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Opened 5 years ago
Closed 3 years ago
#3601 closed defect (fixed)
_show_selected_unparameterised_residue: not enough values to unpack
| 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-3.10.0-1062.9.1.el7.x86_64-x86_64-with-centos-7.7.1908-Core
ChimeraX Version: 1.0 (2020-06-04 23:15:07 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.0 (2020-06-04)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/home/kartikmanne/Documents/CH235
> structures/588AMS_CH235.12-M5-293/RealSpaceRefine_34/588AMS-
> CH235p12-M5-293_apply_ncs_31-coot0-rsr34_real_space_refined.pdb"
Chain information for 588AMS-
CH235p12-M5-293_apply_ncs_31-coot0-rsr34_real_space_refined.pdb #1
---
Chain | Description
A E I | No description available
B F J | No description available
C G K | No description available
D H L | No description available
> set bgColor white
> addh
Summary of feedback from adding hydrogens to 588AMS-
CH235p12-M5-293_apply_ncs_31-coot0-rsr34_real_space_refined.pdb #1
---
notes | No usable SEQRES records for 588AMS-
CH235p12-M5-293_apply_ncs_31-coot0-rsr34_real_space_refined.pdb (#1) chain A;
guessing termini instead
No usable SEQRES records for 588AMS-
CH235p12-M5-293_apply_ncs_31-coot0-rsr34_real_space_refined.pdb (#1) chain B;
guessing termini instead
No usable SEQRES records for 588AMS-
CH235p12-M5-293_apply_ncs_31-coot0-rsr34_real_space_refined.pdb (#1) chain C;
guessing termini instead
No usable SEQRES records for 588AMS-
CH235p12-M5-293_apply_ncs_31-coot0-rsr34_real_space_refined.pdb (#1) chain D;
guessing termini instead
No usable SEQRES records for 588AMS-
CH235p12-M5-293_apply_ncs_31-coot0-rsr34_real_space_refined.pdb (#1) chain E;
guessing termini instead
7 messages similar to the above omitted
Chain-initial residues that are actual N termini: /A BMA 535, /B VAL 518, /C
GLN 1, /D GLU 1, /E BMA 535, /F VAL 518, /G GLN 1, /H GLU 1, /I BMA 535, /J
VAL 518, /K GLN 1, /L GLU 1
Chain-initial residues that are not actual N termini: /A THR 71, /A CYS 157,
/A GLY 312, /A ASN 409, /B GLY 572, /C GLY 134, /E THR 71, /E CYS 157, /E GLY
312, /E ASN 409, /F GLY 572, /G GLY 134, /I THR 71, /I CYS 157, /I GLY 312, /I
ASN 409, /J GLY 572, /K GLY 134
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini: /A VAL 503, /A GLU 62, /A
ASN 147, /A ILE 309, /A ASN 398, /B ASP 664, /B SER 546, /C CYS 216, /C SER
128, /D GLY 212, /E VAL 503, /E GLU 62, /E ASN 147, /E ILE 309, /E ASN 398, /F
ASP 664, /F SER 546, /G CYS 216, /G SER 128, /H GLY 212, /I VAL 503, /I GLU
62, /I ASN 147, /I ILE 309, /I ASN 398, /J ASP 664, /J SER 546, /K CYS 216, /K
SER 128, /L GLY 212
2230 hydrogen bonds
/A VAL 503 is not terminus, removing H atom from 'C'
/A GLU 62 is not terminus, removing H atom from 'C'
/A ASN 147 is not terminus, removing H atom from 'C'
/A ILE 309 is not terminus, removing H atom from 'C'
/A ASN 398 is not terminus, removing H atom from 'C'
25 messages similar to the above omitted
165 hydrogens added
> open "/home/kartikmanne/Documents/CH235
> structures/588AMS_CH235.12-M5-293/cryosparc_P41_J32_009_volume_map_sharp_local.mrc"
Opened cryosparc_P41_J32_009_volume_map_sharp_local.mrc, grid size
320,320,320, pixel 1.07, shown at level 0.659, step 2, values float32
> volume #2 step 1
> clipper associate #2 toModel #1
Chain information for 588AMS-
CH235p12-M5-293_apply_ncs_31-coot0-rsr34_real_space_refined.pdb
---
Chain | Description
1.2/A 1.2/E 1.2/I | No description available
1.2/B 1.2/F 1.2/J | No description available
1.2/C 1.2/G 1.2/K | No description available
1.2/D 1.2/H 1.2/L | No description available
> isolde start
> set selectionWidth 4
Cached rota8000-val data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-leu data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-ile data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-pro data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-phe data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-tyr data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-trp data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-ser data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-thr data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-cys data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-met data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-lys data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-his data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-arg data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-asp data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-asn data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-gln data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-glu data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Done loading forcefield
> clipper spotlight radius 32.00
> select #1
47724 atoms, 48273 bonds, 48 pseudobonds, 13 models selected
Traceback (most recent call last):
File "/home/kartikmanne/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/validation/unparameterised.py", line 48, in
_show_main_frame
self._update_unparameterised_residues_list()
File "/home/kartikmanne/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/validation/unparameterised.py", line 79, in
_update_unparameterised_residues_list
template_dict = find_residue_templates(residues, ff, ligand_db=ligand_db,
logger=self.session.logger)
File "/home/kartikmanne/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 3091, in
find_residue_templates
templates[residues.index(prot_res)] = find_glycan_anchor_name(prot_res)
File "/home/kartikmanne/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/openmm/amberff/glycam.py", line 271, in
find_glycan_anchor_name
residue.name, residue.chain_id, residue.number
RuntimeError: Residue BMA A535 is linked to a glycan, but no parameters are
available for this type of linkage.
RuntimeError: Residue BMA A535 is linked to a glycan, but no parameters are
available for this type of linkage.
File "/home/kartikmanne/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/openmm/amberff/glycam.py", line 271, in
find_glycan_anchor_name
residue.name, residue.chain_id, residue.number
See log for complete Python traceback.
Traceback (most recent call last):
File "/home/kartikmanne/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/validation/unparameterised.py", line 79, in
_update_unparameterised_residues_list
template_dict = find_residue_templates(residues, ff, ligand_db=ligand_db,
logger=self.session.logger)
File "/home/kartikmanne/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 3091, in
find_residue_templates
templates[residues.index(prot_res)] = find_glycan_anchor_name(prot_res)
File "/home/kartikmanne/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/openmm/amberff/glycam.py", line 271, in
find_glycan_anchor_name
residue.name, residue.chain_id, residue.number
RuntimeError: Residue BMA A535 is linked to a glycan, but no parameters are
available for this type of linkage.
RuntimeError: Residue BMA A535 is linked to a glycan, but no parameters are
available for this type of linkage.
File "/home/kartikmanne/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/openmm/amberff/glycam.py", line 271, in
find_glycan_anchor_name
residue.name, residue.chain_id, residue.number
See log for complete Python traceback.
