FindHBond: accPhiPsi() takes exactly N arguments

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.22621
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "E:/Modle Building/231204-Trimer/Trimer_BA.1_32503_coot_1.pdb"

Summary of feedback from opening E:/Modle
Building/231204-Trimer/Trimer_BA.1_32503_coot_1.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 15 15 PRO I
292 THR I 299 1 8  
Start residue of secondary structure not found: HELIX 16 16 CYS I 735 TYR I
738 1 4  
Start residue of secondary structure not found: HELIX 17 17 GLU I 745 LEU I
750 1 6  
Start residue of secondary structure not found: HELIX 18 18 CYS I 757 PHE I
779 1 23  
Start residue of secondary structure not found: HELIX 19 19 PRO I 814 PHE I
820 1 7  
87 messages similar to the above omitted  
End residue of secondary structure not found: SHEET 131 13113 ASN G 391 ILE G
399 0  
End residue of secondary structure not found: SHEET 132 13213 GLY G 428 ASN G
434 0  
Start residue of secondary structure not found: SHEET 133 13313 LEU G 449 ARG
G 451 0  
Start residue of secondary structure not found: SHEET 135 13513 TYR G 505 GLU
G 513 0  
  
Chain information for Trimer_BA.1_32503_coot_1.pdb #1  
---  
Chain | Description  
A B | No description available  
C E | No description available  
D | No description available  
F H | No description available  
G | No description available  
  

> open "E:/Modle Building/231204-Trimer/emd_32503.mrc"

Opened emd_32503.mrc as #2, grid size 320,320,320, pixel 1.06, shown at level
0.00548, step 2, values float32  

> ui tool show ISOLDE

> set selectionWidth 4

> isolde set simFidelityMode Highest/Slowest

ISOLDE: setting sim fidelity mode to Highest/Slowest  
nonbonded_cutoff_distance = 1.700000  
use_gbsa = True  
gbsa_cutoff = 2.000000  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 319 residues in model #1 to IUPAC-IUB
standards.  
Chain information for Trimer_BA.1_32503_coot_1.pdb  
---  
Chain | Description  
1.2/A 1.2/B | No description available  
1.2/C 1.2/E | No description available  
1.2/D | No description available  
1.2/F 1.2/H | No description available  
1.2/G | No description available  
  
ISOLDE: created disulfide bonds between the following residues:  
H333-H358; G1079-G1123; F535-F587; H535-H587; G735-G757; F1079-F1123;
H388-H522; G376-G429; D22-D95; G535-G587; H15-H134; H1079-H1123; G1029-G1040;
G614-G646; H735-H757; F333-F358; F1029-F1040; H1029-H1040; A22-A95; F477-F485;
E22-E96; F735-F757; G129-G161; F388-F522; H376-H429; F376-F429; H659-H668;
G288-G298; G333-G358; G740-G746; G659-G668; F740-F746; H740-H746; F288-F298;
F614-F646; G15-G134; H288-H298; C22-C96; H129-H161; H477-H485; F129-F161;
B22-B95; F15-F134; G388-G522; H614-H646; F659-F668  

> clipper associate #2 toModel #1

Opened emd_32503.mrc as #1.1.1.1, grid size 320,320,320, pixel 1.06, shown at
step 1, values float32  

