![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 2 years ago
Last modified 2 years ago
#10066 assigned defect
ISOLDE: stop sim: 'AdaptiveDistanceRestraintMgr' object has no attribute '_c_pointer'
| Reported by: | Owned by: | Tristan Croll | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Third Party | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-5.15.0-86-generic-x86_64-with-glibc2.31
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
This error upon clicking stop sim: Error processing trigger "sim terminated":
AttributeError: 'AdaptiveDistanceRestraintMgr' object has no attribute '_c_pointer'
File "/programs/x86_64-linux/chimerax/1.5_c8/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/isolde/molobject.py", line 2978, in intra_restraints
return self._plural_restraint_getter(f(self._c_pointer, atoms._c_pointers, n))
See log for complete Python traceback.
Log:
UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open
> /home/drichman/Documents/EXP36/2023-10_best_maps/sessions/2q2e_70bp_bulkfit_J530.cxs
Opened J530_005_map_flip_emready_1p4385apix_240box.mrc as #1.1.1.1, grid size
240,240,240, pixel 1.45, shown at level 3.43, step 1, values float32
Opened J530_005_volume_map_flip.mrc as #2.1.1.1, grid size 240,240,240, pixel
1.44, shown at level 0.241, step 1, values float32
Restoring stepper: 2q2e_comb_mapcent.pdb
Log from Tue Oct 24 16:53:55 2023UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open
> /home/drichman/Documents/EXP36/2023-10_best_maps/sessions/2q2e_bulkfit_J530.cxs
Opened J530_005_map_flip_emready_1p4385apix_240box.mrc as #1.1.1.1, grid size
240,240,240, pixel 1.45, shown at level 6.88, step 1, values float32
Restoring stepper: 2q2e_comb_mapcent.pdb
Log from Tue Oct 24 15:58:25 2023UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open 2q2e_aligned_withJ530_isolde.cxs
Opened J530_005_map_flip_emready_1p4385apix_240box.mrc as #1.1.1.1, grid size
240,240,240, pixel 1.45, shown at level 5.91, step 1, values float32
Log from Mon Oct 23 20:20:41 2023UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open
> /Users/drichman/Documents/EXP36/2023-10_best_maps/sessions/2q2e_aligned_withJ530.cxs
Opened J530_005_map_flip_emready_1p4385apix_240box.mrc as #2, grid size
240,240,240, pixel 1.45, shown at level 4.28, step 1, values float32
Log from Mon Oct 23 19:46:45 2023UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/drichman/Documents/EXP36/2023-10_best_maps/models/2q2e_mapcentered.cif
Summary of feedback from opening
/Users/drichman/Documents/EXP36/2023-10_best_maps/models/2q2e_mapcentered.cif
---
warnings | Unknown polymer entity '1' near line 10437
Unknown polymer entity '2' near line 12969
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Chain information for 2q2e_mapcentered.cif
---
Chain | Description
1.1/A | No description available
1.2/A | No description available
1.1/B | No description available
1.2/B | No description available
> open
> /Users/drichman/Documents/EXP36/2023-10_best_maps/maps/J530_005_map_flip_emready_1p4385apix_240box.mrc
Opened J530_005_map_flip_emready_1p4385apix_240box.mrc as #2, grid size
240,240,240, pixel 1.45, shown at level 0.248, step 1, values float32
> volume #2 level 4.281
> save
> /Users/drichman/Documents/EXP36/2023-10_best_maps/sessions/2q2e_aligned_withJ530.cxs
——— End of log from Mon Oct 23 19:46:45 2023 ———
opened ChimeraX session
> isolde start
> set selectionWidth 4
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 76 residues in model #1.1 to IUPAC-IUB
standards.
> clipper associate #2 toModel #3
Opened J530_005_map_flip_emready_1p4385apix_240box.mrc as #3.1.1.1, grid size
240,240,240, pixel 1.45, shown at step 1, values float32
> close
> open
> /Users/drichman/Documents/EXP36/2023-10_best_maps/models/2q2e_mapcentered.cif
Summary of feedback from opening
/Users/drichman/Documents/EXP36/2023-10_best_maps/models/2q2e_mapcentered.cif
---
warnings | Unknown polymer entity '1' near line 10437
Unknown polymer entity '2' near line 12969
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Chain information for 2q2e_mapcentered.cif
---
Chain | Description
1.1/A | No description available
1.2/A | No description available
1.1/B | No description available
1.2/B | No description available
> combine
Remapping chain ID 'A' in 2q2e_mapcentered.cif #1.2 to 'C'
Remapping chain ID 'B' in 2q2e_mapcentered.cif #1.2 to 'D'
> close #1
> select add #2
14078 atoms, 14340 bonds, 24 pseudobonds, 1794 residues, 2 models selected
> select subtract #2
Nothing selected
> select add #2
14078 atoms, 14340 bonds, 24 pseudobonds, 1794 residues, 2 models selected
> select subtract #2
Nothing selected
> close #2.1
> select add #2
14078 atoms, 14340 bonds, 1794 residues, 1 model selected
> select subtract #2
Nothing selected
> select add #2
14078 atoms, 14340 bonds, 1794 residues, 1 model selected
> select subtract #2
Nothing selected
> save
> /Users/drichman/Documents/EXP36/2023-10_best_maps/models/2q2e_combined_mapcentered.cif
> relModel #2
Not saving entity_poly_seq for non-authoritative sequences
> save
> /Users/drichman/Documents/EXP36/2023-10_best_maps/models/2q2e_combined_mapcentered_transfcoords.cif
Not saving entity_poly_seq for non-authoritative sequences
> close
> open
> /Users/drichman/Documents/EXP36/2023-10_best_maps/models/2q2e_combined_mapcentered.cif
Summary of feedback from opening
/Users/drichman/Documents/EXP36/2023-10_best_maps/models/2q2e_combined_mapcentered.cif
---
warnings | Unknown polymer entity '3' near line 10166
Unknown polymer entity '4' near line 12698
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Chain information for 2q2e_combined_mapcentered.cif #1
---
Chain | Description
A | No description available
B | No description available
> close
> open
> /Users/drichman/Documents/EXP36/2023-10_best_maps/models/2q2e_combined_mapcentered_transfcoords.cif
Summary of feedback from opening
/Users/drichman/Documents/EXP36/2023-10_best_maps/models/2q2e_combined_mapcentered_transfcoords.cif
---
warnings | Unknown polymer entity '3' near line 10166
Unknown polymer entity '4' near line 12698
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Chain information for 2q2e_combined_mapcentered_transfcoords.cif #1
---
Chain | Description
A | No description available
B | No description available
> close
> open
> /Users/drichman/Documents/EXP36/2023-10_best_maps/models/2q2e_mapcentered.cif
Summary of feedback from opening
/Users/drichman/Documents/EXP36/2023-10_best_maps/models/2q2e_mapcentered.cif
---
warnings | Unknown polymer entity '1' near line 10437
Unknown polymer entity '2' near line 12969
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Chain information for 2q2e_mapcentered.cif
---
Chain | Description
1.1/A | No description available
1.2/A | No description available
1.1/B | No description available
1.2/B | No description available
> combine close true
Remapping chain ID 'A' in 2q2e_mapcentered.cif #1.2 to 'C'
Remapping chain ID 'B' in 2q2e_mapcentered.cif #1.2 to 'D'
> select add #1
14078 atoms, 14340 bonds, 24 pseudobonds, 1794 residues, 2 models selected
> select subtract #1
Nothing selected
> log metadata #1
No models had metadata
> log chains #1
Chain information for combination #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
> close #1.1
> select add #1
14078 atoms, 14340 bonds, 1794 residues, 1 model selected
> select subtract #1
Nothing selected
> log metadata #1
The model has no metadata
> log chains #1
Chain information for combination #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
> save
> /Users/drichman/Documents/EXP36/2023-10_best_maps/models/2q2e_comb_mapcent.pdb
> relModel #1
> close
> open
> /Users/drichman/Documents/EXP36/2023-10_best_maps/models/2q2e_comb_mapcent.pdb
Chain information for 2q2e_comb_mapcent.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
> select /A:15-367
2532 atoms, 2579 bonds, 315 residues, 1 model selected
> select /B:11-616
4507 atoms, 4591 bonds, 582 residues, 1 model selected
> select /A:15-367
2532 atoms, 2579 bonds, 315 residues, 1 model selected
> select /B:11-616
4507 atoms, 4591 bonds, 582 residues, 1 model selected
> select /C:15-367
2532 atoms, 2579 bonds, 315 residues, 1 model selected
> select /D:11-616
4507 atoms, 4591 bonds, 582 residues, 1 model selected
> select /B:11-616
4507 atoms, 4591 bonds, 582 residues, 1 model selected
> select /D:11-616
4507 atoms, 4591 bonds, 582 residues, 1 model selected
> select clear
> open
> /Users/drichman/Documents/EXP36/2023-10_best_maps/maps/J530_005_map_flip_emready_1p4385apix_240box.mrc
Opened J530_005_map_flip_emready_1p4385apix_240box.mrc as #2, grid size
240,240,240, pixel 1.45, shown at level 0.248, step 1, values float32
> volume #2 level 5.941
> save
> /Users/drichman/Documents/EXP36/2023-10_best_maps/sessions/2q2e_aligned_withJ530.cxs
> addh
Summary of feedback from adding hydrogens to 2q2e_comb_mapcent.pdb #1
---
warnings | Not adding hydrogens to /B LYS 11 CB because it is missing heavy-
atom bond partners
Not adding hydrogens to /B LYS 12 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /B GLN 13 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /B LYS 14 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /B SER 15 CB because it is missing heavy-atom bond
partners
21 messages similar to the above omitted
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /B GLU 605 N; /D GLU 605 N; /B PRO 408 N; /D PRO 408 N
notes | Termini for 2q2e_comb_mapcent.pdb (#1) chain A determined from SEQRES
records
Termini for 2q2e_comb_mapcent.pdb (#1) chain B determined from SEQRES records
Termini for 2q2e_comb_mapcent.pdb (#1) chain C determined from SEQRES records
Termini for 2q2e_comb_mapcent.pdb (#1) chain D determined from SEQRES records
Chain-initial residues that are actual N termini: /C LEU 15, /D LYS 11
Chain-initial residues that are not actual N termini: /A LEU 15, /A SER 68, /A
THR 82, /A HIS 169, /A VAL 174, /A PHE 279, /B LYS 11, /B PHE 103, /B SER 109,
/B PRO 260, /B LEU 271, /B ALA 539, /B LYS 556, /B THR 613
Chain-final residues that are actual C termini: /C GLY 367, /D LYS 616
Chain-final residues that are not actual C termini: /A SER 43, /A LYS 80, /A
GLY 164, /A LYS 172, /A ALA 270, /A GLY 367, /B GLY 100, /B LYS 107, /B GLU
254, /B LYS 268, /B ASN 534, /B VAL 552, /B GLU 605, /B LYS 616
Missing OXT added to C-terminal residue /C GLY 367
Missing OXT added to C-terminal residue /D LYS 616
863 hydrogen bonds
Adding 'H' to /A LEU 15
Adding 'H' to /A SER 68
Adding 'H' to /A THR 82
Adding 'H' to /A HIS 169
Adding 'H' to /A VAL 174
8 messages similar to the above omitted
/A SER 43 is not terminus, removing H atom from 'C'
/A LYS 80 is not terminus, removing H atom from 'C'
/A GLY 164 is not terminus, removing H atom from 'C'
/A LYS 172 is not terminus, removing H atom from 'C'
/A ALA 270 is not terminus, removing H atom from 'C'
8 messages similar to the above omitted
14147 hydrogens added
> isolde start
> set selectionWidth 4
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 152 residues in model #1 to IUPAC-IUB
standards.