Traceback (most recent call last):
File "/home/kartikmanne/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/isolde.py", line 2735, in _start_sim_or_toggle_pause
self.start_sim()
File "/home/kartikmanne/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/isolde.py", line 2755, in start_sim
self.params, self.sim_params, excluded_residues = self.ignored_residues)
File "/home/kartikmanne/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 612, in __init__
raise e
File "/home/kartikmanne/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__
isolde.forcefield_mgr)
File "/home/kartikmanne/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1323, in __init__
template_dict = find_residue_templates(sim_construct.all_residues, ff,
ligand_db=ligand_db, logger=session.logger)
File "/home/kartikmanne/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 3091, in
find_residue_templates
templates[residues.index(prot_res)] = find_glycan_anchor_name(prot_res)
File "/home/kartikmanne/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/openmm/amberff/glycam.py", line 271, in
find_glycan_anchor_name
residue.name, residue.chain_id, residue.number
RuntimeError: Residue BMA A535 is linked to a glycan, but no parameters are
available for this type of linkage.
RuntimeError: Residue BMA A535 is linked to a glycan, but no parameters are
available for this type of linkage.
File "/home/kartikmanne/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/openmm/amberff/glycam.py", line 271, in
find_glycan_anchor_name
residue.name, residue.chain_id, residue.number
See log for complete Python traceback.
Traceback (most recent call last):
File "/home/kartikmanne/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/isolde.py", line 2755, in start_sim
self.params, self.sim_params, excluded_residues = self.ignored_residues)
File "/home/kartikmanne/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 612, in __init__
raise e
File "/home/kartikmanne/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__
isolde.forcefield_mgr)
File "/home/kartikmanne/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1344, in __init__
sim_params, residue_templates)
File "/home/kartikmanne/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1426, in
_create_openmm_system
raise RuntimeError('Unparameterised residue detected')
RuntimeError: Unparameterised residue detected
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/kartikmanne/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/isolde.py", line 2735, in _start_sim_or_toggle_pause
self.start_sim()
File "/home/kartikmanne/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/isolde.py", line 2768, in start_sim
self._unparam_mgr._sim_unparam_res_cb()
File "/home/kartikmanne/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/validation/unparameterised.py", line 204, in
_sim_unparam_res_cb
self._show_main_frame()
File "/home/kartikmanne/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/validation/unparameterised.py", line 48, in
_show_main_frame
self._update_unparameterised_residues_list()
File "/home/kartikmanne/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/validation/unparameterised.py", line 79, in
_update_unparameterised_residues_list
template_dict = find_residue_templates(residues, ff, ligand_db=ligand_db,
logger=self.session.logger)
File "/home/kartikmanne/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 3091, in
find_residue_templates
templates[residues.index(prot_res)] = find_glycan_anchor_name(prot_res)
File "/home/kartikmanne/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/openmm/amberff/glycam.py", line 271, in
find_glycan_anchor_name
residue.name, residue.chain_id, residue.number
RuntimeError: Residue BMA A535 is linked to a glycan, but no parameters are
available for this type of linkage.
RuntimeError: Residue BMA A535 is linked to a glycan, but no parameters are
available for this type of linkage.
File "/home/kartikmanne/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/openmm/amberff/glycam.py", line 271, in
find_glycan_anchor_name
residue.name, residue.chain_id, residue.number
See log for complete Python traceback.
Traceback (most recent call last):
File "/home/kartikmanne/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/validation/unparameterised.py", line 79, in
_update_unparameterised_residues_list
template_dict = find_residue_templates(residues, ff, ligand_db=ligand_db,
logger=self.session.logger)
File "/home/kartikmanne/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 3091, in
find_residue_templates
templates[residues.index(prot_res)] = find_glycan_anchor_name(prot_res)
File "/home/kartikmanne/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/openmm/amberff/glycam.py", line 271, in
find_glycan_anchor_name
residue.name, residue.chain_id, residue.number
RuntimeError: Residue BMA A535 is linked to a glycan, but no parameters are
available for this type of linkage.
RuntimeError: Residue BMA A535 is linked to a glycan, but no parameters are
available for this type of linkage.
File "/home/kartikmanne/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/openmm/amberff/glycam.py", line 271, in
find_glycan_anchor_name
residue.name, residue.chain_id, residue.number
See log for complete Python traceback.
> delete H
> addh
Summary of feedback from adding hydrogens to 588AMS-
CH235p12-M5-293_apply_ncs_31-coot0-rsr34_real_space_refined.pdb #1.2
---
notes | No usable SEQRES records for 588AMS-
CH235p12-M5-293_apply_ncs_31-coot0-rsr34_real_space_refined.pdb (#1.2) chain
A; guessing termini instead
No usable SEQRES records for 588AMS-
CH235p12-M5-293_apply_ncs_31-coot0-rsr34_real_space_refined.pdb (#1.2) chain
B; guessing termini instead
No usable SEQRES records for 588AMS-
CH235p12-M5-293_apply_ncs_31-coot0-rsr34_real_space_refined.pdb (#1.2) chain
C; guessing termini instead
No usable SEQRES records for 588AMS-
CH235p12-M5-293_apply_ncs_31-coot0-rsr34_real_space_refined.pdb (#1.2) chain
D; guessing termini instead
No usable SEQRES records for 588AMS-
CH235p12-M5-293_apply_ncs_31-coot0-rsr34_real_space_refined.pdb (#1.2) chain
E; guessing termini instead
7 messages similar to the above omitted
Chain-initial residues that are actual N termini: /A BMA 535, /B VAL 518, /C
GLN 1, /D GLU 1, /E BMA 535, /F VAL 518, /G GLN 1, /H GLU 1, /I BMA 535, /J
VAL 518, /K GLN 1, /L GLU 1
Chain-initial residues that are not actual N termini: /A THR 71, /A CYS 157,
/A GLY 312, /A ASN 409, /B GLY 572, /C GLY 134, /E THR 71, /E CYS 157, /E GLY
312, /E ASN 409, /F GLY 572, /G GLY 134, /I THR 71, /I CYS 157, /I GLY 312, /I
ASN 409, /J GLY 572, /K GLY 134
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini: /A VAL 503, /A GLU 62, /A
ASN 147, /A ILE 309, /A ASN 398, /B ASP 664, /B SER 546, /C CYS 216, /C SER
128, /D GLY 212, /E VAL 503, /E GLU 62, /E ASN 147, /E ILE 309, /E ASN 398, /F
ASP 664, /F SER 546, /G CYS 216, /G SER 128, /H GLY 212, /I VAL 503, /I GLU
62, /I ASN 147, /I ILE 309, /I ASN 398, /J ASP 664, /J SER 546, /K CYS 216, /K
SER 128, /L GLY 212
2683 hydrogen bonds
Adding 'H' to /A THR 71
Adding 'H' to /A CYS 157
Adding 'H' to /A GLY 312
Adding 'H' to /A ASN 409
Adding 'H' to /B GLY 572
13 messages similar to the above omitted
/A VAL 503 is not terminus, removing H atom from 'C'
/A GLU 62 is not terminus, removing H atom from 'C'
/A ASN 147 is not terminus, removing H atom from 'C'
/A ILE 309 is not terminus, removing H atom from 'C'
/A ASN 398 is not terminus, removing H atom from 'C'
25 messages similar to the above omitted
23652 hydrogens added
> isolde start
> set selectionWidth 4
Done loading forcefield
Traceback (most recent call last):
File "/home/kartikmanne/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/validation/unparameterised.py", line 48, in
_show_main_frame
self._update_unparameterised_residues_list()
File "/home/kartikmanne/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/validation/unparameterised.py", line 79, in
_update_unparameterised_residues_list
template_dict = find_residue_templates(residues, ff, ligand_db=ligand_db,
logger=self.session.logger)
File "/home/kartikmanne/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 3091, in
find_residue_templates
templates[residues.index(prot_res)] = find_glycan_anchor_name(prot_res)
File "/home/kartikmanne/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/openmm/amberff/glycam.py", line 271, in
find_glycan_anchor_name
residue.name, residue.chain_id, residue.number
RuntimeError: Residue BMA A535 is linked to a glycan, but no parameters are
available for this type of linkage.
