.mrc, grid size
375,375,375, pixel 1.05, shown at level 0.0163, step 2, values float32
> volume zone #2 nearAtoms ciiic range 12 minimalBounds true newMap true
> close #2
> volume #5 level 0.01698
> volume #6 level 0.03273
> name civknee /g,h,i,j
Opened 375_Box_postprocess_Default_Bfactor_1_048pix_job1646.mrc, grid size
375,375,375, pixel 1.05, shown at level 0.0136, step 2, values float32
> volume zone #2 nearAtoms civknee range 12 minimalBounds true newMap true
> volume #7 level 0.01537
> close #2
> name civbutt /g,h,i,j
> name civknee /k,l,m,n,o
> close #7
Opened 375_Box_Default_Bfactor_1048pix_postprocess_job1619.mrc, grid size
375,375,375, pixel 1.05, shown at level 0.011, step 2, values float32
> volume zone #2 nearAtoms civbutt range 12 minimalBounds true newMap true
> volume #7 level 0.01555
> close #2
Opened 375_Box_postprocess_Default_Bfactor_1_048pix_job1646.mrc, grid size
375,375,375, pixel 1.05, shown at level 0.0136, step 2, values float32
> volume zone #2 nearAtoms civknee range 12 minimalBounds true newMap true
> volume #8 level 0.02758
> close #2
> clipper associate #3-8 toModel #1
Chain information for
N_module_from_3NDsubunits_from_Qsite_from_CIVknee_from_CIV_butt_from_CIII_coot_edited_7July20_.cif
---
Chain | Description
1.2/A | ?
1.2/B | ?
1.2/C | ?
1.2/D | ?
1.2/E | ?
1.2/F | ?
1.2/G | ?
1.2/H | ?
1.2/I | ?
1.2/J | ?
1.2/K | ?
1.2/L | ?
1.2/M | ?
1.2/N | ?
1.2/P | ?
1.2/Q | ?
1.2/R | ?
1.2/Z | ?
1.2/a | ?
1.2/b 1.2/e | ?
1.2/c | ?
1.2/d | ?
1.2/f | ?
1.2/g 1.2/k | ?
1.2/h 1.2/l | ?
1.2/i 1.2/m | ?
1.2/j 1.2/n | ?
1.2/o | ?
1.2/p | ?
1.2/q | ?
> isolde start
> set selectionWidth 4
Done loading forcefield
> select nmodule
22840 atoms, 23089 bonds, 19 pseudobonds, 2 models selected
> select 1module
Expected an objects specifier or a keyword
> select qmodule
40981 atoms, 41451 bonds, 12 pseudobonds, 2 models selected
> select clear
> select threend
28780 atoms, 29111 bonds, 2 pseudobonds, 2 models selected
> select clear
> select ciiic
34200 atoms, 34630 bonds, 32 pseudobonds, 3 models selected
> select clear
> select civbutt
21188 atoms, 21475 bonds, 15 pseudobonds, 2 models selected
> select clear
> select civknee
22294 atoms, 22584 bonds, 17 pseudobonds, 3 models selected
> select nmodule
22840 atoms, 23089 bonds, 19 pseudobonds, 2 models selected
> select qmodule
40981 atoms, 41451 bonds, 12 pseudobonds, 2 models selected
> clipper set contourSensitivity 0.25
> select threend
28780 atoms, 29111 bonds, 2 pseudobonds, 2 models selected
> set bgColor white
> select ciiic
34200 atoms, 34630 bonds, 32 pseudobonds, 3 models selected
> select civknee
22294 atoms, 22584 bonds, 17 pseudobonds, 3 models selected
> select civbutt
21188 atoms, 21475 bonds, 15 pseudobonds, 2 models selected
> select civknee
22294 atoms, 22584 bonds, 17 pseudobonds, 3 models selected
> select clear
> save ready_all_maps_masked.cxs
opened ChimeraX session
> isolde start
> set selectionWidth 4
Done loading forcefield
> select clear
Failed to add
/run/media/tic20/storage/structure_dump/cimr/yaikhomba/ligands/CDL.xml:
Residue template USER_CDL with the same override level 0 already exists.
Failed to add
/run/media/tic20/storage/structure_dump/cimr/yaikhomba/ligands/cua.xml: Found
multiple definitions for atom type: CUA_Cu
Failed to add
/run/media/tic20/storage/structure_dump/cimr/yaikhomba/ligands/EHZ.xml:
Residue template USER_EHZ with the same override level 0 already exists.
Failed to add
/run/media/tic20/storage/structure_dump/cimr/yaikhomba/ligands/hea.xml:
Residue template USER_HEA with the same override level 0 already exists.