Chain information for 2q2e_comb_mapcent.pdb
---
Chain | Description
1.2/A | No description available
1.2/B | No description available
1.2/C | No description available
1.2/D | No description available
> clipper associate #2 toModel #1
Opened J530_005_map_flip_emready_1p4385apix_240box.mrc as #1.1.1.1, grid size
240,240,240, pixel 1.45, shown at step 1, values float32
> view matrix models #1.2,1,0,0,-0.42875,0,1,0,-1.1419,0,0,1,-30.888
> view matrix models #1.2,1,0,0,-0.27005,0,1,0,-0.19072,0,0,1,-0.14362
> isolde sim start sel
ISOLDE: stopped sim
Fetching CCD PRO_LL from http://ligand-
expo.rcsb.org/reports/P/PRO_LL/PRO_LL.cif
Fetching CCD ALA_LL from http://ligand-
expo.rcsb.org/reports/A/ALA_LL/ALA_LL.cif
Fetching CCD SER_LL_DHG from http://ligand-
expo.rcsb.org/reports/S/SER_LL_DHG/SER_LL_DHG.cif
Fetching CCD SER_LL from http://ligand-
expo.rcsb.org/reports/S/SER_LL/SER_LL.cif
Fetching CCD ALA_LEO2 from http://ligand-
expo.rcsb.org/reports/A/ALA_LEO2/ALA_LEO2.cif
Fetching CCD SER_LSN3_DHG from http://ligand-
expo.rcsb.org/reports/S/SER_LSN3_DHG/SER_LSN3_DHG.cif
Fetching CCD ALA_LFZW from http://ligand-
expo.rcsb.org/reports/A/ALA_LFZW/ALA_LFZW.cif
Fetching CCD CYS_LL_DHG from http://ligand-
expo.rcsb.org/reports/C/CYS_LL_DHG/CYS_LL_DHG.cif
Fetching CCD THR_LL_DHG1 from http://ligand-
expo.rcsb.org/reports/T/THR_LL_DHG1/THR_LL_DHG1.cif
Fetching CCD SER_LEO2_DHG from http://ligand-
expo.rcsb.org/reports/S/SER_LEO2_DHG/SER_LEO2_DHG.cif
Fetching CCD CYS_LL from http://ligand-
expo.rcsb.org/reports/C/CYS_LL/CYS_LL.cif
Fetching CCD THR_LL from http://ligand-
expo.rcsb.org/reports/T/THR_LL/THR_LL.cif
Fetching CCD VAL_LL from http://ligand-
expo.rcsb.org/reports/V/VAL_LL/VAL_LL.cif
Fetching CCD SER_LEO2 from http://ligand-
expo.rcsb.org/reports/S/SER_LEO2/SER_LEO2.cif
Fetching CCD CYS_LSN3_DHG from http://ligand-
expo.rcsb.org/reports/C/CYS_LSN3_DHG/CYS_LSN3_DHG.cif
Fetching CCD THR_LSN3_DHG1 from http://ligand-
expo.rcsb.org/reports/T/THR_LSN3_DHG1/THR_LSN3_DHG1.cif
Fetching CCD SER_LFZW_DHG from http://ligand-
expo.rcsb.org/reports/S/SER_LFZW_DHG/SER_LFZW_DHG.cif
Fetching CCD SER_LFZW from http://ligand-
expo.rcsb.org/reports/S/SER_LFZW/SER_LFZW.cif
Fetching CCD PCA from http://ligand-expo.rcsb.org/reports/P/PCA/PCA.cif
Fetching CCD ASP_LL_DHD2 from http://ligand-
expo.rcsb.org/reports/A/ASP_LL_DHD2/ASP_LL_DHD2.cif
Fetching CCD ASN_LL from http://ligand-
expo.rcsb.org/reports/A/ASN_LL/ASN_LL.cif
Fetching CCD ASP_LL from http://ligand-
expo.rcsb.org/reports/A/ASP_LL/ASP_LL.cif
Fetching CCD PRO_LEO2 from http://ligand-
expo.rcsb.org/reports/P/PRO_LEO2/PRO_LEO2.cif
Fetching CCD HY3 from http://ligand-expo.rcsb.org/reports/H/HY3/HY3.cif
Fetching CCD CYS_LEO2_DHG from http://ligand-
expo.rcsb.org/reports/C/CYS_LEO2_DHG/CYS_LEO2_DHG.cif
Fetching CCD ASP_LSN3_DHD2 from http://ligand-
expo.rcsb.org/reports/A/ASP_LSN3_DHD2/ASP_LSN3_DHD2.cif
Fetching CCD AYA from http://ligand-expo.rcsb.org/reports/A/AYA/AYA.cif
Fetching CCD THR_LEO2_DHG1 from http://ligand-
expo.rcsb.org/reports/T/THR_LEO2_DHG1/THR_LEO2_DHG1.cif
Fetching CCD ILE_LL from http://ligand-
expo.rcsb.org/reports/I/ILE_LL/ILE_LL.cif
Fetching CCD LEU_LL from http://ligand-
expo.rcsb.org/reports/L/LEU_LL/LEU_LL.cif
Fetching CCD CYS_LEO2 from http://ligand-
expo.rcsb.org/reports/C/CYS_LEO2/CYS_LEO2.cif
Fetching CCD THR_LEO2 from http://ligand-
expo.rcsb.org/reports/T/THR_LEO2/THR_LEO2.cif
Fetching CCD VAL_LEO2 from http://ligand-
expo.rcsb.org/reports/V/VAL_LEO2/VAL_LEO2.cif
Fetching CCD CSO from http://ligand-expo.rcsb.org/reports/C/CSO/CSO.cif
Fetching CCD PRO_LFZW from http://ligand-
expo.rcsb.org/reports/P/PRO_LFZW/PRO_LFZW.cif
Fetching CCD THR_LFZW_DHG1 from http://ligand-
expo.rcsb.org/reports/T/THR_LFZW_DHG1/THR_LFZW_DHG1.cif
Fetching CCD ORN from http://ligand-expo.rcsb.org/reports/O/ORN/ORN.cif
Fetching CCD CYS_LFZW from http://ligand-
expo.rcsb.org/reports/C/CYS_LFZW/CYS_LFZW.cif
Fetching CCD THR_LFZW from http://ligand-
expo.rcsb.org/reports/T/THR_LFZW/THR_LFZW.cif
Fetching CCD VAL_LFZW from http://ligand-
expo.rcsb.org/reports/V/VAL_LFZW/VAL_LFZW.cif
Fetching CCD MET_LL from http://ligand-
expo.rcsb.org/reports/M/MET_LL/MET_LL.cif
Fetching CCD CSS from http://ligand-expo.rcsb.org/reports/C/CSS/CSS.cif
Fetching CCD GLU_LL_DHE2 from http://ligand-
expo.rcsb.org/reports/G/GLU_LL_DHE2/GLU_LL_DHE2.cif
Residue GLU B605 has only 1 atoms in common with the template. At least 3 are
needed to rebuild automatically. Try deleting this residue and replacing it
with "isolde add aa GLU
> delete atoms (#!1.2 & sel)
> delete bonds (#!1.2 & sel)
Traceback (most recent call last):
File
"/opt/sbgrid/i386-mac/chimerax/1.5/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/isolde/ui/validation_tab/unparameterised.py", line 160, in
_table_item_clicked_cb
residue.atoms.displays = True
File "atomic_cpp/cymol.pyx", line 996, in
chimerax.atomic.cymol.CyResidue.atoms.__get__
RuntimeError: Residue already deleted
RuntimeError: Residue already deleted
File "atomic_cpp/cymol.pyx", line 996, in
chimerax.atomic.cymol.CyResidue.atoms.__get__
See log for complete Python traceback.