RuntimeError: Residue BMA A535 is linked to a glycan, but no parameters are
available for this type of linkage.
File "/home/kartikmanne/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/openmm/amberff/glycam.py", line 271, in
find_glycan_anchor_name
residue.name, residue.chain_id, residue.number
See log for complete Python traceback.
> ui tool show ISOLDE
> set selectionWidth 4
Done loading forcefield
Traceback (most recent call last):
File "/home/kartikmanne/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/isolde.py", line 2608, in _xtal_mask_to_selection
self._xtal_mask_to_atoms(sel, focus)
File "/home/kartikmanne/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/isolde.py", line 2617, in _xtal_mask_to_atoms
atoms, 0, context, cutoff, focus=focus)
File "/home/kartikmanne/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/symmetry.py", line 973, in
isolate_and_cover_selection
extra_padding=extra_padding)
File "/home/kartikmanne/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/map_mgr.py", line 358, in cover_atoms
zm.set_symmetry_map(atoms, transforms, transform_indices)
File "/home/kartikmanne/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 111, in set_symmetry_map
self.structure = self._unique_structure(atoms)
File "/home/kartikmanne/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 177, in
_unique_structure
raise TypeError('All atoms for zone mask must be from a single model!')
TypeError: All atoms for zone mask must be from a single model!
TypeError: All atoms for zone mask must be from a single model!
File "/home/kartikmanne/.local/share/ChimeraX/1.0/site-
packages/chimerax/clipper/maps/mask_handler.py", line 177, in
_unique_structure
raise TypeError('All atoms for zone mask must be from a single model!')
See log for complete Python traceback.
Traceback (most recent call last):
File "/home/kartikmanne/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/validation/unparameterised.py", line 48, in
_show_main_frame
self._update_unparameterised_residues_list()
File "/home/kartikmanne/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/validation/unparameterised.py", line 79, in
_update_unparameterised_residues_list
template_dict = find_residue_templates(residues, ff, ligand_db=ligand_db,
logger=self.session.logger)
File "/home/kartikmanne/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 3091, in
find_residue_templates
templates[residues.index(prot_res)] = find_glycan_anchor_name(prot_res)
File "/home/kartikmanne/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/openmm/amberff/glycam.py", line 271, in
find_glycan_anchor_name
residue.name, residue.chain_id, residue.number
RuntimeError: Residue BMA A535 is linked to a glycan, but no parameters are
available for this type of linkage.
RuntimeError: Residue BMA A535 is linked to a glycan, but no parameters are
available for this type of linkage.
File "/home/kartikmanne/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/openmm/amberff/glycam.py", line 271, in
find_glycan_anchor_name
residue.name, residue.chain_id, residue.number
See log for complete Python traceback.
> close session
Deleting atomic symmetry model...
> open "/home/kartikmanne/Documents/CH235
> structures/588AMS_CH235.12-M5-293/RealSpaceRefine_34/588AMS-
> CH235p12-M5-293_apply_ncs_31-coot0-rsr34_real_space_refined-coot-0.pdb"
Chain information for 588AMS-
CH235p12-M5-293_apply_ncs_31-coot0-rsr34_real_space_refined-coot-0.pdb #1
---
Chain | Description
A E I | No description available
B F J | No description available
C G K | No description available
D H L | No description available
> addh
Summary of feedback from adding hydrogens to 588AMS-
CH235p12-M5-293_apply_ncs_31-coot0-rsr34_real_space_refined-coot-0.pdb #1
---
notes | No usable SEQRES records for 588AMS-
CH235p12-M5-293_apply_ncs_31-coot0-rsr34_real_space_refined-coot-0.pdb (#1)
chain A; guessing termini instead
No usable SEQRES records for 588AMS-
CH235p12-M5-293_apply_ncs_31-coot0-rsr34_real_space_refined-coot-0.pdb (#1)
chain B; guessing termini instead
No usable SEQRES records for 588AMS-
CH235p12-M5-293_apply_ncs_31-coot0-rsr34_real_space_refined-coot-0.pdb (#1)
chain C; guessing termini instead
No usable SEQRES records for 588AMS-
CH235p12-M5-293_apply_ncs_31-coot0-rsr34_real_space_refined-coot-0.pdb (#1)
chain D; guessing termini instead
No usable SEQRES records for 588AMS-
CH235p12-M5-293_apply_ncs_31-coot0-rsr34_real_space_refined-coot-0.pdb (#1)
chain E; guessing termini instead
7 messages similar to the above omitted
Chain-initial residues that are actual N termini: /A NAG 534, /B VAL 518, /C
GLN 1, /D GLU 1, /E BMA 535, /F VAL 518, /G GLN 1, /H GLU 1, /I BMA 535, /J
VAL 518, /K GLN 1, /L GLU 1
Chain-initial residues that are not actual N termini: /A THR 71, /A CYS 157,
/A GLY 312, /A ASN 409, /B GLY 572, /C GLY 134, /E THR 71, /E CYS 157, /E GLY
312, /E ASN 409, /F GLY 572, /G GLY 134, /I THR 71, /I CYS 157, /I GLY 312, /I
ASN 409, /J GLY 572, /K GLY 134
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini: /A VAL 503, /A GLU 62, /A
ASN 147, /A ILE 309, /A ASN 398, /B ASP 664, /B SER 546, /C CYS 216, /C SER
128, /D GLY 212, /E VAL 503, /E GLU 62, /E ASN 147, /E ILE 309, /E ASN 398, /F
ASP 664, /F SER 546, /G CYS 216, /G SER 128, /H GLY 212, /I VAL 503, /I GLU
62, /I ASN 147, /I ILE 309, /I ASN 398, /J ASP 664, /J SER 546, /K CYS 216, /K
SER 128, /L GLY 212
2226 hydrogen bonds
/A VAL 503 is not terminus, removing H atom from 'C'
/A GLU 62 is not terminus, removing H atom from 'C'
/A ASN 147 is not terminus, removing H atom from 'C'
/A ILE 309 is not terminus, removing H atom from 'C'
/A ASN 398 is not terminus, removing H atom from 'C'
25 messages similar to the above omitted
133 hydrogens added
> open "/home/kartikmanne/Documents/CH235
> structures/588AMS_CH235.12-M5-293/cryosparc_P41_J32_009_volume_map_sharp_local.mrc"
Opened cryosparc_P41_J32_009_volume_map_sharp_local.mrc, grid size
320,320,320, pixel 1.07, shown at level 0.659, step 2, values float32
> volume #2 step 1
