Opened 4 years ago

Closed 4 years ago

#5404 closed defect (fixed)

Fix residue: Not enough connected atoms to form a dihedral

Reported by: chimerax-bug-report@… Owned by: Tristan Croll
Priority: normal Milestone:
Component: Third Party Version:
Keywords: Cc: pett
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-3.10.0-1160.36.2.el7.x86_64-x86_64-with-glibc2.14
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /home/local/CORNELL/cryosparc/Desktop/FS_J81_TIMCRY/TIM_J129.pdb format
> pdb

TIM_J129.pdb title:  
Alphafold V2.0 prediction for protein timeless (P49021) [more info...]  
  
Chain information for TIM_J129.pdb #1  
---  
Chain | Description  
A | protein timeless  
  

> open /home/local/CORNELL/cryosparc/Desktop/FS_J81_TIMCRY/J129/J129_zfilp.mrc

Opened J129_zfilp.mrc as #2, grid size 300,300,300, pixel 1.03, shown at level
0.0901, step 2, values float32  

> clipper associate #2 toModel #1

Opened J129_zfilp.mrc as #1.1.1.1, grid size 300,300,300, pixel 1.03, shown at
level 0.659, step 1, values float32  
TIM_J129.pdb title:  
Alphafold V2.0 prediction for protein timeless (P49021) [more info...]  
  
Chain information for TIM_J129.pdb  
---  
Chain | Description  
1.2/A | protein timeless  
  

> isolde start

> set selectionWidth 4

Done loading forcefield  

> addh

Summary of feedback from adding hydrogens to TIM_J129.pdb #1.2  
---  
warnings | Not adding hydrogens to /A PHE 783 CE1 because it is missing heavy-
atom bond partners  
Not adding hydrogens to /A PHE 783 CZ because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A ALA 784 CA because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A THR 785 CA because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A THR 785 CB because it is missing heavy-atom bond
partners  
10 messages similar to the above omitted  
notes | Termini for TIM_J129.pdb (#1.2) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini: /A MET 1, /A ALA 784, /A LEU
786, /A GLU 787, /A VAL 788, /A MET 789  
Chain-initial residues that are not actual N termini: /A THR 575, /A HIS 790,
/A VAL 992  
Chain-final residues that are actual C termini: /A ALA 784, /A THR 785, /A LEU
786, /A GLU 787, /A VAL 788, /A MET 789  
Chain-final residues that are not actual C termini: /A PHE 248, /A PHE 783, /A
MET 862, /A ALA 1128  
Missing OXT added to C-terminal residue /A THR 785  
Missing OXT added to C-terminal residue /A LEU 786  
Missing OXT added to C-terminal residue /A VAL 788  
donor: /A GLN 829 NE2 acceptor: /A MET 789 O  
  
Traceback (most recent call last):  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 280, in execute  
cmd.run(cmd_text)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.8/site-
packages/chimerax/addh/cmd.py", line 63, in cmd_addh  
add_h_func(session, structures, template=template, in_isolation=in_isolation,
**prot_schemes)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.8/site-
packages/chimerax/addh/cmd.py", line 170, in hbond_add_hydrogens  
add_hydrogens(session, atoms, type_info_for_atom, naming_schemas,
hydrogen_totals,  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.8/site-
packages/chimerax/addh/hbond.py", line 245, in add_hydrogens  
hbonds = find_hbonds(session, s_list, dist_slop=rec_dist_slop,
angle_slop=rec_angle_slop)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.8/site-
packages/chimerax/hbonds/hbond.py", line 606, in find_hbonds  
if not geom_func(donor_atom, donor_hyds, *args):  
TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given  
  
TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given  
  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.8/site-
packages/chimerax/hbonds/hbond.py", line 606, in find_hbonds  
if not geom_func(donor_atom, donor_hyds, *args):  
  
See log for complete Python traceback.  
  

> hide HC

> select #1

9282 atoms, 9395 bonds, 673 residues, 12 models selected  

> isolde sim start sel

ISOLDE: stopped sim  
Traceback (most recent call last):  
File "/users/cryosparc/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/validation/unparameterised.py", line 174, in
_fix_selected_unparameterised_residue  
residue, template_name, ccd_template = item.data  
TypeError: cannot unpack non-iterable builtin_function_or_method object  
  
TypeError: cannot unpack non-iterable builtin_function_or_method object  
  
File "/users/cryosparc/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/validation/unparameterised.py", line 174, in
_fix_selected_unparameterised_residue  
residue, template_name, ccd_template = item.data  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/users/cryosparc/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/validation/unparameterised.py", line 174, in
_fix_selected_unparameterised_residue  
residue, template_name, ccd_template = item.data  
TypeError: cannot unpack non-iterable builtin_function_or_method object  
  
TypeError: cannot unpack non-iterable builtin_function_or_method object  
  
File "/users/cryosparc/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/validation/unparameterised.py", line 174, in
_fix_selected_unparameterised_residue  
residue, template_name, ccd_template = item.data  
  
See log for complete Python traceback.  
  
Deleted the following atoms from residue MET A862: HN, H  
Residue MET A789 has only 2 connected atoms in common with template MET_LL. At
least 3 matching atoms are needed.  
Traceback (most recent call last):  
File "/users/cryosparc/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/validation/unparameterised.py", line 174, in
_fix_selected_unparameterised_residue  
residue, template_name, ccd_template = item.data  
TypeError: cannot unpack non-iterable builtin_function_or_method object  
  
TypeError: cannot unpack non-iterable builtin_function_or_method object  
  
File "/users/cryosparc/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/validation/unparameterised.py", line 174, in
_fix_selected_unparameterised_residue  
residue, template_name, ccd_template = item.data  
  
See log for complete Python traceback.  
  