Fetching CCD SAC from http://ligand-expo.rcsb.org/reports/S/SAC/SAC.cif
Deleted the following atoms from residue SER C43: HN, H
Traceback (most recent call last):
File
"/opt/sbgrid/i386-mac/chimerax/1.5/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/isolde/ui/validation_tab/unparameterised.py", line 160, in
_table_item_clicked_cb
residue.atoms.displays = True
File "atomic_cpp/cymol.pyx", line 996, in
chimerax.atomic.cymol.CyResidue.atoms.__get__
RuntimeError: Residue already deleted
RuntimeError: Residue already deleted
File "atomic_cpp/cymol.pyx", line 996, in
chimerax.atomic.cymol.CyResidue.atoms.__get__
See log for complete Python traceback.
Fetching CCD LYS_LL from http://ligand-
expo.rcsb.org/reports/L/LYS_LL/LYS_LL.cif
Fetching CCD LYS_LL_DHZ3 from http://ligand-
expo.rcsb.org/reports/L/LYS_LL_DHZ3/LYS_LL_DHZ3.cif
Fetching CCD LYS_LEO2 from http://ligand-
expo.rcsb.org/reports/L/LYS_LEO2/LYS_LEO2.cif
Fetching CCD LYZ from http://ligand-expo.rcsb.org/reports/L/LYZ/LYZ.cif
Fetching CCD MLZ from http://ligand-expo.rcsb.org/reports/M/MLZ/MLZ.cif
Fetching CCD LYS_LFZW from http://ligand-
expo.rcsb.org/reports/L/LYS_LFZW/LYS_LFZW.cif
Deleted the following atoms from residue LYS C80: H, HN
Traceback (most recent call last):
File
"/opt/sbgrid/i386-mac/chimerax/1.5/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/isolde/ui/validation_tab/unparameterised.py", line 182, in
_fix_button_clicked_cb
indices = [i for i in range(table.rowCount()) if table.item(i,
0).data(USER_ROLE)[0].name == residue.name]
File
"/opt/sbgrid/i386-mac/chimerax/1.5/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/isolde/ui/validation_tab/unparameterised.py", line 182, in
<listcomp>
indices = [i for i in range(table.rowCount()) if table.item(i,
0).data(USER_ROLE)[0].name == residue.name]
File "atomic_cpp/cymol.pyx", line 1217, in
chimerax.atomic.cymol.CyResidue.name.__get__
RuntimeError: Residue already deleted
RuntimeError: Residue already deleted
File "atomic_cpp/cymol.pyx", line 1217, in
chimerax.atomic.cymol.CyResidue.name.__get__
See log for complete Python traceback.
Deleted the following atoms from residue LYS C172: H, HN
Deleted the following atoms from residue LYS D107: HN, H
Deleted the following atoms from residue LYS D268: HN, H
Residue GLU D605 has only 1 atoms in common with the template. At least 3 are
needed to rebuild automatically. Try deleting this residue and replacing it
with "isolde add aa GLU
> delete atoms (#!1.2 & sel)
> delete bonds (#!1.2 & sel)
Fetching CCD GLU_LL from http://ligand-
expo.rcsb.org/reports/G/GLU_LL/GLU_LL.cif
Fetching CCD GLU_LSN3_DHE2 from http://ligand-
expo.rcsb.org/reports/G/GLU_LSN3_DHE2/GLU_LSN3_DHE2.cif
Fetching CCD GLU_LEO2_DHE2 from http://ligand-
expo.rcsb.org/reports/G/GLU_LEO2_DHE2/GLU_LEO2_DHE2.cif
Fetching CCD GLU_LFZW_DHE2 from http://ligand-
expo.rcsb.org/reports/G/GLU_LFZW_DHE2/GLU_LFZW_DHE2.cif
Fetching CCD NLG from http://ligand-expo.rcsb.org/reports/N/NLG/NLG.cif
Deleted the following atoms from residue GLU D254: HN, H
Fetching CCD GLY_LL from http://ligand-
expo.rcsb.org/reports/G/GLY_LL/GLY_LL.cif
Deleted the following atoms from residue GLY D100: HN, H
Fetching CCD ASN_LEO2 from http://ligand-
expo.rcsb.org/reports/A/ASN_LEO2/ASN_LEO2.cif
Deleted the following atoms from residue ASN D534: HN, H
Deleted the following atoms from residue GLY C164: HN, H
Deleted the following atoms from residue ALA C270: HN, H
Deleted the following atoms from residue VAL D552: HN, H
Traceback (most recent call last):
File
"/opt/sbgrid/i386-mac/chimerax/1.5/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/isolde/ui/validation_tab/unparameterised.py", line 160, in
_table_item_clicked_cb
residue.atoms.displays = True
File "atomic_cpp/cymol.pyx", line 996, in
chimerax.atomic.cymol.CyResidue.atoms.__get__
RuntimeError: Residue already deleted
RuntimeError: Residue already deleted
File "atomic_cpp/cymol.pyx", line 996, in
chimerax.atomic.cymol.CyResidue.atoms.__get__
See log for complete Python traceback.
Traceback (most recent call last):
File
"/opt/sbgrid/i386-mac/chimerax/1.5/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/isolde/ui/validation_tab/unparameterised.py", line 160, in
_table_item_clicked_cb
residue.atoms.displays = True
File "atomic_cpp/cymol.pyx", line 996, in
chimerax.atomic.cymol.CyResidue.atoms.__get__
RuntimeError: Residue already deleted
RuntimeError: Residue already deleted
File "atomic_cpp/cymol.pyx", line 996, in
chimerax.atomic.cymol.CyResidue.atoms.__get__
See log for complete Python traceback.
Traceback (most recent call last):
File
"/opt/sbgrid/i386-mac/chimerax/1.5/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/isolde/ui/validation_tab/unparameterised.py", line 160, in
_table_item_clicked_cb
residue.atoms.displays = True
File "atomic_cpp/cymol.pyx", line 996, in
chimerax.atomic.cymol.CyResidue.atoms.__get__
RuntimeError: Residue already deleted
RuntimeError: Residue already deleted
File "atomic_cpp/cymol.pyx", line 996, in
chimerax.atomic.cymol.CyResidue.atoms.__get__
See log for complete Python traceback.