> clipper associate #2 toModel #1
Chain information for 588AMS-
CH235p12-M5-293_apply_ncs_31-coot0-rsr34_real_space_refined-coot-0.pdb
---
Chain | Description
1.2/A 1.2/E 1.2/I | No description available
1.2/B 1.2/F 1.2/J | No description available
1.2/C 1.2/G 1.2/K | No description available
1.2/D 1.2/H 1.2/L | No description available
> isolde start
> set selectionWidth 4
Done loading forcefield
Traceback (most recent call last):
File "/home/kartikmanne/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/validation/unparameterised.py", line 48, in
_show_main_frame
self._update_unparameterised_residues_list()
File "/home/kartikmanne/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/validation/unparameterised.py", line 79, in
_update_unparameterised_residues_list
template_dict = find_residue_templates(residues, ff, ligand_db=ligand_db,
logger=self.session.logger)
File "/home/kartikmanne/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 3091, in
find_residue_templates
templates[residues.index(prot_res)] = find_glycan_anchor_name(prot_res)
File "/home/kartikmanne/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/openmm/amberff/glycam.py", line 271, in
find_glycan_anchor_name
residue.name, residue.chain_id, residue.number
RuntimeError: Residue BMA E535 is linked to a glycan, but no parameters are
available for this type of linkage.
RuntimeError: Residue BMA E535 is linked to a glycan, but no parameters are
available for this type of linkage.
File "/home/kartikmanne/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/openmm/amberff/glycam.py", line 271, in
find_glycan_anchor_name
residue.name, residue.chain_id, residue.number
See log for complete Python traceback.
> close session
Deleting atomic symmetry model...
> open "/home/kartikmanne/Documents/CH235
> structures/588AMS_CH235.12-M5-293/RealSpaceRefine_34/588AMS-
> CH235p12-M5-293_apply_ncs_31-coot0-rsr34_real_space_refined-coot-0.pdb"
Chain information for 588AMS-
CH235p12-M5-293_apply_ncs_31-coot0-rsr34_real_space_refined-coot-0.pdb #1
---
Chain | Description
A E I | No description available
B F J | No description available
C G K | No description available
D H L | No description available
> addh
Summary of feedback from adding hydrogens to 588AMS-
CH235p12-M5-293_apply_ncs_31-coot0-rsr34_real_space_refined-coot-0.pdb #1
---
notes | No usable SEQRES records for 588AMS-
CH235p12-M5-293_apply_ncs_31-coot0-rsr34_real_space_refined-coot-0.pdb (#1)
chain A; guessing termini instead
No usable SEQRES records for 588AMS-
CH235p12-M5-293_apply_ncs_31-coot0-rsr34_real_space_refined-coot-0.pdb (#1)
chain B; guessing termini instead
No usable SEQRES records for 588AMS-
CH235p12-M5-293_apply_ncs_31-coot0-rsr34_real_space_refined-coot-0.pdb (#1)
chain C; guessing termini instead
No usable SEQRES records for 588AMS-
CH235p12-M5-293_apply_ncs_31-coot0-rsr34_real_space_refined-coot-0.pdb (#1)
chain D; guessing termini instead
No usable SEQRES records for 588AMS-
CH235p12-M5-293_apply_ncs_31-coot0-rsr34_real_space_refined-coot-0.pdb (#1)
chain E; guessing termini instead
7 messages similar to the above omitted
Chain-initial residues that are actual N termini: /A NAG 534, /B VAL 518, /C
GLN 1, /D GLU 1, /E NAG 534, /F VAL 518, /G GLN 1, /H GLU 1, /I NAG 534, /J
VAL 518, /K GLN 1, /L GLU 1
Chain-initial residues that are not actual N termini: /A THR 71, /A CYS 157,
/A GLY 312, /A ASN 409, /B GLY 572, /C GLY 134, /E THR 71, /E CYS 157, /E GLY
312, /E ASN 409, /F GLY 572, /G GLY 134, /I THR 71, /I CYS 157, /I GLY 312, /I
ASN 409, /J GLY 572, /K GLY 134
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini: /A VAL 503, /A GLU 62, /A
ASN 147, /A ILE 309, /A ASN 398, /B ASP 664, /B SER 546, /C CYS 216, /C SER
128, /D GLY 212, /E VAL 503, /E GLU 62, /E ASN 147, /E ILE 309, /E ASN 398, /F
ASP 664, /F SER 546, /G CYS 216, /G SER 128, /H GLY 212, /I VAL 503, /I GLU
62, /I ASN 147, /I ILE 309, /I ASN 398, /J ASP 664, /J SER 546, /K CYS 216, /K
SER 128, /L GLY 212
2218 hydrogen bonds
/A VAL 503 is not terminus, removing H atom from 'C'
/A GLU 62 is not terminus, removing H atom from 'C'
/A ASN 147 is not terminus, removing H atom from 'C'
/A ILE 309 is not terminus, removing H atom from 'C'
/A ASN 398 is not terminus, removing H atom from 'C'
25 messages similar to the above omitted
69 hydrogens added
> open "/home/kartikmanne/Documents/CH235
> structures/588AMS_CH235.12-M5-293/cryosparc_P41_J32_009_volume_map_sharp_local.mrc"
Opened cryosparc_P41_J32_009_volume_map_sharp_local.mrc, grid size
320,320,320, pixel 1.07, shown at level 0.659, step 2, values float32
> volume #2 step 1
> clipper associate #2 toModel #1
Chain information for 588AMS-
CH235p12-M5-293_apply_ncs_31-coot0-rsr34_real_space_refined-coot-0.pdb
---
Chain | Description
1.2/A 1.2/E 1.2/I | No description available
1.2/B 1.2/F 1.2/J | No description available
1.2/C 1.2/G 1.2/K | No description available
1.2/D 1.2/H 1.2/L | No description available
> isolde start
> set selectionWidth 4
Done loading forcefield
Fetching CCD ASN_LL from http://ligand-
expo.rcsb.org/reports/A/ASN_LL/ASN_LL.cif
Fetching CCD ASN_LSN3 from http://ligand-
expo.rcsb.org/reports/A/ASN_LSN3/ASN_LSN3.cif
Fetching CCD ASN_LEO2 from http://ligand-
expo.rcsb.org/reports/A/ASN_LEO2/ASN_LEO2.cif
Deleted the following atoms from residue ASN I392: HD22
Deleted the following atoms from residue ASN I386: HD22
Deleted the following atoms from residue ASN I339: HD22
Deleted the following atoms from residue ASN I262: HD22
Deleted the following atoms from residue ASN I197: HD22
Deleted the following atoms from residue ASN E392: HD22
Deleted the following atoms from residue ASN E386: HD22
Deleted the following atoms from residue ASN E339: HD22
Deleted the following atoms from residue ASN E262: HD22
Deleted the following atoms from residue ASN E197: HD22
Deleted the following atoms from residue ASN A392: HD22
Deleted the following atoms from residue ASN A386: HD22
Deleted the following atoms from residue ASN A339: HD22
Deleted the following atoms from residue ASN A262: HD22
