ISOLDE: Failed to add atoms; more than its assigned geometry can support

[22111510066@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.26100
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
Failed to add atoms ['HD21', 'HD22'] to atom ND2 because this will lead to having 4 atoms attached, which is more than its assigned geometry can support. This is probably due to an error in the MD template (ASN). 

Log:
Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  
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 "D:/documents/FDU/SunChenLab_Local/Project 01-Spike
> design/P0104-Intermediate of SARS
> spike/G4_SARS_pH_ACE2_BOG_4d/J162_local_S2_C3_3dot24/J162_008_volume_map_deep.mrc"

Opened J162_008_volume_map_deep.mrc as #1, grid size 400,400,400, pixel 0.932,
shown at level 7.96e-05, step 2, values float32  

> open "D:/documents/FDU/SunChenLab_Local/Project 01-Spike
> design/P0104-Intermediate of SARS
> spike/G4_SARS_pH_ACE2_BOG_4d/model_building/S2-coot-9_SS_real_space_refined.pdb"

Chain information for S2-coot-9_SS_real_space_refined.pdb #2  
---  
Chain | Description  
A | No description available  
B C | No description available  
  

> 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 60 residues in model #2 to IUPAC-IUB
standards.  
Chain information for S2-coot-9_SS_real_space_refined.pdb  
---  
Chain | Description  
2.2/A | No description available  
2.2/B 2.2/C | No description available  
  

> clipper associate #1 toModel #2

Opened J162_008_volume_map_deep.mrc as #2.1.1.1, grid size 400,400,400, pixel
0.932, shown at step 1, values float32  

> isolde sim start /A-C

Sim termination reason: None  
ISOLDE: stopped sim  

> addh #2.2

Summary of feedback from adding hydrogens to
S2-coot-9_SS_real_space_refined.pdb #2.2  
---  
notes | No usable SEQRES records for S2-coot-9_SS_real_space_refined.pdb
(#2.2) chain A; guessing termini instead  
No usable SEQRES records for S2-coot-9_SS_real_space_refined.pdb (#2.2) chain
B; guessing termini instead  
No usable SEQRES records for S2-coot-9_SS_real_space_refined.pdb (#2.2) chain
C; guessing termini instead  
Chain-initial residues that are actual N termini: /A TYR 689, /B TYR 689, /C
TYR 689  
Chain-initial residues that are not actual N termini: /A ARG 758, /A LEU 876,
/B LEU 876, /C LEU 876  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A VAL 1119, /A GLU 755,
/A THR 863, /B VAL 1119, /B SER 861, /C VAL 1119, /C SER 861  
741 hydrogen bonds  
Adding 'H' to /A ARG 758  
Adding 'H' to /A LEU 876  
Adding 'H' to /B LEU 876  
Adding 'H' to /C LEU 876  
/A VAL 1119 is not terminus, removing H atom from 'C'  
/B VAL 1119 is not terminus, removing H atom from 'C'  
/C VAL 1119 is not terminus, removing H atom from 'C'  
9873 hydrogens added  
  
Failed to add atoms ['HD21', 'HD22'] to atom ND2 because this will lead to
having 4 atoms attached, which is more than its assigned geometry can support.
This is probably due to an error in the MD template (ASN). If this template is
built into ISOLDE, please report this using Help/Report a bug  
Traceback (most recent call last):  
File "C:\Users\qyn20\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\ui\validation_tab\unparameterised.py", line 176, in
_fix_button_clicked_cb  
data = item.data(0, USER_ROLE)  
AttributeError: 'NoneType' object has no attribute 'data'  
  
AttributeError: 'NoneType' object has no attribute 'data'  
  
File "C:\Users\qyn20\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\ui\validation_tab\unparameterised.py", line 176, in
_fix_button_clicked_cb  
data = item.data(0, USER_ROLE)  
  
See log for complete Python traceback.  
  
Failed to add atoms ['HD21', 'HD22'] to atom ND2 because this will lead to
having 4 atoms attached, which is more than its assigned geometry can support.
This is probably due to an error in the MD template (ASN). If this template is
built into ISOLDE, please report this using Help/Report a bug  




OpenGL version: 3.3.0 NVIDIA 572.47
OpenGL renderer: NVIDIA GeForce RTX 3070 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

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CPU: 20 12th Gen Intel(R) Core(TM) i7-12700H
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[Eric Pettersen]

Reported by QYN