> reset
Unknown command: reset
> select clear
> select add #1.2
28230 atoms, 28494 bonds, 1792 residues, 11 models selected
> select add #1.2
28230 atoms, 28494 bonds, 1792 residues, 11 models selected
> select add #1.2
28230 atoms, 28494 bonds, 1792 residues, 11 models selected
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop discardTo start
> select clear
> save
> /Users/drichman/Documents/EXP36/2023-10_best_maps/sessions/2q2e_aligned_withJ530_isolde.cxs
——— End of log from Mon Oct 23 20:20:41 2023 ———
opened ChimeraX session
> isolde start
> set selectionWidth 4
> select add #1.1
28230 atoms, 28494 bonds, 1792 residues, 6 models selected
> select subtract #1.1
28230 atoms, 28494 bonds, 1792 residues, 1 model selected
> select add #1
28230 atoms, 28494 bonds, 1792 residues, 17 models selected
> select add #1
28230 atoms, 28494 bonds, 1792 residues, 17 models selected
> select subtract #1.1
28230 atoms, 28494 bonds, 1792 residues, 12 models selected
> select subtract #1.3
28230 atoms, 28494 bonds, 1792 residues, 11 models selected
> select clear
> show cartoons
> hide atoms
> select clear
> clipper spotlight
> select clear
[Repeated 1 time(s)]
> addh
Summary of feedback from adding hydrogens to 2q2e_comb_mapcent.pdb #1.2
---
warnings | Not adding hydrogens to /B LYS 11 CB because it is missing heavy-
atom bond partners
Not adding hydrogens to /B LYS 12 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /B GLN 13 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /B LYS 14 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /B SER 15 CB because it is missing heavy-atom bond
partners
15 messages similar to the above omitted
notes | Termini for 2q2e_comb_mapcent.pdb (#1.2) chain A determined from
SEQRES records
Termini for 2q2e_comb_mapcent.pdb (#1.2) chain B determined from SEQRES
records
Termini for 2q2e_comb_mapcent.pdb (#1.2) chain C determined from SEQRES
records
Termini for 2q2e_comb_mapcent.pdb (#1.2) chain D determined from SEQRES
records
Chain-initial residues that are actual N termini: /C LEU 15, /D LYS 11
Chain-initial residues that are not actual N termini: /A LEU 15, /A SER 68, /A
THR 82, /A HIS 169, /A VAL 174, /A PHE 279, /B LYS 11, /B PHE 103, /B SER 109,
/B PRO 260, /B LEU 271, /B ALA 539, /B LYS 556, /B THR 613, /D THR 613
Chain-final residues that are actual C termini: /C GLY 367, /D LYS 616
Chain-final residues that are not actual C termini: /A SER 43, /A LYS 80, /A
GLY 164, /A LYS 172, /A ALA 270, /A GLY 367, /B GLY 100, /B LYS 107, /B GLU
254, /B LYS 268, /B ASN 534, /B VAL 552, /B VAL 604, /B LYS 616, /D VAL 604
823 hydrogen bonds
Adding 'H' to /D THR 613
/A SER 43 is not terminus, removing H atom from 'C'
/A LYS 80 is not terminus, removing H atom from 'C'
/A GLY 164 is not terminus, removing H atom from 'C'
/A LYS 172 is not terminus, removing H atom from 'C'
/A ALA 270 is not terminus, removing H atom from 'C'
10 messages similar to the above omitted
9 hydrogens added
> select #1/B
9086 atoms, 9171 bonds, 581 residues, 1 model selected
> select clear
> clipper spotlight
> select clear
> select add #1
28239 atoms, 28503 bonds, 1792 residues, 17 models selected
> clipper isolate sel maskRadius 4.0 focus false
> isolde sim start sel
ISOLDE: stopped sim
Fetching CCD SAC from http://ligand-expo.rcsb.org/reports/S/SAC/SAC.cif
Deleted the following atoms from residue SER C43: H1
Fetching CCD GLY_LL from http://ligand-
expo.rcsb.org/reports/G/GLY_LL/GLY_LL.cif
Deleted the following atoms from residue GLY C164: H1
Fetching CCD LYS_LL from http://ligand-
expo.rcsb.org/reports/L/LYS_LL/LYS_LL.cif
Fetching CCD LYS_LL_DHZ3 from http://ligand-
expo.rcsb.org/reports/L/LYS_LL_DHZ3/LYS_LL_DHZ3.cif
Fetching CCD LYS_LEO2 from http://ligand-
expo.rcsb.org/reports/L/LYS_LEO2/LYS_LEO2.cif
Fetching CCD LYZ from http://ligand-expo.rcsb.org/reports/L/LYZ/LYZ.cif
Fetching CCD MLZ from http://ligand-expo.rcsb.org/reports/M/MLZ/MLZ.cif
Fetching CCD LYS_LFZW from http://ligand-
expo.rcsb.org/reports/L/LYS_LFZW/LYS_LFZW.cif
Deleted the following atoms from residue LYS C80: H1
Deleted the following atoms from residue LYS C172: H1
Deleted the following atoms from residue ALA C270: H1
Deleted the following atoms from residue GLY D100: H1
Deleted the following atoms from residue LYS D107: H1
Fetching CCD GLU_LL from http://ligand-
expo.rcsb.org/reports/G/GLU_LL/GLU_LL.cif
Fetching CCD GLU_LSN3_DHE2 from http://ligand-
expo.rcsb.org/reports/G/GLU_LSN3_DHE2/GLU_LSN3_DHE2.cif
Fetching CCD GLU_LEO2_DHE2 from http://ligand-
expo.rcsb.org/reports/G/GLU_LEO2_DHE2/GLU_LEO2_DHE2.cif
Fetching CCD GLU_LFZW_DHE2 from http://ligand-
expo.rcsb.org/reports/G/GLU_LFZW_DHE2/GLU_LFZW_DHE2.cif
Fetching CCD NLG from http://ligand-expo.rcsb.org/reports/N/NLG/NLG.cif
Deleted the following atoms from residue GLU D254: H1
Deleted the following atoms from residue LYS D268: H1
Fetching CCD ASN_LEO2 from http://ligand-
expo.rcsb.org/reports/A/ASN_LEO2/ASN_LEO2.cif
Deleted the following atoms from residue ASN D534: H1
Deleted the following atoms from residue VAL D552: H1
> select clear
> select add #1.2
28228 atoms, 28492 bonds, 1792 residues, 11 models selected
> isolde sim start sel
Launching using CUDA failed with the below message. Falling back to using
OpenCL.
Error loading CUDA module: CUDA_ERROR_UNSUPPORTED_PTX_VERSION (222)
ISOLDE: started sim
> show sel cartoons
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1/B
9086 atoms, 9171 bonds, 581 residues, 1 model selected
> clipper isolate sel maskRadius 4.0 focus false
> clipper spotlight
> isolde restrain distances "#1/B"
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
> isolde adjust distances #1 displayThreshold 0.5
> isolde adjust distances #1 displayThreshold 0.1
> isolde adjust distances #1 displayThreshold 0.5
> show sel atoms
> select clear
> hide sideonly
> hide ~@CA
> select #1/B
9086 atoms, 9171 bonds, 581 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> ui mousemode right "isolde tug selection"
> close #1.2.9
> isolde sim stop
Traceback (most recent call last):
File "/programs/x86_64-linux/chimerax/1.5_c8/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/triggerset.py", line 134,
in invoke
return self._func(self._name, data)
File "/programs/x86_64-linux/chimerax/1.5_c8/libexec/UCSF-
ChimeraX/lib/python3.9/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1040, in
_sim_end_cb
self._adr_sim_end_cb()
File "/programs/x86_64-linux/chimerax/1.5_c8/libexec/UCSF-
ChimeraX/lib/python3.9/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1157, in
_adr_sim_end_cb
restraints = adrm.intra_restraints(self.sim_construct.all_atoms)
File "/programs/x86_64-linux/chimerax/1.5_c8/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/isolde/molobject.py", line 2978,
in intra_restraints
return self._plural_restraint_getter(f(self._c_pointer, atoms._c_pointers, n))
AttributeError: 'AdaptiveDistanceRestraintMgr' object has no attribute
'_c_pointer'
Error processing trigger "sim terminated":
AttributeError: 'AdaptiveDistanceRestraintMgr' object has no attribute
'_c_pointer'
File "/programs/x86_64-linux/chimerax/1.5_c8/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/isolde/molobject.py", line 2978,
in intra_restraints
return self._plural_restraint_getter(f(self._c_pointer, atoms._c_pointers, n))
See log for complete Python traceback.
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 38 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select #1
28228 atoms, 28492 bonds, 584 pseudobonds, 1792 residues, 18 models selected
> select clear
> select #1/D
9101 atoms, 9186 bonds, 6 pseudobonds, 581 residues, 2 models selected
> show sel cartoons
> select up
28228 atoms, 28492 bonds, 1792 residues, 1 model selected
> select down
9101 atoms, 9186 bonds, 581 residues, 1 model selected
> select #1/D
9101 atoms, 9186 bonds, 581 residues, 1 model selected
> clipper isolate sel maskRadius 4.0 focus false
> clipper spotlight
> isolde sim start sel
ISOLDE: started sim
> show sel cartoons
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> hide ~@CA
> show sel atoms
> hide ~@CA
> hide sel cartoons
> show sel cartoons
> hide sideonly
> show sel atoms
> hide sideonly
> hide ~@CA
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde restrain distances #1/D
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
> isolde sim start sel
ISOLDE: started sim
> ui mousemode right "isolde tug selection"
> show sel atoms
> close #1.2.9
> ui mousemode right "isolde tug atom"
> isolde sim stop
Traceback (most recent call last):
File "/programs/x86_64-linux/chimerax/1.5_c8/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/triggerset.py", line 134,
in invoke
return self._func(self._name, data)
File "/programs/x86_64-linux/chimerax/1.5_c8/libexec/UCSF-
ChimeraX/lib/python3.9/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1040, in
_sim_end_cb
self._adr_sim_end_cb()
File "/programs/x86_64-linux/chimerax/1.5_c8/libexec/UCSF-
ChimeraX/lib/python3.9/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1157, in
_adr_sim_end_cb
restraints = adrm.intra_restraints(self.sim_construct.all_atoms)
File "/programs/x86_64-linux/chimerax/1.5_c8/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/isolde/molobject.py", line 2978,
in intra_restraints
return self._plural_restraint_getter(f(self._c_pointer, atoms._c_pointers, n))
AttributeError: 'AdaptiveDistanceRestraintMgr' object has no attribute
'_c_pointer'
Error processing trigger "sim terminated":
AttributeError: 'AdaptiveDistanceRestraintMgr' object has no attribute
'_c_pointer'
File "/programs/x86_64-linux/chimerax/1.5_c8/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/isolde/molobject.py", line 2978,
in intra_restraints
return self._plural_restraint_getter(f(self._c_pointer, atoms._c_pointers, n))
See log for complete Python traceback.