Deleted the following atoms from residue ASN A197: HD22
Fetching CCD A2G from http://ligand-expo.rcsb.org/reports/A/A2G/A2G.cif
Fetching CCD NGA from http://ligand-expo.rcsb.org/reports/N/NGA/NGA.cif
Fetching CCD BM3 from http://ligand-expo.rcsb.org/reports/B/BM3/BM3.cif
Fetching CCD BM7 from http://ligand-expo.rcsb.org/reports/B/BM7/BM7.cif
Fetching CCD NDG from http://ligand-expo.rcsb.org/reports/N/NDG/NDG.cif
Deleted the following atoms from residue NAG I532: H11, H12
Deleted the following atoms from residue NAG I528: H11
Deleted the following atoms from residue NAG I522: H11
Deleted the following atoms from residue NAG E532: H12, H11
Deleted the following atoms from residue NAG E528: H11
Deleted the following atoms from residue NAG E522: H11
Deleted the following atoms from residue NAG A532: H11, H12
Deleted the following atoms from residue NAG A528: H11
Deleted the following atoms from residue NAG A522: H11
Fetching CCD CYS_LL from http://ligand-
expo.rcsb.org/reports/C/CYS_LL/CYS_LL.cif
Fetching CCD CYS_LL_DHG from http://ligand-
expo.rcsb.org/reports/C/CYS_LL_DHG/CYS_LL_DHG.cif
Fetching CCD CYS_LSN3 from http://ligand-
expo.rcsb.org/reports/C/CYS_LSN3/CYS_LSN3.cif
Fetching CCD CYS_LSN3_DHG from http://ligand-
expo.rcsb.org/reports/C/CYS_LSN3_DHG/CYS_LSN3_DHG.cif
Fetching CCD CYS_LEO2 from http://ligand-
expo.rcsb.org/reports/C/CYS_LEO2/CYS_LEO2.cif
Fetching CCD CYS_LEO2_DHG from http://ligand-
expo.rcsb.org/reports/C/CYS_LEO2_DHG/CYS_LEO2_DHG.cif
Fetching CCD CSO from http://ligand-expo.rcsb.org/reports/C/CSO/CSO.cif
Fetching CCD CYS_LFZW from http://ligand-
expo.rcsb.org/reports/C/CYS_LFZW/CYS_LFZW.cif
Fetching CCD CSS from http://ligand-expo.rcsb.org/reports/C/CSS/CSS.cif
Fetching CCD SC2 from http://ligand-expo.rcsb.org/reports/S/SC2/SC2.cif
Traceback (most recent call last):
File "/home/kartikmanne/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/validation/unparameterised.py", line 113, in
_show_selected_unparameterised_residue
residue, by_name, by_comp = item.data
ValueError: not enough values to unpack (expected 3, got 2)
ValueError: not enough values to unpack (expected 3, got 2)
File "/home/kartikmanne/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/validation/unparameterised.py", line 113, in
_show_selected_unparameterised_residue
residue, by_name, by_comp = item.data
See log for complete Python traceback.
Traceback (most recent call last):
File "/home/kartikmanne/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/validation/unparameterised.py", line 113, in
_show_selected_unparameterised_residue
residue, by_name, by_comp = item.data
ValueError: not enough values to unpack (expected 3, got 2)
ValueError: not enough values to unpack (expected 3, got 2)
File "/home/kartikmanne/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/validation/unparameterised.py", line 113, in
_show_selected_unparameterised_residue
residue, by_name, by_comp = item.data
See log for complete Python traceback.
Traceback (most recent call last):
File "/home/kartikmanne/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/validation/unparameterised.py", line 113, in
_show_selected_unparameterised_residue
residue, by_name, by_comp = item.data
ValueError: not enough values to unpack (expected 3, got 2)
ValueError: not enough values to unpack (expected 3, got 2)
File "/home/kartikmanne/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/validation/unparameterised.py", line 113, in
_show_selected_unparameterised_residue
residue, by_name, by_comp = item.data
See log for complete Python traceback.
> select #1
47448 atoms, 47985 bonds, 48 pseudobonds, 13 models selected
Traceback (most recent call last):
File "/home/kartikmanne/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/validation/unparameterised.py", line 113, in
_show_selected_unparameterised_residue
residue, by_name, by_comp = item.data
ValueError: not enough values to unpack (expected 3, got 2)
ValueError: not enough values to unpack (expected 3, got 2)
File "/home/kartikmanne/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/validation/unparameterised.py", line 113, in
_show_selected_unparameterised_residue
residue, by_name, by_comp = item.data
See log for complete Python traceback.
Traceback (most recent call last):
File "/home/kartikmanne/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/validation/unparameterised.py", line 113, in
_show_selected_unparameterised_residue
residue, by_name, by_comp = item.data
ValueError: not enough values to unpack (expected 3, got 2)
ValueError: not enough values to unpack (expected 3, got 2)
File "/home/kartikmanne/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/validation/unparameterised.py", line 113, in
_show_selected_unparameterised_residue
residue, by_name, by_comp = item.data
See log for complete Python traceback.
Traceback (most recent call last):
File "/home/kartikmanne/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/validation/unparameterised.py", line 113, in
_show_selected_unparameterised_residue
residue, by_name, by_comp = item.data
ValueError: not enough values to unpack (expected 3, got 2)
ValueError: not enough values to unpack (expected 3, got 2)
File "/home/kartikmanne/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/validation/unparameterised.py", line 113, in
_show_selected_unparameterised_residue
residue, by_name, by_comp = item.data
See log for complete Python traceback.
Traceback (most recent call last):
File "/home/kartikmanne/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/validation/unparameterised.py", line 113, in
_show_selected_unparameterised_residue
residue, by_name, by_comp = item.data
ValueError: not enough values to unpack (expected 3, got 2)
ValueError: not enough values to unpack (expected 3, got 2)
File "/home/kartikmanne/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/validation/unparameterised.py", line 113, in
_show_selected_unparameterised_residue
residue, by_name, by_comp = item.data
See log for complete Python traceback.