Failed to add
/run/media/tic20/storage/structure_dump/cimr/yaikhomba/ligands/hec.xml:
Residue template USER_HEC with the same override level 0 already exists.
Failed to add
/run/media/tic20/storage/structure_dump/cimr/yaikhomba/ligands/NDP.xml:
Residue template USER_NDP with the same override level 0 already exists.
Failed to add
/run/media/tic20/storage/structure_dump/cimr/yaikhomba/ligands/P5S.xml:
Residue template USER_P5S with the same override level 0 already exists.
Failed to add
/run/media/tic20/storage/structure_dump/cimr/yaikhomba/ligands/PC1.xml:
Residue template USER_PC1 with the same override level 0 already exists.
Failed to add
/run/media/tic20/storage/structure_dump/cimr/yaikhomba/ligands/T7X.xml:
Residue template USER_T7X with the same override level 0 already exists.
Failed to add
/run/media/tic20/storage/structure_dump/cimr/yaikhomba/ligands/U10.xml:
Residue template USER_U10 with the same override level 0 already exists.
> ui tool 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")
Loading residue template for 3PE from internal database
Loading residue template for 3PH from internal database
Loading residue template for FMN from internal database
Loading residue template for PGT from internal database
> select clear
> preset custom "make bond"
> open /home/tic20/chimerax_presets/make_bond.py
executed make_bond.py
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset custom "make bond"
> open /home/tic20/chimerax_presets/make_bond.py
executed make_bond.py
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset custom "make bond"
> open /home/tic20/chimerax_presets/make_bond.py
executed make_bond.py
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset custom "make bond"
> open /home/tic20/chimerax_presets/make_bond.py
executed make_bond.py
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset custom "make bond"
> open /home/tic20/chimerax_presets/make_bond.py
executed make_bond.py
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset custom "make bond"
> open /home/tic20/chimerax_presets/make_bond.py
executed make_bond.py
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset custom "make bond"
> open /home/tic20/chimerax_presets/make_bond.py
executed make_bond.py
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset custom "make bond"
> open /home/tic20/chimerax_presets/make_bond.py
executed make_bond.py
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset custom "make bond"
> open /home/tic20/chimerax_presets/make_bond.py
executed make_bond.py
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset custom "make bond"
> open /home/tic20/chimerax_presets/make_bond.py
executed make_bond.py
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset custom "make bond"
> open /home/tic20/chimerax_presets/make_bond.py
executed make_bond.py
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset custom "make bond"
> open /home/tic20/chimerax_presets/make_bond.py
executed make_bond.py
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset custom "make bond"
> open /home/tic20/chimerax_presets/make_bond.py
executed make_bond.py
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset custom "make bond"
> open /home/tic20/chimerax_presets/make_bond.py
executed make_bond.py
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset custom "make bond"
> open /home/tic20/chimerax_presets/make_bond.py
executed make_bond.py
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset custom "make bond"
> open /home/tic20/chimerax_presets/make_bond.py
executed make_bond.py
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset custom "make bond"
> open /home/tic20/chimerax_presets/make_bond.py
executed make_bond.py
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset custom "make bond"
> open /home/tic20/chimerax_presets/make_bond.py
executed make_bond.py
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset custom "make bond"
> open /home/tic20/chimerax_presets/make_bond.py
executed make_bond.py
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset custom "make bond"
> open /home/tic20/chimerax_presets/make_bond.py
executed make_bond.py
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset custom "make bond"
> open /home/tic20/chimerax_presets/make_bond.py
executed make_bond.py
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset custom "make bond"
> open /home/tic20/chimerax_presets/make_bond.py
executed make_bond.py
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset custom "make bond"
> open /home/tic20/chimerax_presets/make_bond.py
executed make_bond.py
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset custom "make bond"
> open /home/tic20/chimerax_presets/make_bond.py
executed make_bond.py
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset custom "make bond"
> open /home/tic20/chimerax_presets/make_bond.py
executed make_bond.py
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset custom "make bond"
> open /home/tic20/chimerax_presets/make_bond.py
executed make_bond.py
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset custom "make bond"
> open /home/tic20/chimerax_presets/make_bond.py
executed make_bond.py
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset custom "make bond"
> open /home/tic20/chimerax_presets/make_bond.py
executed make_bond.py
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset custom "make bond"
> open /home/tic20/chimerax_presets/make_bond.py
executed make_bond.py
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset custom "make bond"
> open /home/tic20/chimerax_presets/make_bond.py
executed make_bond.py
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset custom "make bond"
> open /home/tic20/chimerax_presets/make_bond.py
executed make_bond.py
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset custom "make bond"
> open /home/tic20/chimerax_presets/make_bond.py
executed make_bond.py
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset custom "make bond"