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 34 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> hide ~@CA
> ui tool show "Ramachandran Plot"
> select #1
28228 atoms, 28492 bonds, 1151 pseudobonds, 1792 residues, 18 models selected
> select #1/A,B,C,D
28228 atoms, 28492 bonds, 1151 pseudobonds, 1792 residues, 2 models selected
> isolde restrain distances #1/A
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
> select #1/A
5014 atoms, 5061 bonds, 315 residues, 1 model selected
> show sel atoms
> close #1.2.9
> isolde restrain distances #1/A:15-144
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
> select #1/A:15-144
1733 atoms, 1748 bonds, 105 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> hide ~@CA
> close #1.2.9
> isolde sim stop
Traceback (most recent call last):
File "/programs/x86_64-linux/chimerax/1.5_c8/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/triggerset.py", line 134,
in invoke
return self._func(self._name, data)
File "/programs/x86_64-linux/chimerax/1.5_c8/libexec/UCSF-
ChimeraX/lib/python3.9/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1040, in
_sim_end_cb
self._adr_sim_end_cb()
File "/programs/x86_64-linux/chimerax/1.5_c8/libexec/UCSF-
ChimeraX/lib/python3.9/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1157, in
_adr_sim_end_cb
restraints = adrm.intra_restraints(self.sim_construct.all_atoms)
File "/programs/x86_64-linux/chimerax/1.5_c8/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/isolde/molobject.py", line 2978,
in intra_restraints
return self._plural_restraint_getter(f(self._c_pointer, atoms._c_pointers, n))
AttributeError: 'AdaptiveDistanceRestraintMgr' object has no attribute
'_c_pointer'
Error processing trigger "sim terminated":
AttributeError: 'AdaptiveDistanceRestraintMgr' object has no attribute
'_c_pointer'
File "/programs/x86_64-linux/chimerax/1.5_c8/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/isolde/molobject.py", line 2978,
in intra_restraints
return self._plural_restraint_getter(f(self._c_pointer, atoms._c_pointers, n))
See log for complete Python traceback.
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 8 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde restrain distances #1/A:145-367
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
> select #1/A:145-367
3281 atoms, 3312 bonds, 206 pseudobonds, 210 residues, 2 models selected
> show
> hide ~@CA
> select clear
> select #1/A:145-367
3281 atoms, 3312 bonds, 206 pseudobonds, 210 residues, 2 models selected
> hide ~@CA
> show
> hide ~@CA
> isolde sim start sel
ISOLDE: started sim
> close #1.2.9
> isolde sim stop
Traceback (most recent call last):
File "/programs/x86_64-linux/chimerax/1.5_c8/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/triggerset.py", line 134,
in invoke
return self._func(self._name, data)
File "/programs/x86_64-linux/chimerax/1.5_c8/libexec/UCSF-
ChimeraX/lib/python3.9/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1040, in
_sim_end_cb
self._adr_sim_end_cb()
File "/programs/x86_64-linux/chimerax/1.5_c8/libexec/UCSF-
ChimeraX/lib/python3.9/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1157, in
_adr_sim_end_cb
restraints = adrm.intra_restraints(self.sim_construct.all_atoms)
File "/programs/x86_64-linux/chimerax/1.5_c8/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/isolde/molobject.py", line 2978,
in intra_restraints
return self._plural_restraint_getter(f(self._c_pointer, atoms._c_pointers, n))
AttributeError: 'AdaptiveDistanceRestraintMgr' object has no attribute
'_c_pointer'
Error processing trigger "sim terminated":
AttributeError: 'AdaptiveDistanceRestraintMgr' object has no attribute
'_c_pointer'
File "/programs/x86_64-linux/chimerax/1.5_c8/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/isolde/molobject.py", line 2978,
in intra_restraints
return self._plural_restraint_getter(f(self._c_pointer, atoms._c_pointers, n))
See log for complete Python traceback.
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 9 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde restrain distances #1/C:15-144
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
> select #1/C:15-144
1739 atoms, 1754 bonds, 102 pseudobonds, 105 residues, 2 models selected
> isolde sim start sel
ISOLDE: started sim
> ui mousemode right "isolde tug selection"
> close #1.2.9
> isolde sim stop
Traceback (most recent call last):
File "/programs/x86_64-linux/chimerax/1.5_c8/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/triggerset.py", line 134,
in invoke
return self._func(self._name, data)
File "/programs/x86_64-linux/chimerax/1.5_c8/libexec/UCSF-
ChimeraX/lib/python3.9/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1040, in
_sim_end_cb
self._adr_sim_end_cb()
File "/programs/x86_64-linux/chimerax/1.5_c8/libexec/UCSF-
ChimeraX/lib/python3.9/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1157, in
_adr_sim_end_cb
restraints = adrm.intra_restraints(self.sim_construct.all_atoms)
File "/programs/x86_64-linux/chimerax/1.5_c8/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/isolde/molobject.py", line 2978,
in intra_restraints
return self._plural_restraint_getter(f(self._c_pointer, atoms._c_pointers, n))
AttributeError: 'AdaptiveDistanceRestraintMgr' object has no attribute
'_c_pointer'
Error processing trigger "sim terminated":
AttributeError: 'AdaptiveDistanceRestraintMgr' object has no attribute
'_c_pointer'
File "/programs/x86_64-linux/chimerax/1.5_c8/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/isolde/molobject.py", line 2978,
in intra_restraints
return self._plural_restraint_getter(f(self._c_pointer, atoms._c_pointers, n))
See log for complete Python traceback.
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 7 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde restrain distances #1/C:145-367
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
> select #1/C:145-367
3288 atoms, 3319 bonds, 206 pseudobonds, 210 residues, 2 models selected
> isolde sim start sel
ISOLDE: started sim
> ui mousemode right "isolde tug selection"
> close #1.2.9
> isolde sim stop
Traceback (most recent call last):
File "/programs/x86_64-linux/chimerax/1.5_c8/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/triggerset.py", line 134,
in invoke
return self._func(self._name, data)
File "/programs/x86_64-linux/chimerax/1.5_c8/libexec/UCSF-
ChimeraX/lib/python3.9/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1040, in
_sim_end_cb
self._adr_sim_end_cb()
File "/programs/x86_64-linux/chimerax/1.5_c8/libexec/UCSF-
ChimeraX/lib/python3.9/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1157, in
_adr_sim_end_cb
restraints = adrm.intra_restraints(self.sim_construct.all_atoms)
File "/programs/x86_64-linux/chimerax/1.5_c8/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/isolde/molobject.py", line 2978,
in intra_restraints
return self._plural_restraint_getter(f(self._c_pointer, atoms._c_pointers, n))
AttributeError: 'AdaptiveDistanceRestraintMgr' object has no attribute
'_c_pointer'
Error processing trigger "sim terminated":
AttributeError: 'AdaptiveDistanceRestraintMgr' object has no attribute
'_c_pointer'
File "/programs/x86_64-linux/chimerax/1.5_c8/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/isolde/molobject.py", line 2978,
in intra_restraints
return self._plural_restraint_getter(f(self._c_pointer, atoms._c_pointers, n))
See log for complete Python traceback.
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 9 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select
28228 atoms, 28492 bonds, 1764 pseudobonds, 1792 residues, 18 models selected
> select #1/A,B,C,D
28228 atoms, 28492 bonds, 1764 pseudobonds, 1792 residues, 2 models selected
> save
> /home/drichman/Documents/EXP36/2023-10_best_maps/models/2q2e_bulkfit_J530.pdb
> save
> /home/drichman/Documents/EXP36/2023-10_best_maps/models/2q2e_bulkfit_J530.cif
> relModel #1.2
> isolde sim start sel
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 69 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> save
> /home/drichman/Documents/EXP36/2023-10_best_maps/sessions/2q2e_bulkfit_J530.cxs
Taking snapshot of stepper: 2q2e_comb_mapcent.pdb
——— End of log from Tue Oct 24 15:58:25 2023 ———
opened ChimeraX session
> hide sel cartoons
[Repeated 1 time(s)]
> hide sel atoms
> show sel atoms
> style sel stick
Changed 22 atom styles
> style sel sphere
Changed 22 atom styles
> style sel stick
Changed 22 atom styles
> show sel cartoons
> hide sel atoms
> show sel cartoons
> hide sel cartoons
> show sel atoms
> hide sel atoms
> isolde start
> set selectionWidth 4
> open
> /home/drichman/Documents/EXP36/2023-10_best_maps/models/70bp_DNA_bend_roughplace.pdb
Chain information for 70bp_DNA_bend_roughplace.pdb #2
---
Chain | Description
A | No description available
B | No description available
> select #2
2870 atoms, 3218 bonds, 140 residues, 1 model selected
> select clear
> select #2
2870 atoms, 3218 bonds, 140 residues, 1 model selected
> hide #!1 models
> show #!1 models
> hide #!1.1 models
> show #!1.1 models
> open
> /home/drichman/Documents/EXP36/2023-10_best_maps/maps/J530_005_volume_map_flip.mrc
Opened J530_005_volume_map_flip.mrc as #3, grid size 240,240,240, pixel 1.44,
shown at level 0.0547, step 1, values float32
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
Chain information for 70bp_DNA_bend_roughplace.pdb
---