> delete H
> addh
Summary of feedback from adding hydrogens to 588AMS-
CH235p12-M5-293_apply_ncs_31-coot0-rsr34_real_space_refined-coot-0.pdb #1.2
---
notes | No usable SEQRES records for 588AMS-
CH235p12-M5-293_apply_ncs_31-coot0-rsr34_real_space_refined-coot-0.pdb (#1.2)
chain A; guessing termini instead
No usable SEQRES records for 588AMS-
CH235p12-M5-293_apply_ncs_31-coot0-rsr34_real_space_refined-coot-0.pdb (#1.2)
chain B; guessing termini instead
No usable SEQRES records for 588AMS-
CH235p12-M5-293_apply_ncs_31-coot0-rsr34_real_space_refined-coot-0.pdb (#1.2)
chain C; guessing termini instead
No usable SEQRES records for 588AMS-
CH235p12-M5-293_apply_ncs_31-coot0-rsr34_real_space_refined-coot-0.pdb (#1.2)
chain D; guessing termini instead
No usable SEQRES records for 588AMS-
CH235p12-M5-293_apply_ncs_31-coot0-rsr34_real_space_refined-coot-0.pdb (#1.2)
chain E; guessing termini instead
7 messages similar to the above omitted
Chain-initial residues that are actual N termini: /A NAG 534, /B VAL 518, /C
GLN 1, /D GLU 1, /E NAG 534, /F VAL 518, /G GLN 1, /H GLU 1, /I NAG 534, /J
VAL 518, /K GLN 1, /L GLU 1
Chain-initial residues that are not actual N termini: /A THR 71, /A CYS 157,
/A GLY 312, /A ASN 409, /B GLY 572, /C GLY 134, /E THR 71, /E CYS 157, /E GLY
312, /E ASN 409, /F GLY 572, /G GLY 134, /I THR 71, /I CYS 157, /I GLY 312, /I
ASN 409, /J GLY 572, /K GLY 134
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini: /A VAL 503, /A GLU 62, /A
ASN 147, /A ILE 309, /A ASN 398, /B ASP 664, /B SER 546, /C CYS 216, /C SER
128, /D GLY 212, /E VAL 503, /E GLU 62, /E ASN 147, /E ILE 309, /E ASN 398, /F
ASP 664, /F SER 546, /G CYS 216, /G SER 128, /H GLY 212, /I VAL 503, /I GLU
62, /I ASN 147, /I ILE 309, /I ASN 398, /J ASP 664, /J SER 546, /K CYS 216, /K
SER 128, /L GLY 212
2660 hydrogen bonds
Adding 'H' to /A THR 71
Adding 'H' to /A CYS 157
Adding 'H' to /A GLY 312
Adding 'H' to /A ASN 409
Adding 'H' to /B GLY 572
13 messages similar to the above omitted
/A VAL 503 is not terminus, removing H atom from 'C'
/A GLU 62 is not terminus, removing H atom from 'C'
/A ASN 147 is not terminus, removing H atom from 'C'
/A ILE 309 is not terminus, removing H atom from 'C'
/A ASN 398 is not terminus, removing H atom from 'C'
25 messages similar to the above omitted
23532 hydrogens added
Fetching CCD ASP_LL_DHD2 from http://ligand-
expo.rcsb.org/reports/A/ASP_LL_DHD2/ASP_LL_DHD2.cif
Fetching CCD ASP_LL from http://ligand-
expo.rcsb.org/reports/A/ASP_LL/ASP_LL.cif
Fetching CCD ASP_LSN3_DHD2 from http://ligand-
expo.rcsb.org/reports/A/ASP_LSN3_DHD2/ASP_LSN3_DHD2.cif
Fetching CCD ASP_LEO2_DHD2 from http://ligand-
expo.rcsb.org/reports/A/ASP_LEO2_DHD2/ASP_LEO2_DHD2.cif
Fetching CCD ASP_LFZW_DHD2 from http://ligand-
expo.rcsb.org/reports/A/ASP_LFZW_DHD2/ASP_LFZW_DHD2.cif
Fetching CCD HIS_LEO2_DHE2 from http://ligand-
expo.rcsb.org/reports/H/HIS_LEO2_DHE2/HIS_LEO2_DHE2.cif
Fetching CCD HIS_LEO2_DHD1 from http://ligand-
expo.rcsb.org/reports/H/HIS_LEO2_DHD1/HIS_LEO2_DHD1.cif
Fetching CCD HIS_LEO2 from http://ligand-
expo.rcsb.org/reports/H/HIS_LEO2/HIS_LEO2.cif
Fetching CCD HIS_LFZW_DHE2 from http://ligand-
expo.rcsb.org/reports/H/HIS_LFZW_DHE2/HIS_LFZW_DHE2.cif
Fetching CCD HIS_LFZW_DHD1 from http://ligand-
expo.rcsb.org/reports/H/HIS_LFZW_DHD1/HIS_LFZW_DHD1.cif
Fetching CCD HIS_LFZW from http://ligand-
expo.rcsb.org/reports/H/HIS_LFZW/HIS_LFZW.cif
Deleted the following atoms from residue NAG I534: HO4
Deleted the following atoms from residue NAG E534: HO4
Deleted the following atoms from residue NAG A534: HO4
Deleted the following atoms from residue NAG I532: HO4, H11, H12
Deleted the following atoms from residue NAG I528: H11, HO4, H12
Deleted the following atoms from residue NAG I522: H11, HO4, H12
Deleted the following atoms from residue NAG E532: H12, HO4, H11
Deleted the following atoms from residue NAG E528: H12, H11, HO4
Deleted the following atoms from residue NAG E522: HO4, H11, H12
Deleted the following atoms from residue NAG A532: HO4, H12, H11
Deleted the following atoms from residue NAG A528: H12, HO4, H11
Deleted the following atoms from residue NAG A522: H12, H11, HO4
> select #1
47439 atoms, 47976 bonds, 48 pseudobonds, 19 models selected
> select #1
47451 atoms, 47988 bonds, 48 pseudobonds, 19 models selected
Traceback (most recent call last):
File "/home/kartikmanne/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/validation/unparameterised.py", line 113, in
_show_selected_unparameterised_residue
residue, by_name, by_comp = item.data
ValueError: not enough values to unpack (expected 3, got 2)
ValueError: not enough values to unpack (expected 3, got 2)
File "/home/kartikmanne/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/validation/unparameterised.py", line 113, in
_show_selected_unparameterised_residue
residue, by_name, by_comp = item.data
See log for complete Python traceback.
Traceback (most recent call last):
File "/home/kartikmanne/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/validation/unparameterised.py", line 113, in
_show_selected_unparameterised_residue
residue, by_name, by_comp = item.data
ValueError: not enough values to unpack (expected 3, got 2)
ValueError: not enough values to unpack (expected 3, got 2)
File "/home/kartikmanne/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/validation/unparameterised.py", line 113, in
_show_selected_unparameterised_residue
residue, by_name, by_comp = item.data
See log for complete Python traceback.