> isolde sim start /F-H,A-E

Sim termination reason: None  
ISOLDE: stopped sim  

> addh #1.2

Summary of feedback from adding hydrogens to Trimer_BA.1_32503_coot_1.pdb #1.2  
---  
notes | No usable SEQRES records for Trimer_BA.1_32503_coot_1.pdb (#1.2) chain
A; guessing termini instead  
No usable SEQRES records for Trimer_BA.1_32503_coot_1.pdb (#1.2) chain B;
guessing termini instead  
No usable SEQRES records for Trimer_BA.1_32503_coot_1.pdb (#1.2) chain C;
guessing termini instead  
No usable SEQRES records for Trimer_BA.1_32503_coot_1.pdb (#1.2) chain D;
guessing termini instead  
No usable SEQRES records for Trimer_BA.1_32503_coot_1.pdb (#1.2) chain E;
guessing termini instead  
3 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /A GLU 1, /B GLU 1, /C GLU
1, /D GLU 1, /E GLU 1, /F GLN 14, /G GLN 14, /H GLN 14  
Chain-initial residues that are not actual N termini: /D ARG 19, /D VAL 67, /D
ALA 91, /F MET 148, /F ASN 180, /F ALA 259, /F TYR 633, /F SER 688, /F ALA
843, /G MET 148, /G ASN 180, /G ALA 259, /G VAL 347, /G GLU 403, /G ASP 439,
/G LEU 452, /G ASN 457, /G PRO 488, /G ARG 506, /G TYR 633, /G SER 688, /G ALA
843, /H MET 148, /H ASN 180, /H ALA 259, /H TYR 633, /H SER 688, /H ALA 843  
Chain-final residues that are actual C termini: /C SER 120, /E SER 120, /F SER
1144, /G SER 1144, /H SER 1144  
Chain-final residues that are not actual C termini: /A VAL 116, /B VAL 116, /D
VAL 114, /D GLY 9, /D ASN 60, /D MET 82, /F HIS 141, /F LEU 171, /F ARG 243,
/F GLN 625, /F THR 675, /F VAL 823, /G HIS 141, /G LEU 171, /G ARG 243, /G PHE
344, /G VAL 398, /G TRP 433, /G TYR 448, /G ARG 454, /G THR 467, /G TYR 498,
/G GLN 625, /G THR 675, /G VAL 823, /H HIS 141, /H LEU 171, /H ARG 243, /H GLN
625, /H THR 675, /H VAL 823  
donor: /F SER 527 OG acceptor: /F LYS 525 OXT  
  
Traceback (most recent call last):  
File "C:\Users\jxh57\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\ui\validation_tab\unparameterised.py", line 76, in
_populate_unparameterised_residue_table  
self._ask_to_add_hydrogens_if_necessary(residues)  
File "C:\Users\jxh57\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\ui\validation_tab\unparameterised.py", line 224, in
_ask_to_add_hydrogens_if_necessary  
run(self.session, f'addh #{residues.unique_structures[0].id_string}')  
File "D:\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "D:\ChimeraX\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "D:\ChimeraX\ChimeraX\bin\lib\site-packages\chimerax\addh\cmd.py", line
66, in cmd_addh  
add_h_func(session, structures, template=template, in_isolation=in_isolation,
**prot_schemes)  
File "D:\ChimeraX\ChimeraX\bin\lib\site-packages\chimerax\addh\cmd.py", line
173, in hbond_add_hydrogens  
add_hydrogens(session, atoms, type_info_for_atom, naming_schemas,
hydrogen_totals,  
File "D:\ChimeraX\ChimeraX\bin\lib\site-packages\chimerax\addh\hbond.py", line
248, in add_hydrogens  
hbonds = find_hbonds(session, s_list, dist_slop=rec_dist_slop,
angle_slop=rec_angle_slop)  
File "D:\ChimeraX\ChimeraX\bin\lib\site-packages\chimerax\hbonds\hbond.py",
line 603, 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 "D:\ChimeraX\ChimeraX\bin\lib\site-packages\chimerax\hbonds\hbond.py",
line 603, in find_hbonds  
if not geom_func(donor_atom, donor_hyds, *args):  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 527.99
OpenGL renderer: NVIDIA GeForce RTX 3060 Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: zh_CN.cp936
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: windows

Manufacturer: LENOVO
Model: 82RF
OS: Microsoft Windows 11 家庭中文版 (Build 22621)
Memory: 16,890,978,304
MaxProcessMemory: 137,438,953,344
CPU: 20 12th Gen Intel(R) Core(TM) i9-12900H
OSLanguage: zh-CN

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