Chain | Description
2.2/A | No description available
2.2/B | No description available
> clipper associate #3 toModel #2
Opened J530_005_volume_map_flip.mrc as #2.1.1.1, grid size 240,240,240, pixel
1.44, shown at step 1, values float32
> hide #!1 models
> hide #!2.1 models
> show #!2.1 models
> hide #!2 models
> show #!2 models
3 models selected
> select clear
> select #2.2
2870 atoms, 3218 bonds, 140 residues, 6 models selected
> isolde sim start sel
ISOLDE: stopped sim
> addh #2.2
Summary of feedback from adding hydrogens to 70bp_DNA_bend_roughplace.pdb #2.2
---
warnings | Not adding hydrogens to 70bp_DNA_bend_roughplace.pdb #2.2/A A 1 P
because it is missing heavy-atom bond partners
Not adding hydrogens to 70bp_DNA_bend_roughplace.pdb #2.2/A A 1 C2' because it
is missing heavy-atom bond partners
Not adding hydrogens to 70bp_DNA_bend_roughplace.pdb #2.2/A G 3 C2' because it
is missing heavy-atom bond partners
Not adding hydrogens to 70bp_DNA_bend_roughplace.pdb #2.2/A C 4 C2' because it
is missing heavy-atom bond partners
Not adding hydrogens to 70bp_DNA_bend_roughplace.pdb #2.2/A C 7 C2' because it
is missing heavy-atom bond partners
91 messages similar to the above omitted
notes | Termini for 70bp_DNA_bend_roughplace.pdb (#2.2) chain A determined
from SEQRES records
Termini for 70bp_DNA_bend_roughplace.pdb (#2.2) chain B determined from SEQRES
records
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini:
188 hydrogen bonds
1400 hydrogens added
Deleted the following atoms from residue A B139: 1H5', 2H5', O2P, 1H6, O1P,
2H6
Deleted the following atoms from residue A B136: 1H6, O2P, 1H5', 2H5', O1P,
2H6
Deleted the following atoms from residue A B135: 1H5', 2H5', 1H6, O2P, 2H6,
O1P
Deleted the following atoms from residue A B131: O1P, 2H6, O2P, 2H5', 1H5',
1H6
Deleted the following atoms from residue A B128: 2H5', O1P, O2P, 2H6, 1H5',
1H6
Deleted the following atoms from residue A B126: O2P, 2H6, 2H5', O1P, 1H5',
1H6
Deleted the following atoms from residue A B125: 2H6, 1H6, 1H5', O1P, 2H5',
O2P
Deleted the following atoms from residue A B111: O2P, 1H5', 2H6, 2H5', O1P,
1H6
Deleted the following atoms from residue A B109: 1H5', O2P, 2H6, 2H5', 1H6,
O1P
Deleted the following atoms from residue A B105: O1P, 1H6, 2H5', O2P, 2H6,
1H5'
Deleted the following atoms from residue A B103: O2P, 2H5', 2H6, 1H5', O1P,
1H6
Deleted the following atoms from residue A B99: 1H5', 2H5', O2P, 1H6, O1P, 2H6
Deleted the following atoms from residue A B97: O1P, 1H5', 2H6, O2P, 1H6, 2H5'
Deleted the following atoms from residue A B96: O1P, 1H6, 1H5', 2H5', O2P, 2H6
Deleted the following atoms from residue A B90: O2P, 1H6, O1P, 1H5', 2H5', 2H6
Deleted the following atoms from residue A B89: O2P, 1H5', O1P, 1H6, 2H5', 2H6
Deleted the following atoms from residue A B88: 2H6, 1H5', O1P, 2H5', O2P, 1H6
Deleted the following atoms from residue A B84: 2H6, 1H5', O2P, 1H6, O1P, 2H5'
Deleted the following atoms from residue A B82: O2P, 2H6, 1H5', O1P, 1H6, 2H5'
Deleted the following atoms from residue A B76: O2P, 2H5', 2H6, O1P, 1H5', 1H6
Deleted the following atoms from residue A B75: O2P, 1H6, O1P, 2H6, 2H5', 1H5'
Deleted the following atoms from residue A B73: O1P, 1H6, 2H6, O2P, 1H5', 2H5'
Deleted the following atoms from residue A B72: O2P, 2H5', 1H6, O1P, 1H5', 2H6
Deleted the following atoms from residue A A67: 1H5', 2H6, O1P, 2H5', O2P, 1H6
Deleted the following atoms from residue A A50: O1P, 2H5', 2H6, O2P, 1H5', 1H6
Deleted the following atoms from residue A A48: 1H5', 2H5', O2P, 1H6, 2H6, O1P
Deleted the following atoms from residue A A47: O2P, 1H5', 1H6, O1P, 2H5', 2H6
Deleted the following atoms from residue A A43: O1P, 2H6, 1H5', O2P, 1H6, 2H5'
Deleted the following atoms from residue A A40: O2P, 1H5', 2H5', 2H6, O1P, 1H6
Deleted the following atoms from residue A A37: 1H5', O1P, O2P, 2H5', 1H6, 2H6
Deleted the following atoms from residue A A34: 1H5', 2H5', 1H6, 2H6, O2P, O1P
Deleted the following atoms from residue A A31: O1P, 1H6, 1H5', 2H6, O2P, 2H5'
Deleted the following atoms from residue A A28: O1P, 1H5', 2H5', 2H6, O2P, 1H6
Deleted the following atoms from residue A A26: O1P, 1H5', 2H5', O2P, 2H6, 1H6
Deleted the following atoms from residue A A25: O1P, 2H5', 2H6, O2P, 1H5', 1H6
Deleted the following atoms from residue A A22: O2P, 1H5', 2H6, O1P, 1H6, 2H5'
Deleted the following atoms from residue A A21: 2H6, 1H5', O1P, 1H6, O2P, 2H5'
Deleted the following atoms from residue A A20: 1H5', 2H5', 1H6, 2H6, O1P, O2P
Deleted the following atoms from residue A A19: O1P, 1H5', 2H5', O2P, 1H6, 2H6
Deleted the following atoms from residue A A18: O1P, 2H5', 2H6, O2P, 1H5', 1H6
Deleted the following atoms from residue A A14: O2P, 2H6, O1P, 2H5', 1H6, 1H5'
Deleted the following atoms from residue A A12: O1P, 2H5', 1H6, 1H5', O2P, 2H6
Deleted the following atoms from residue A A11: 1H6, O1P, O2P, 2H5', 2H6, 1H5'
Deleted the following atoms from residue A A9: 2H6, 1H5', 1H6, O2P, 2H5', O1P
Deleted the following atoms from residue A A8: O1P, 1H6, 2H6, 1H5', 2H5', O2P
Deleted the following atoms from residue A A1: 1H6, O1P, O2P, 2H6, 1H5', 2H5'
Fetching CCD GNG from http://ligand-expo.rcsb.org/reports/G/GNG/GNG.cif
Fetching CCD GMP from http://ligand-expo.rcsb.org/reports/G/GMP/GMP.cif
Deleted the following atoms from residue G A3: O1P, 2H5', O2P, 1H2, 1H5', 2H2
Deleted the following atoms from residue C B138: O1P, 1H5', 1H4, 2H5', 2H4,
O2P
Deleted the following atoms from residue C B124: 1H4, 2H5', 2H4, O1P, 1H5',
O2P
Deleted the following atoms from residue C B118: 1H4, O2P, 2H5', 2H4, O1P,
1H5'
Deleted the following atoms from residue C B117: 1H5', 2H5', O2P, 1H4, O1P,
2H4
Deleted the following atoms from residue C B114: 2H4, 1H5', O1P, 2H5', O2P,
1H4
Deleted the following atoms from residue C B112: O2P, 1H5', 1H4, O1P, 2H5',
2H4
Deleted the following atoms from residue C B108: O2P, 1H5', 2H4, O1P, 2H5',
1H4
Deleted the following atoms from residue C B106: 1H5', 2H5', O2P, 2H4, O1P,
1H4
Deleted the following atoms from residue C B102: 1H5', O2P, 2H5', 1H4, O1P,
2H4
Deleted the following atoms from residue C B100: O1P, 1H5', 2H5', O2P, 2H4,
1H4
Deleted the following atoms from residue C B85: 1H5', O2P, 2H5', O1P, 2H4, 1H4
Deleted the following atoms from residue C B83: O2P, 1H4, O1P, 2H5', 1H5', 2H4
Deleted the following atoms from residue C B80: 1H5', 2H5', O2P, 2H4, O1P, 1H4
Deleted the following atoms from residue C A70: 1H5', 1H4, HO3', 2H5', 2H4,
O2P, O1P
Deleted the following atoms from residue C A64: O1P, 1H5', 1H4, 2H4, O2P, 2H5'
Deleted the following atoms from residue C A63: 1H5', 1H4, 2H5', O2P, O1P, 2H4
Deleted the following atoms from residue C A62: 1H5', 2H5', O2P, 2H4, O1P, 1H4
Deleted the following atoms from residue C A60: 2H5', 1H5', O2P, 1H4, O1P, 2H4
Deleted the following atoms from residue C A55: 1H5', 1H4, O1P, 2H5', 2H4, O2P
Deleted the following atoms from residue C A54: O1P, 2H5', 1H5', O2P, 2H4, 1H4
Deleted the following atoms from residue C A49: 1H4, 1H5', O2P, 2H4, O1P, 2H5'
Deleted the following atoms from residue C A46: O2P, 2H5', 1H5', O1P, 2H4, 1H4
Deleted the following atoms from residue C A7: O2P, 2H5', 1H5', O1P, 2H4, 1H4
Deleted the following atoms from residue C A4: 1H5', 2H5', 2H4, O2P, O1P, 1H4
Deleted the following atoms from residue G B137: O1P, 2H2, 1H5', O2P, 2H5',
1H2
Deleted the following atoms from residue G B134: O1P, 1H2, 2H5', 1H5', O2P,
2H2
Deleted the following atoms from residue G B95: 1H5', 2H5', O1P, 2H2, 1H2, O2P
Deleted the following atoms from residue G B92: 2H2, 1H2, O2P, O1P, 2H5', 1H5'
Deleted the following atoms from residue G B87: O2P, 1H2, 2H2, O1P, 1H5', 2H5'
Deleted the following atoms from residue G B86: O1P, 1H2, 2H5', 1H5', O2P, 2H2
Deleted the following atoms from residue G B81: 1H5', 1H2, O2P, 2H5', O1P, 2H2
Deleted the following atoms from residue G B79: O1P, 1H5', O2P, 2H5', 1H2, 2H2
Deleted the following atoms from residue G B78: 2H2, 2H5', 1H5', O1P, O2P, 1H2
Deleted the following atoms from residue G B77: 2H2, 1H2, O2P, O1P, 2H5', 1H5'
Deleted the following atoms from residue G B71: 1H2, 1H5', O2P, 2H2, O1P, 2H5'
Deleted the following atoms from residue G A61: O1P, 1H5', 2H5', O2P, 1H2, 2H2
Deleted the following atoms from residue G A58: O2P, 2H2, 1H5', O1P, 1H2, 2H5'
Deleted the following atoms from residue G A56: 1H5', 2H5', O1P, O2P, 1H2, 2H2
Deleted the following atoms from residue G A41: 2H2, O1P, O2P, 1H5', 1H2, 2H5'
Deleted the following atoms from residue G A39: O1P, 1H2, 2H2, 1H5', O2P, 2H5'
Deleted the following atoms from residue G A35: O1P, 2H5', 1H2, O2P, 2H2, 1H5'
Deleted the following atoms from residue G A33: O1P, 1H5', 1H2, 2H5', O2P, 2H2
Deleted the following atoms from residue G A29: O1P, 1H5', 1H2, O2P, 2H2, 2H5'
Deleted the following atoms from residue G A27: 1H5', 2H5', O1P, O2P, 2H2, 1H2
Deleted the following atoms from residue G A24: 1H2, 1H5', O1P, 2H2, O2P, 2H5'
Deleted the following atoms from residue G A23: 2H2, 1H5', O2P, 1H2, O1P, 2H5'
Deleted the following atoms from residue G A17: 1H5', O1P, 1H2, 2H5', O2P, 2H2
> select up
34 atoms, 36 bonds, 1 residue, 1 model selected
> select down
25 atoms, 27 bonds, 1 residue, 1 model selected
> select #2.2
4551 atoms, 4899 bonds, 140 residues, 11 models selected
> isolde sim start sel
Launching using CUDA failed with the below message. Falling back to using
OpenCL.