Deleted the following atoms from residue LEU A786: N, C, O, CA, CB, CD2, OXT,
HB1, HB2  
Traceback (most recent call last):  
File "/users/cryosparc/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/validation/unparameterised.py", line 185, in
_fix_selected_unparameterised_residue  
fix_residue_to_match_md_template(self.session, r, template,
cif_template=ccd_template)  
File "/users/cryosparc/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/atomic/template_utils.py", line 329, in
fix_residue_to_match_md_template  
fix_residue_from_template(residue, cif_template, template_indices=ccd_indices)  
File "/users/cryosparc/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/atomic/template_utils.py", line 278, in
fix_residue_from_template  
build_next_atom_from_geometry(residue, ra, tn, ta)  
File "/users/cryosparc/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/atomic/template_utils.py", line 512, in
build_next_atom_from_geometry  
raise TypeError('No n3 found - Not enough connected atoms to form a
dihedral!')  
TypeError: No n3 found - Not enough connected atoms to form a dihedral!  
  
TypeError: No n3 found - Not enough connected atoms to form a dihedral!  
  
File "/users/cryosparc/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/atomic/template_utils.py", line 512, in
build_next_atom_from_geometry  
raise TypeError('No n3 found - Not enough connected atoms to form a
dihedral!')  
  
See log for complete Python traceback.  
  

> hide HC

> select #1

9464 atoms, 9578 bonds, 673 residues, 18 models selected  

> isolde sim start #1

> set selectionWidth 4

ISOLDE: stopped sim  
Done loading forcefield  
Traceback (most recent call last):  
File "/users/cryosparc/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/validation/unparameterised.py", line 174, in
_fix_selected_unparameterised_residue  
residue, template_name, ccd_template = item.data  
TypeError: cannot unpack non-iterable builtin_function_or_method object  
  
TypeError: cannot unpack non-iterable builtin_function_or_method object  
  
File "/users/cryosparc/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/validation/unparameterised.py", line 174, in
_fix_selected_unparameterised_residue  
residue, template_name, ccd_template = item.data  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/users/cryosparc/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/validation/unparameterised.py", line 174, in
_fix_selected_unparameterised_residue  
residue, template_name, ccd_template = item.data  
TypeError: cannot unpack non-iterable builtin_function_or_method object  
  
TypeError: cannot unpack non-iterable builtin_function_or_method object  
  
File "/users/cryosparc/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/validation/unparameterised.py", line 174, in
_fix_selected_unparameterised_residue  
residue, template_name, ccd_template = item.data  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/users/cryosparc/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/validation/unparameterised.py", line 185, in
_fix_selected_unparameterised_residue  
fix_residue_to_match_md_template(self.session, r, template,
cif_template=ccd_template)  
File "/users/cryosparc/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/atomic/template_utils.py", line 329, in
fix_residue_to_match_md_template  
fix_residue_from_template(residue, cif_template, template_indices=ccd_indices)  
File "/users/cryosparc/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/atomic/template_utils.py", line 278, in
fix_residue_from_template  
build_next_atom_from_geometry(residue, ra, tn, ta)  
File "/users/cryosparc/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/atomic/template_utils.py", line 512, in
build_next_atom_from_geometry  
raise TypeError('No n3 found - Not enough connected atoms to form a
dihedral!')  
TypeError: No n3 found - Not enough connected atoms to form a dihedral!  
  
TypeError: No n3 found - Not enough connected atoms to form a dihedral!  
  
File "/users/cryosparc/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/atomic/template_utils.py", line 512, in
build_next_atom_from_geometry  
raise TypeError('No n3 found - Not enough connected atoms to form a
dihedral!')  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 460.67
OpenGL renderer: GeForce RTX 3090/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: To Be Filled By O.E.M.
Model: To Be Filled By O.E.M.
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
Virutal Machine: none
CPU: 48 AMD Ryzen Threadripper 3960X 24-Core Processor
Cache Size: 512 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:           125G        7.2G        7.6G        227M        110G        117G
	Swap:           15G        1.0G         14G

Graphics:
	01:00.0 VGA compatible controller [0300]: NVIDIA Corporation Device [10de:2204] (rev a1)	
	Subsystem: Gigabyte Technology Co., Ltd Device [1458:403b]	
	Kernel driver in use: nvidia
Locale: ('en_US', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.12.5
    cftime: 1.5.0
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0.1
    ChimeraX-AddH: 2.1.6
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AmberInfo: 1.0
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    ChimeraX-Atomic: 1.13.2
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    ChimeraX-CrystalContacts: 1.0
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    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.3
    ChimeraX-DistUI: 1.0
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    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.0
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.1
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    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.2.1
    ChimeraX-MDcrds: 2.2
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
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    ChimeraX-MMTF: 2.1
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    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
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    ChimeraX-ReadPbonds: 1.0
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    ChimeraX-RotamerLibsDynameomics: 2.0
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    ChimeraX-SaveCommand: 1.4
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    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
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    Pygments: 2.7.1
    PyOpenGL: 3.1.5
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    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
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    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.1
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    tifffile: 2020.9.3
    tinyarray: 1.2.3
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    traitlets: 5.0.5
    urllib3: 1.25.11
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.0
    wheel-filename: 1.2.0

Change History (2)

comment:1 by pett, 4 years ago

Cc: pett added
Component: Unassigned → Third Party
Owner: set to Tristan Croll
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Fix residue: Not enough connected atoms to form a dihedral

Probably badly incomplete or disconnected structure

comment:2 by Tristan Croll, 4 years ago

Resolution: → fixed
Status: assigned → closed

I *think* everything in here has been taken care of by recent bug-fixes...

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