Traceback (most recent call last):
File "/home/kartikmanne/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/validation/unparameterised.py", line 113, in
_show_selected_unparameterised_residue
residue, by_name, by_comp = item.data
ValueError: not enough values to unpack (expected 3, got 2)
ValueError: not enough values to unpack (expected 3, got 2)
File "/home/kartikmanne/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/validation/unparameterised.py", line 113, in
_show_selected_unparameterised_residue
residue, by_name, by_comp = item.data
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 430.40
OpenGL renderer: GeForce RTX 2080 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: TYAN
Model: B7105F48TV8HR-2T-G
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
CPU: 64 Intel(R) Xeon(R) Silver 4216 CPU @ 2.10GHz
Cache Size: 22528 KB
Memory:
total used free shared buff/cache available
Mem: 187G 10G 169G 240M 7.0G 175G
Swap: 9G 0B 9G
Graphics:
04:00.0 VGA compatible controller [0300]: ASPEED Technology, Inc. ASPEED Graphics Family [1a03:2000] (rev 41)
Subsystem: ASPEED Technology, Inc. ASPEED Graphics Family [1a03:2000]
Kernel driver in use: ast
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.8
Change History (9)
comment:1 by , 5 years ago
| Component: | Unassigned → Third Party |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → _show_selected_unparameterised_residue: not enough values to unpack |
follow-up: 3 comment:3 by , 5 years ago
Hi Tristan,
__ I was waiting for the release actually.
I have been building glycans using coot 0.9 EL-->modules-->Glyco-->N-linked glycan addition. I have only been choosing what are being suggested and possible.
I tried removing all the glycans and then run it on ISOLDE simulation, it works fine now. But that also means I have to rebuild the glycans after ISOLDE simulation and that changes the model/clashes a little bit.
Any thoughts?
Thanks,
Kartik
On 8/5/20, 5:39 PM, "ChimeraX" <ChimeraX-bugs-admin@cgl.ucsf.edu> wrote:
#3601: _show_selected_unparameterised_residue: not enough values to unpack
-------------------------------------+---------------------------
Reporter: kartik.manne@… | Owner: Tristan Croll
Type: defect | Status: assigned
Priority: normal | Milestone:
Component: Third Party | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
-------------------------------------+---------------------------
Comment (by Tristan Croll):
{{{
Wow, that was quick - haven’t even announced it yet! Will look into the
headline error in the morning, but there’s still something badly wrong
with your glycans - ISOLDE’s telling you that some of the sugar residues
are linked to others in ways that are not biologically possible.
}}}
--
Ticket URL: <https://urldefense.com/v3/__https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/3601*comment:2__;Iw!!OToaGQ!--aiYkFrDujoI1Wshd1kS1pNGuxJpRRxSBcogK4stvB_6tHardajSYuP3Mer5ZxLWp0$ >
ChimeraX <https://urldefense.com/v3/__http://www.rbvi.ucsf.edu/chimerax/__;!!OToaGQ!--aiYkFrDujoI1Wshd1kS1pNGuxJpRRxSBcogK4stvB_6tHardajSYuP3Merpv_45PQ$ >
ChimeraX Issue Tracker
follow-up: 4 comment:4 by , 5 years ago
This actually looks like it's being caused by a bug in the ChimeraX PDB
reader. In the PDB file Kartik sent me, some of the glycans appear as
HETATMs *before* the first amino acid residue of the chain they're part
of:
{{{
HETATM 396 HO3 NAG A 534 197.121 183.929 145.850 1.00124.14
H
HETATM 397 HO6 NAG A 534 198.128 178.244 148.262 1.00124.14
H
HETATM 398 C1 BMA A 535 198.987 181.656 145.981 1.00114.98
C
HETATM 399 C2 BMA A 535 200.153 181.067 145.212 1.00114.98
C
HETATM 400 C3 BMA A 535 201.302 181.315 146.179 1.00114.98
C
HETATM 401 C4 BMA A 535 201.480 182.827 146.365 1.00114.98
C
HETATM 402 C5 BMA A 535 200.208 183.307 147.064 1.00114.98
C
HETATM 403 C6 BMA A 535 200.163 184.747 147.547 1.00114.98
C
HETATM 404 O2 BMA A 535 200.240 181.710 143.942 1.00114.98
O
HETATM 405 O3 BMA A 535 202.537 180.636 145.942 1.00114.98
O
HETATM 406 O4 BMA A 535 202.643 183.129 147.132 1.00114.98
O
HETATM 407 O5 BMA A 535 199.159 183.052 146.149 1.00114.98
O
HETATM 408 O6 BMA A 535 201.055 185.594 146.842 1.00114.98
O
HETATM 409 H2 BMA A 535 199.995 179.987 145.098 1.00114.98
H
HETATM 410 H3 BMA A 535 200.933 180.875 147.093 1.00114.98
H
HETATM 411 H4 BMA A 535 201.580 183.320 145.393 1.00114.98
H
HETATM 412 H5 BMA A 535 200.017 182.719 147.968 1.00114.98
H
HETATM 413 H61 BMA A 535 200.400 184.754 148.611 1.00114.98
H
HETATM 414 H62 BMA A 535 199.142 185.117 147.438 1.00114.98
H
HETATM 415 HO2 BMA A 535 199.505 182.333 143.859 1.00114.98
H
HETATM 416 HO4 BMA A 535 203.368 182.547 146.874 1.00114.98
H
ATOM 417 N GLU A 32 198.567 176.510 228.289 1.00147.83
A N
ATOM 418 CA GLU A 32 197.692 175.328 228.511 1.00147.83
A C
ATOM 419 C GLU A 32 196.210 175.734 228.483 1.00147.83
A C
ATOM 420 O GLU A 32 195.908 176.911 228.335 1.00147.83
A O
}}}
What's breaking ISOLDE is that BMA A 535 is being assigned residue type
PT_AMINO. For each sugar residue ISOLDE looks through its bonded
neighbors to see if any are amino acids, and then looks up a map to see
if it has parameters for that amino acid-sugar link. For obvious reasons
it doesn't find BMA in that map, and everything falls apart. Kartik,
it'd be really helpful if you could share this file with the ChimeraX
team for debugging. Meanwhile, everything *should work if you move the
sugars to after the protein component of each chain.
On 2020-08-05 22:51, ChimeraX wrote:
follow-up: 5 comment:5 by , 5 years ago
Hey Tristan,
Do you want me to share the pdb file by replying all (like this)?
Also, what does that mean when you say "move the sugars to after the protein component of each chain."?
Manually cut and paste the glycans in the pdb file to the end of each chain?
Thanks,
Kartik
Kartik Manne, Ph.D.