Error loading CUDA module: CUDA_ERROR_UNSUPPORTED_PTX_VERSION (222)
ISOLDE: started sim
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde restrain distances #2.2
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!2.1 models
> select clear
> isolde release distances
Missing or invalid "atoms" argument: empty atom specifier
> select #2.2
4551 atoms, 4899 bonds, 140 residues, 11 models selected
> remove distances sel
Unknown command: isolde remove distances sel
> save
> /home/drichman/Documents/EXP36/2023-10_best_maps/models/2q2e_70bp_bulkfit_J530.pdb
> save
> /home/drichman/Documents/EXP36/2023-10_best_maps/sessions/2q2e_70bp_bulkfit_J530.cxs
Taking snapshot of stepper: 2q2e_comb_mapcent.pdb
——— End of log from Tue Oct 24 16:53:55 2023 ———
opened ChimeraX session
> show #!2.1 models
> hide #!2.1 models
> isolde start
> set selectionWidth 4
> show #!2.1 models
> hide #!1.1 models
> select #2.2/A:0-10,B:130-140
323 atoms, 346 bonds, 10 residues, 1 model selected
> select #2.2/A:0-10,B:100-140
323 atoms, 346 bonds, 10 residues, 1 model selected
> select #2.2/A:0-10,#2.2/B:100-140
Expected an objects specifier or a keyword
> select #2.2/A:0-10 and /B:100-140
Expected a keyword
> select #2.2/A:0-10&/B:100-140
Nothing selected
> select #2.2/A:0-10 & /B:100-140
Nothing selected
> select #2.2/A:0-10 & #2.2/B:100-140
Nothing selected
> select #2.2/A:0-10
323 atoms, 346 bonds, 10 residues, 1 model selected
> select #2.2/A:0-10 && #2.2/B:100-140
Expected a keyword
> select #2.2/A:0-10
323 atoms, 346 bonds, 10 residues, 1 model selected
> select #2.2/A:0-10
323 atoms, 346 bonds, 10 residues, 1 model selected
> select #2.2/B:100-140
1318 atoms, 1412 bonds, 41 residues, 1 model selected
> select #2.2/A:0-10,#2.2/B:100-140
Expected an objects specifier or a keyword
> select #2.2/A:0-10, /B:100-140
Expected an objects specifier or a keyword
> select #2.2/A:0-10, /B:120-140
Expected an objects specifier or a keyword
> select #2.2/A:0-10, B:120-140
323 atoms, 346 bonds, 10 residues, 1 model selected
> select #2.2/A:0-10, /B:120-140
Expected an objects specifier or a keyword
> select #2.2/A,B
4551 atoms, 4899 bonds, 140 residues, 1 model selected
> select #2.2/A:1-10,B
323 atoms, 346 bonds, 10 residues, 1 model selected
> select #2.2/A,B:1-10
323 atoms, 346 bonds, 10 residues, 1 model selected
> select #2.2/A,B
4551 atoms, 4899 bonds, 140 residues, 1 model selected
> select clear
> select #2.2/A,B
4551 atoms, 4899 bonds, 140 residues, 1 model selected
> select #2.2/A:1-10,B
323 atoms, 346 bonds, 10 residues, 1 model selected
> select #2.2/A:1-20,B
651 atoms, 701 bonds, 20 residues, 1 model selected
> select #2.2/A:1-20,B:120-140
651 atoms, 701 bonds, 20 residues, 1 model selected
> select #2.2/A:1-20/B:120-140
1333 atoms, 1433 bonds, 41 residues, 1 model selected
> hide ~@CA
> isolde sim start sel
Launching using CUDA failed with the below message. Falling back to using
OpenCL.
Error loading CUDA module: CUDA_ERROR_UNSUPPORTED_PTX_VERSION (222)
ISOLDE: started sim
> ui mousemode right "isolde tug selection"
> isolde sim pause
> show sel atoms
> hide ~@CA
> show sel cartoons
> isolde sim resume
> ui mousemode right "isolde tug residue"
> ui mousemode right "isolde tug atom"
> show sel atoms
> hide sel atoms
> ui mousemode right "isolde tug atom"
> ui mousemode right "isolde tug residue"
> ui mousemode right "isolde tug atom"
> ui mousemode right "isolde tug selection"
> select #2.2/A:5-15
356 atoms, 382 bonds, 11 residues, 1 model selected
> select #2.2/B:125-135
359 atoms, 386 bonds, 11 residues, 1 model selected
> select #2.2/B:130-135
196 atoms, 210 bonds, 6 residues, 1 model selected
> select #2.2/B:135-140
197 atoms, 212 bonds, 6 residues, 1 model selected
> select #2.2/B:132-140
295 atoms, 317 bonds, 9 residues, 1 model selected
> select #2.2/B:133-140
263 atoms, 283 bonds, 8 residues, 1 model selected
> select #2.2/B:138-140
97 atoms, 103 bonds, 3 residues, 1 model selected
> select #2.2/B:135-140
197 atoms, 212 bonds, 6 residues, 1 model selected
> close #2.2.9
> select #2.2/A:1-10
323 atoms, 346 bonds, 10 residues, 1 model selected
> select #2.2/A:10-15
195 atoms, 209 bonds, 6 residues, 1 model selected
> select #2.2/A:10-13
130 atoms, 139 bonds, 4 residues, 1 model selected
> select #2.2/A:1-5
162 atoms, 173 bonds, 5 residues, 1 model selected
> select #2.2/B:135-140
197 atoms, 212 bonds, 6 residues, 1 model selected
> select #2.2/B:138-140
97 atoms, 103 bonds, 3 residues, 1 model selected
> select #2.2/B:136-138
98 atoms, 105 bonds, 3 residues, 1 model selected
> ui mousemode right "isolde tug atom"
> ui mousemode right "isolde tug selection"
> select #2.2/B:137
34 atoms, 36 bonds, 1 residue, 1 model selected
> select #2.2/A:1-5
162 atoms, 173 bonds, 5 residues, 1 model selected
> select #2.2/A:1-5/B:135-140
359 atoms, 385 bonds, 11 residues, 1 model selected
> select #2.2/A:1-5/B:135-140
359 atoms, 385 bonds, 11 residues, 1 model selected
> select #2.2/A:6-10/B:135-140
358 atoms, 384 bonds, 11 residues, 1 model selected
> isolde restrain distances #2.2
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
> show sel atoms
> isolde sim pause
> isolde sim resume
> isolde sim stop
Traceback (most recent call last):
File "/programs/x86_64-linux/chimerax/1.5_c8/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/triggerset.py", line 134,
in invoke
return self._func(self._name, data)
File "/programs/x86_64-linux/chimerax/1.5_c8/libexec/UCSF-
ChimeraX/lib/python3.9/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1040, in
_sim_end_cb
self._adr_sim_end_cb()
File "/programs/x86_64-linux/chimerax/1.5_c8/libexec/UCSF-
ChimeraX/lib/python3.9/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1157, in
_adr_sim_end_cb
restraints = adrm.intra_restraints(self.sim_construct.all_atoms)
File "/programs/x86_64-linux/chimerax/1.5_c8/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/isolde/molobject.py", line 2978,
in intra_restraints
return self._plural_restraint_getter(f(self._c_pointer, atoms._c_pointers, n))
AttributeError: 'AdaptiveDistanceRestraintMgr' object has no attribute
'_c_pointer'
Error processing trigger "sim terminated":
AttributeError: 'AdaptiveDistanceRestraintMgr' object has no attribute
'_c_pointer'
File "/programs/x86_64-linux/chimerax/1.5_c8/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/isolde/molobject.py", line 2978,
in intra_restraints
return self._plural_restraint_getter(f(self._c_pointer, atoms._c_pointers, n))
See log for complete Python traceback.