> open /home/tic20/chimerax_presets/make_bond.py
executed make_bond.py
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset custom "make bond"
> open /home/tic20/chimerax_presets/make_bond.py
executed make_bond.py
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset custom "make bond"
> open /home/tic20/chimerax_presets/make_bond.py
executed make_bond.py
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset custom "make bond"
> open /home/tic20/chimerax_presets/make_bond.py
executed make_bond.py
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset custom "make bond"
> open /home/tic20/chimerax_presets/make_bond.py
executed make_bond.py
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> delete sel
> preset custom "make bond"
> open /home/tic20/chimerax_presets/make_bond.py
executed make_bond.py
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset custom "make bond"
> open /home/tic20/chimerax_presets/make_bond.py
executed make_bond.py
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset custom "make bond"
> open /home/tic20/chimerax_presets/make_bond.py
executed make_bond.py
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset custom "make bond"
> open /home/tic20/chimerax_presets/make_bond.py
executed make_bond.py
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset custom "make bond"
> open /home/tic20/chimerax_presets/make_bond.py
executed make_bond.py
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset custom "make bond"
> open /home/tic20/chimerax_presets/make_bond.py
executed make_bond.py
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset custom "make bond"
> open /home/tic20/chimerax_presets/make_bond.py
executed make_bond.py
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset custom "make bond"
> open /home/tic20/chimerax_presets/make_bond.py
executed make_bond.py
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset custom "make bond"
> open /home/tic20/chimerax_presets/make_bond.py
executed make_bond.py
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset custom "make bond"
> open /home/tic20/chimerax_presets/make_bond.py
executed make_bond.py
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset custom "make bond"
> open /home/tic20/chimerax_presets/make_bond.py
executed make_bond.py
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset custom "make bond"
> open /home/tic20/chimerax_presets/make_bond.py
executed make_bond.py
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset custom "make bond"
> open /home/tic20/chimerax_presets/make_bond.py
executed make_bond.py
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset custom "make bond"
> open /home/tic20/chimerax_presets/make_bond.py
executed make_bond.py
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset custom "make bond"
> open /home/tic20/chimerax_presets/make_bond.py
executed make_bond.py
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset custom "make bond"
> open /home/tic20/chimerax_presets/make_bond.py
executed make_bond.py
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset custom "make bond"
> open /home/tic20/chimerax_presets/make_bond.py
executed make_bond.py
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> delete sel
> isolde ignore sel
ISOLDE: currently ignoring 1 residues in model 1.2
> isolde restrain distances ~sel kappa 40
> select #1
167690 atoms, 169773 bonds, 95 pseudobonds, 35 models selected
> select clear
> select clear
> select clear
> select clear
> select clear
> select clear
> select ciiic
34200 atoms, 34654 bonds, 32 pseudobonds, 3 models selected
> select civbutt
21186 atoms, 21488 bonds, 15 pseudobonds, 2 models selected
> select civknee
22292 atoms, 22597 bonds, 17 pseudobonds, 3 models selected
> select threend
28780 atoms, 29111 bonds, 2 pseudobonds, 2 models selected
> select civbutt
21186 atoms, 21488 bonds, 15 pseudobonds, 2 models selected
> select clear
> close #1.2.11
> view /A:280
No objects specified.
> open 3hb3
3hb3 title:
High resolution crystal structure of Paracoccus denitrificans cytochrome c
oxidase [more info...]
Chain information for 3hb3 #2
---
Chain | Description
A | Cytochrome c oxidase subunit 1-beta
B | Cytochrome c oxidase subunit 2
C | antibody FV fragment
D | antibody FV fragment
Non-standard residues in 3hb3 #2
---
CA — calcium ion
CU1 — copper (I) ion
HEA — heme-A
LDA — lauryl dimethylamine-N-oxide
LMT — dodecyl-β-D-maltoside
MN — manganese (II) ion
PEO — hydrogen peroxide
> matchmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker
N_module_from_3NDsubunits_from_Qsite_from_CIVknee_from_CIV_butt_from_CIII_coot_edited_7July20_.cif,
chain g (#1.2) with 3hb3, chain A (#2), sequence alignment score = 2889.7
RMSD between 523 pruned atom pairs is 0.486 angstroms; (across all 529 pairs:
0.619)
> view #2/A:280
> ui mousemode right distance
> distance #2/A:276@NE2 #2/A:280@CE2
Distance between 3hb3 #2/A HIS 276 NE2 and TYR 280 CE2: 1.521Å
> delete sel
> delete sel
> hide #!1 models
> ui mousemode right distance
> distance #2/A:276@ND1 #2/A:561@CU
Distance between 3hb3 #2/A HIS 276 ND1 and CU1 561 CU: 2.022Å
> distance #2/A:325@NE2 #2/A:561@CU
Distance between 3hb3 #2/A HIS 325 NE2 and CU1 561 CU: 2.026Å
> distance #2/A:326@NE2 #2/A:561@CU
Distance between 3hb3 #2/A HIS 326 NE2 and CU1 561 CU: 2.023Å
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> select clear
> show #!2 models
> select clear
> hide #!2 models
> hide #!3 models
> select up
213 atoms, 219 bonds, 1 model selected
> select up
10119 atoms, 10283 bonds, 1 model selected
> select down
213 atoms, 219 bonds, 1 model selected
> select clear
> select /U10
Nothing selected
> select :U10
765 atoms, 765 bonds, 1 model selected
> select #1:U10
765 atoms, 765 bonds, 1 model selected
> select clear
> view sel
> select clear
> select up
153 atoms, 153 bonds, 1 model selected
> show sel
> select clear
Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.