Postdoctoral Associate
Priyamvada Acharya's lab
Duke Human Vaccine Institute
(919)681-3917 (office)
(248)631-8230 (mobile)
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Wednesday, August 5, 2020 6:40 PM
To: Kartik Manne, Ph.D. <kartik.manne@duke.edu>; tic20@cam.ac.uk <tic20@cam.ac.uk>
Subject: Re: [ChimeraX] #3601: _show_selected_unparameterised_residue: not enough values to unpack
#3601: _show_selected_unparameterised_residue: not enough values to unpack
-------------------------------------+---------------------------
Reporter: kartik.manne@… | Owner: Tristan Croll
Type: defect | Status: assigned
Priority: normal | Milestone:
Component: Third Party | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
-------------------------------------+---------------------------
Comment (by Tristan Croll):
{{{
This actually looks like it's being caused by a bug in the ChimeraX PDB
reader. In the PDB file Kartik sent me, some of the glycans appear as
HETATMs *before* the first amino acid residue of the chain they're part
of:
{{{
HETATM 396 HO3 NAG A 534 197.121 183.929 145.850 1.00124.14
H
HETATM 397 HO6 NAG A 534 198.128 178.244 148.262 1.00124.14
H
HETATM 398 C1 BMA A 535 198.987 181.656 145.981 1.00114.98
C
HETATM 399 C2 BMA A 535 200.153 181.067 145.212 1.00114.98
C
HETATM 400 C3 BMA A 535 201.302 181.315 146.179 1.00114.98
C
HETATM 401 C4 BMA A 535 201.480 182.827 146.365 1.00114.98
C
HETATM 402 C5 BMA A 535 200.208 183.307 147.064 1.00114.98
C
HETATM 403 C6 BMA A 535 200.163 184.747 147.547 1.00114.98
C
HETATM 404 O2 BMA A 535 200.240 181.710 143.942 1.00114.98
O
HETATM 405 O3 BMA A 535 202.537 180.636 145.942 1.00114.98
O
HETATM 406 O4 BMA A 535 202.643 183.129 147.132 1.00114.98
O
HETATM 407 O5 BMA A 535 199.159 183.052 146.149 1.00114.98
O
HETATM 408 O6 BMA A 535 201.055 185.594 146.842 1.00114.98
O
HETATM 409 H2 BMA A 535 199.995 179.987 145.098 1.00114.98
H
HETATM 410 H3 BMA A 535 200.933 180.875 147.093 1.00114.98
H
HETATM 411 H4 BMA A 535 201.580 183.320 145.393 1.00114.98
H
HETATM 412 H5 BMA A 535 200.017 182.719 147.968 1.00114.98
H
HETATM 413 H61 BMA A 535 200.400 184.754 148.611 1.00114.98
H
HETATM 414 H62 BMA A 535 199.142 185.117 147.438 1.00114.98
H
HETATM 415 HO2 BMA A 535 199.505 182.333 143.859 1.00114.98
H
HETATM 416 HO4 BMA A 535 203.368 182.547 146.874 1.00114.98
H
ATOM 417 N GLU A 32 198.567 176.510 228.289 1.00147.83
A N
ATOM 418 CA GLU A 32 197.692 175.328 228.511 1.00147.83
A C
ATOM 419 C GLU A 32 196.210 175.734 228.483 1.00147.83
A C
ATOM 420 O GLU A 32 195.908 176.911 228.335 1.00147.83
A O
}}}
What's breaking ISOLDE is that BMA A 535 is being assigned residue type
PT_AMINO. For each sugar residue ISOLDE looks through its bonded
neighbors to see if any are amino acids, and then looks up a map to see
if it has parameters for that amino acid-sugar link. For obvious reasons
it doesn't find BMA in that map, and everything falls apart. Kartik,
it'd be really helpful if you could share this file with the ChimeraX
team for debugging. Meanwhile, everything *should work if you move the
sugars to after the protein component of each chain.
On 2020-08-05 22:51, ChimeraX wrote:
}}}
--
Ticket URL: <https://urldefense.com/v3/__https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/3601*comment:4__;Iw!!OToaGQ!55bwx27FWbPwMb0VdYN6oK88FZS7itTH6FPuWEMaU79-AjiUA-XZlWCtAMrMu-vUDjM$ >
ChimeraX <https://urldefense.com/v3/__http://www.rbvi.ucsf.edu/chimerax/__;!!OToaGQ!55bwx27FWbPwMb0VdYN6oK88FZS7itTH6FPuWEMaU79-AjiUA-XZlWCtAMrM2Y-onY4$ >
ChimeraX Issue Tracker
follow-up: 6 comment:6 by , 5 years ago
Yep - if you reply to the bug tracker email with the file attached, they’ll get it. It can also be removed from the bug tracker history immediately to ensure it stays confidential. And yes - I just confirmed that simply cutting and pasting the sugars in the PDB file to appear after the end of their protein chains fixes the problem. One other note: pay close attention to the geometry at the Asn-Nag bond - it’s very common to see the sugar flipped 180 degrees from what it should be, which throws out the geometry of the whole glycan. Looked to me like the stem of the glycan containing BMA535 might be flipped in this way.
comment:7 by , 5 years ago
You don't need to send the PDB file. This is a problem with the PDB file, not the PDB reader. Residues of a chain have to be in chain order as listed by the SEQRES records. branched residues and/or bound ligands have to be after the first TER card of the chain.
follow-up: 8 comment:8 by , 5 years ago
Hi Eric,
Thanks for the feedback.
It works now.
Thank you both,
Kartik
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Wednesday, August 5, 2020 7:03 PM
Cc: Kartik Manne, Ph.D. <kartik.manne@duke.edu>; tic20@cam.ac.uk <tic20@cam.ac.uk>
Subject: Re: [ChimeraX] #3601: _show_selected_unparameterised_residue: not enough values to unpack
#3601: _show_selected_unparameterised_residue: not enough values to unpack
-------------------------------------+---------------------------
Reporter: kartik.manne@… | Owner: Tristan Croll
Type: defect | Status: assigned
Priority: normal | Milestone:
Component: Third Party | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
-------------------------------------+---------------------------
Comment (by Eric Pettersen):
You don't need to send the PDB file. This is a problem with the PDB file,
not the PDB reader. Residues of a chain have to be in chain order as
listed by the SEQRES records. branched residues and/or bound ligands have
to be after the first TER card of the chain.
--
Ticket URL: <https://urldefense.com/v3/__https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/3601*comment:7__;Iw!!OToaGQ!95yZwspaC9c9Frk4Vz7DXUgRlbFMUsy35h1hDiwk4bXC0AZhs6XcLi2sJGiMlAXezio$ >
ChimeraX <https://urldefense.com/v3/__http://www.rbvi.ucsf.edu/chimerax/__;!!OToaGQ!95yZwspaC9c9Frk4Vz7DXUgRlbFMUsy35h1hDiwk4bXC0AZhs6XcLi2sJGiMLjPIPJk$ >
ChimeraX Issue Tracker
comment:9 by , 3 years ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
Sorry for not closing this back then... better late than never!
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