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #1.1/B:235-314
Nothing selected
> select #1.1/B:235-314
Nothing selected
> select #1.2/B:235-314
1170 atoms, 1183 bonds, 70 pseudobonds, 73 residues, 2 models selected
> select #1.2/B:235-314
1170 atoms, 1183 bonds, 70 pseudobonds, 73 residues, 2 models selected
> select #1.2/D:235-314
1174 atoms, 1187 bonds, 70 pseudobonds, 73 residues, 2 models selected
> show #!1.1 models
> hide #!2.1 models
> show #!2.1 models
> hide #!2.1 models
> show #!2.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!2.1 models
> select #1.2/D:235-314
1174 atoms, 1187 bonds, 70 pseudobonds, 73 residues, 2 models selected
> isolde sim start sel
ISOLDE: started sim
> ui mousemode right "isolde tug selection"
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start sel
ISOLDE: started sim
> isolde restrain distances sel
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
> ui mousemode right "isolde tug selection"
> show #!2.1 models
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select up
1461 atoms, 1477 bonds, 92 residues, 1 model selected
> select up
6642 atoms, 6707 bonds, 419 residues, 1 model selected
> select down
1461 atoms, 1477 bonds, 92 residues, 1 model selected
> select down
1329 atoms, 1344 bonds, 84 residues, 1 model selected
> select #1.2/B:235-314
1170 atoms, 1183 bonds, 73 residues, 1 model selected
> select #2.2/A:1-5/B:135-140
359 atoms, 385 bonds, 11 residues, 1 model selected
> select #2.2/A:1-10/B:135-140
520 atoms, 558 bonds, 16 residues, 1 model selected
> select #2.2/A:1-10/B:130-140
683 atoms, 733 bonds, 21 residues, 1 model selected
> select #2.2/A:1-5/B:135-140
359 atoms, 385 bonds, 11 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> hide #!1.1 models
> ui mousemode right "isolde tug selection"
> show sel cartoons
> show sel atoms
> hide sel cartoons
> isolde sim stop
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #2.2/A:130-140/B:1-10
Nothing selected
> show cartoons
> select #2.2/A:130-140/B:1-10
Nothing selected
> select #2.2/A:130-140/B:60-70
Nothing selected
> select #2.2/A:130-140/B:70-80
331 atoms, 358 bonds, 10 residues, 1 model selected
> select #2.2/A:60-70/B:70-80
681 atoms, 731 bonds, 21 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> show sel cartoons
> ui mousemode right "isolde tug selection"
> isolde sim stop discardTo start
reverting to start
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #2.2/A:50-60
354 atoms, 378 bonds, 11 residues, 1 model selected
> select #2.2/A:60-65
190 atoms, 202 bonds, 6 residues, 1 model selected
> select #2.2/A:58-65
256 atoms, 273 bonds, 8 residues, 1 model selected
> select #2.2/A:58-62
162 atoms, 173 bonds, 5 residues, 1 model selected
> isolde sim start sel
ISOLDE: started sim
> show sel cartoons
> show sel atoms
> hide sel atoms
> show all
Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest
bonded heavy atom.
> ui mousemode right "isolde tug selection"
> isolde release distances
Missing or invalid "atoms" argument: empty atom specifier
> close #2.2.9
> isolde sim stop discardTo start
Traceback (most recent call last):
File "/programs/x86_64-linux/chimerax/1.5_c8/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/triggerset.py", line 134,
in invoke
return self._func(self._name, data)
File "/programs/x86_64-linux/chimerax/1.5_c8/libexec/UCSF-
ChimeraX/lib/python3.9/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1040, in
_sim_end_cb
self._adr_sim_end_cb()
File "/programs/x86_64-linux/chimerax/1.5_c8/libexec/UCSF-
ChimeraX/lib/python3.9/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1157, in
_adr_sim_end_cb
restraints = adrm.intra_restraints(self.sim_construct.all_atoms)
File "/programs/x86_64-linux/chimerax/1.5_c8/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/isolde/molobject.py", line 2978,
in intra_restraints
return self._plural_restraint_getter(f(self._c_pointer, atoms._c_pointers, n))
AttributeError: 'AdaptiveDistanceRestraintMgr' object has no attribute
'_c_pointer'
Error processing trigger "sim terminated":
AttributeError: 'AdaptiveDistanceRestraintMgr' object has no attribute
'_c_pointer'
File "/programs/x86_64-linux/chimerax/1.5_c8/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/isolde/molobject.py", line 2978,
in intra_restraints
return self._plural_restraint_getter(f(self._c_pointer, atoms._c_pointers, n))
See log for complete Python traceback.
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
OpenGL version: 3.3.0 NVIDIA 470.199.02
OpenGL renderer: NVIDIA GeForce RTX 2080 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.9.11
Locale: en_US.UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: xcb
XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: System manufacturer
Model: System Product Name
OS: Ubuntu 20.04 Focal Fossa
Architecture: 64bit ELF
Virtual Machine: none
CPU: 32 AMD Ryzen 9 3950X 16-Core Processor
Cache Size: 512 KB
Memory:
total used free shared buff/cache available
Mem: 125Gi 7.7Gi 102Gi 153Mi 15Gi 116Gi
Swap: 2.0Gi 0B 2.0Gi
Graphics:
09:00.0 VGA compatible controller [0300]: NVIDIA Corporation TU102 [GeForce RTX 2080 Ti] [10de:1e04] (rev a1)
Subsystem: eVga.com. Corp. TU102 [GeForce RTX 2080 Ti] [3842:2281]
Kernel driver in use: nvidia
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
asttokens: 2.1.0
Babel: 2.11.0
backcall: 0.2.0
blockdiag: 3.0.0
build: 0.8.0
certifi: 2022.9.24
cftime: 1.6.2
charset-normalizer: 2.1.1
ChimeraX-AddCharge: 1.4
ChimeraX-AddH: 2.2.1
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.6
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.41.5
ChimeraX-AtomicLibrary: 8.0.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.7.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.1
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.19.0
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.2
ChimeraX-CommandLine: 1.2.4
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.5
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.3
ChimeraX-DockPrep: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.5
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-LinuxSupport: 1.0.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.1
ChimeraX-MatchMaker: 2.0.9
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.8
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.6
ChimeraX-ModelPanel: 1.3.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.1
ChimeraX-MouseModes: 1.1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.9.1
ChimeraX-PDB: 2.6.8
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.7.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.1.3
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.24.3
ChimeraX-uniprot: 2.2.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.1.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.1
ChimeraX-WebServices: 1.1.0
ChimeraX-Zone: 1.0.1
colorama: 0.4.5
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.32
debugpy: 1.6.4
decorator: 5.1.1
distro: 1.7.0
docutils: 0.19
entrypoints: 0.4
executing: 1.2.0
filelock: 3.7.1
fonttools: 4.38.0
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.33
imagecodecs: 2022.7.31
imagesize: 1.4.1
importlib-metadata: 5.1.0
ipykernel: 6.15.3
ipython: 8.4.0
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.1.2
jupyter-client: 7.3.4
jupyter-core: 5.1.0
kiwisolver: 1.4.4
line-profiler: 3.5.1
lxml: 4.9.1
lz4: 4.0.2
MarkupSafe: 2.1.1
matplotlib: 3.5.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.0
networkx: 2.8.5
numexpr: 2.8.4
numpy: 1.23.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.2.0
pip: 22.2.2
pkginfo: 1.8.3
platformdirs: 2.5.4
prompt-toolkit: 3.0.33
psutil: 5.9.1
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.12.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2022.6
pyzmq: 24.0.1
qtconsole: 5.3.1
QtPy: 2.3.0
RandomWords: 0.4.0
requests: 2.28.1
scipy: 1.9.0
setuptools: 65.1.1
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 5.1.1
sphinx-autodoc-typehints: 1.19.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tifffile: 2022.7.31
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.2
traitlets: 5.3.0
urllib3: 1.26.13
wcwidth: 0.2.5
webcolors: 1.12
wheel: 0.37.1
wheel-filename: 1.4.1
zipp: 3.11.0
Change History (2)
comment:1 by , 2 years ago
| Component: | Unassigned → Third Party |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → ISOLDE: stop sim: 'AdaptiveDistanceRestraintMgr' object has no attribute '_c_pointer' |
comment:2 by , 2 years ago
This should go away if you update to ChimeraX 1.6 and the matching ISOLDE. Previous versions would get *really* unhappy if you deleted the model while a simulation was still running. On Wed, 25 Oct 2023 at 21:20, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> wrote: > > > >
Note:
See TracTickets
for help on using tickets.
Reported by Dan Richman