ISOLDE: too many hydrogens for SER

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Linux-6.8.0-51-generic-x86_64-with-glibc2.39
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
Serines cannot be parameterised when built in coot first

Failed to add atoms ['HB2', 'HB3'] to atom C because this will lead to having 5 atoms attached, which is more than its assigned geometry can support. This is probably due to an error in the MD template (SER). If this template is built into ISOLDE, please report this using Help/Report a bug


Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
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
> /home/cweidle/Documents/tcdb_scfv6/cryosparc_P303_J2820_010_volume_map_sharp.mrc
> format mrc

Opened cryosparc_P303_J2820_010_volume_map_sharp.mrc as #1, grid size
460,460,460, pixel 0.885, shown at level 0.0348, step 2, values float32  

> open
> /home/cweidle/Documents/tcdb_scfv6/refinement_22Jan25/tcdb_scfv6-coot-49_correctsequence_para2.pdb

Chain information for tcdb_scfv6-coot-49_correctsequence_para2.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> volume #1 step 1

> isolde start

> 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...  
Chain information for tcdb_scfv6-coot-49_correctsequence_para2.pdb  
---  
Chain | Description  
2.2/A | No description available  
2.2/B | No description available  
2.2/C | No description available  
  

> clipper associate #1 toModel #2

Opened cryosparc_P303_J2820_010_volume_map_sharp.mrc as #2.1.1.1, grid size
460,460,460, pixel 0.885, shown at step 1, values float32  

> isolde sim start /B-C,A

Sim termination reason: None  
ISOLDE: stopped sim  
Failed to add atoms ['HB2', 'HB3'] to atom C because this will lead to having
5 atoms attached, which is more than its assigned geometry can support. This
is probably due to an error in the MD template (SER). If this template is
built into ISOLDE, please report this using Help/Report a bug  
Failed to add atoms ['HB2', 'HB3'] to atom C because this will lead to having
5 atoms attached, which is more than its assigned geometry can support. This
is probably due to an error in the MD template (GLYCAM_OLS). If this template
is built into ISOLDE, please report this using Help/Report a bug  
Failed to add atoms ['HB2', 'HB3'] to atom C because this will lead to having
5 atoms attached, which is more than its assigned geometry can support. This
is probably due to an error in the MD template (SER). If this template is
built into ISOLDE, please report this using Help/Report a bug  




OpenGL version: 3.3.0 NVIDIA 565.57.01
OpenGL renderer: NVIDIA GeForce RTX 4070 Ti SUPER/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: en_US.UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:2
Manufacturer: Micro-Star International Co., Ltd.
Model: MS-7D75
OS: Ubuntu 24.04 Noble Numbat
Architecture: 64bit ELF
Virtual Machine: none
CPU: 24 AMD Ryzen 9 7900X 12-Core Processor
Cache Size: 1024 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            61Gi        16Gi        34Gi       722Mi        11Gi        45Gi
	Swap:             0B          0B          0B

Graphics:
	01:00.0 VGA compatible controller [0300]: NVIDIA Corporation AD103 [GeForce RTX 4070 Ti SUPER] [10de:2705] (rev a1)	
	Subsystem: PNY Device [196e:141f]	
	Kernel driver in use: nvidia

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