> select clear
> view sel
> show sel
> select clear
Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.
Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.
Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.
> select clear
> view sel
> show sel
> select clear
Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.
Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.
> select up
123 atoms, 122 bonds, 1 model selected
> select up
123 atoms, 122 bonds, 1 model selected
> isolde ignore ~sel
ISOLDE: currently ignoring 1593 residues in model 2
ISOLDE: currently ignoring 9676 residues in model 1.2
> select clear
> isolde ~ignore
> isolde add ligand CDL
> color sel bychain
> color sel byhetero
> isolde ignore ~sel
ISOLDE: currently ignoring 1593 residues in model 2
ISOLDE: currently ignoring 9677 residues in model 1.2
Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.
Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.
Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.
Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.
Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.
Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.
Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.
Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.
> select up
123 atoms, 122 bonds, 1 model selected
> select up
123 atoms, 122 bonds, 1 model selected
> select up
246 atoms, 244 bonds, 1 model selected
> delete sel
> isolde ~ignore
> select up
256 atoms, 255 bonds, 1 model selected
> isolde add ligand MG
> color sel bychain
> color sel byhetero
> ui mousemode right distance
> distance #1.2/a:1025@OA3 #1.2/a:1026@MG
Distance between
N_module_from_3NDsubunits_from_Qsite_from_CIVknee_from_CIV_butt_from_CIII_coot_edited_7July20_.cif
#1.2/a CDL 1025 OA3 and MG 1026 MG: 6.383Å
> show #!3 models
> select clear
> isolde add ligand SO$
Traceback (most recent call last):
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 258, in execute
cmd.run(cmd_text)
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File "/home/tic20/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/atomic/building/place_ligand.py", line 145, in
place_ligand
tmpl = mmcif.find_template_residue(session, ligand_id)
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/atomic/mmcif/mmcif.py", line 378, in find_template_residue
return _mmcif.find_template_residue(name)
ValueError: No template for residue type SO$
ValueError: No template for residue type SO$
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/atomic/mmcif/mmcif.py", line 378, in find_template_residue
return _mmcif.find_template_residue(name)
See log for complete Python traceback.
> isolde add ligand SO4
> color sel bychain
> color sel byhetero
> ~distances
Unknown command: ~distances
> ~distance
> ui mousemode right distance
> distance #1.2/a:1026@MG #1.2/d:1016@O2
Distance between
N_module_from_3NDsubunits_from_Qsite_from_CIVknee_from_CIV_butt_from_CIII_coot_edited_7July20_.cif
#1.2/a MG 1026 MG and /d SO4 1016 O2: 5.316Å
Loading residue template for SO4 from internal database
> select up
6 atoms, 4 bonds, 1 model selected
> delete sel
> pwd
Current working directory is:
/run/media/tic20/storage/structure_dump/cimr/yaikhomba/jul_2020
> save working.cxs
opened ChimeraX session
OpenGL version: 3.3.0 NVIDIA 450.36.06
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
Memory:
total used free shared buff/cache available
Mem: 62G 3.8G 51G 187M 7.1G 58G
Swap: 4.9G 0B 4.9G
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
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.8
Change History (3)
comment:1 by , 5 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Sessions |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Try to continue on past session-restore error |
| Type: | defect → enhancement |
comment:2 by , 5 years ago
follow-up: 3 comment:3 by , 5 years ago
Well... sort of. This is the related but opposite problem: the session *saved*, but throws an error on trying to *restore* it. On 2020-07-09 19:34, ChimeraX wrote:
Note:
See TracTickets
for help on using tickets.
Same request was made for salvaging session save 7 months ago #2638.