ISOLDE: 5-bond carbon

[guillaume.gaullier@…]

The following bug report has been submitted:
Platform:        Linux-5.14.0-427.37.1.el9_4.x86_64-x86_64-with-glibc2.34
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
I am doing model building/fitting in ISOLDE. Mutating a residue to SER (swapaa sel SER) requires rebuilding the new residue to ISOLDE's template (this is normal), but when trying to do so (using the template matched by residue name), I get the following error message:

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

This problem did not happen with other residues.

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  

> open /home/guillaume/github/chimerax-config/init.cxc

> open commands/alphafold.cxc

> alias afresults mmaker ~$1 to $1; hide ~$1 models; view $1; mseries slider
> all; preset custom 'alphafold results'

> alias afcolor color bfactor $1 palette alphafold

executed alphafold.cxc  

> open commands/backbonetrace.cxc

> alias bbsidechains hide $1 cartoons; hide $1 surfaces; hide $1; show
> $1@CA&protein; show $1@P&nucleic; style $1 stick; show $1&sidechain; show
> $1&~backbone&nucleic; size stickradius 0.1; size pseudobondradius 0.1

> alias bbtrace hide $1 cartoons; hide $1 surfaces; hide $1; show
> $1@CA&protein; show $1@P&nucleic; style $1 stick; size stickradius 0.1; size
> pseudobondradius 0.1

executed backbonetrace.cxc  

> open commands/servalcat.cxc

> alias servalcatresults open refined.mmcif; open diffmap_normalized_fo.mrc;
> open diffmap_normalized_fofc.mrc; isolde start; clipper associate #2 toModel
> #1; clipper associate #3 toModel #1

executed servalcat.cxc  

> open ui/defaults.cxc

> preset custom "guillaume default mol display"

Using preset: Custom / Guillaume Default Mol Display  
Preset expands to these ChimeraX commands:

    
    
    # My usual display mode
    
    graphics silhouettes true
    lighting soft
    set bgcolor grey
    
    

  
executed defaults.cxc  

> open ui/aliases.cxc

> alias cofron cofr centerofview showpivot 6,0.25

> alias cofroff cofr centerofview showpivot false

> alias symclip cofr centerofview; clip near -$1 far $1 position cofr

> alias mapsphere surface unzone ##~num_residues; sel; close #10000; marker
> #10000 position cofr; sel ~sel; surface zone ##~num_residues nearAtoms sel
> distance $1; close #10000

> alias mapunsphere surface unzone ##~num_residues

> alias hidemaps surface unzone ##~num_residues; sel; close #10000; marker
> #10000 position cofr; sel ~sel; surface zone ##~num_residues nearAtoms sel
> distance 0; close #10000

> alias showmaps surface unzone ##~num_residues

executed aliases.cxc  

> open ui/buttons.cxc

> buttonpanel Shortcuts rows 3 columns 4

> buttonpanel Shortcuts add Log command "tool show Log"

> buttonpanel Shortcuts add Models command "tool show 'Model Panel'"

> buttonpanel Shortcuts add Volumes command "tool show 'Volume Viewer'"

> buttonpanel Shortcuts add "Coot mode" command "preset custom 'oli coot mode
> mesh'"

> buttonpanel Shortcuts add cofron command cofron

> buttonpanel Shortcuts add "Clip 10" command "symclip 10"

> buttonpanel Shortcuts add "Show maps" command showmaps

> buttonpanel Shortcuts add "Map sphere 15" command "mapsphere 15"

> buttonpanel Shortcuts add cofroff command cofroff

> buttonpanel Shortcuts add "Clip off" command "clip off"

> buttonpanel Shortcuts add "Hide maps" command hidemaps

> buttonpanel Shortcuts add "Map unsphere" command mapunsphere

executed buttons.cxc  
executed init.cxc  
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open cryosparc_P351_J201_007_volume_map.mrc

Opened cryosparc_P351_J201_007_volume_map.mrc as #1, grid size 648,648,648,
pixel 0.507, shown at step 1, values float32  

> volume #1 region 0,0,0,647,647,647 step 4

[Repeated 1 time(s)]

> volume #1 step 1

> set bgColor white

[Repeated 1 time(s)]

> open /home/guillaume/BlikstadLab/collaborations/Nicholas_Rubisco/model-
> building/rubisco-alphafold-ISOLDE-WIP.cif

Summary of feedback from opening
/home/guillaume/BlikstadLab/collaborations/Nicholas_Rubisco/model-
building/rubisco-alphafold-ISOLDE-WIP.cif  
---  
warnings | Atom HA2 is not in the residue template for ASN /B:8  
Atom HA2 is not in the residue template for LYS /B:37  
  
Chain information for rubisco-alphafold-ISOLDE-WIP.cif #2  
---  
Chain | Description  
A C E G I K M O | Ribulose bisphosphate carboxylase large chain  
B | Ribulose bisphosphate carboxylase small subunit, chloroplastic 1  
D F H J L N P | Ribulose bisphosphate carboxylase small subunit, chloroplastic 1  
  

> isolde start

> set selectionWidth 4

Done loading forcefield  

> 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 rubisco-alphafold-ISOLDE-WIP.cif  
---  
Chain | Description  
2.2/A 2.2/C 2.2/E 2.2/G 2.2/I 2.2/K 2.2/M 2.2/O | Ribulose bisphosphate carboxylase large chain  
2.2/B | Ribulose bisphosphate carboxylase small subunit, chloroplastic 1  
2.2/D 2.2/F 2.2/H 2.2/J 2.2/L 2.2/N 2.2/P | Ribulose bisphosphate carboxylase small subunit, chloroplastic 1  
  

> clipper associate #1 toModel #2

Opened cryosparc_P351_J201_007_volume_map.mrc as #2.1.1.1, grid size
648,648,648, pixel 0.507, shown at step 1, values float32  

> ui tool show "Ramachandran Plot"

> sequence chain /b

Alignment identifier is 2.2/B  

> isolde stepto /b:106

> isolde sim start /B:106

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  

> select up

8 atoms, 7 bonds, 1 residue, 2 models selected  

> swapaa sel ALA

Using Dunbrack library  
Swapping /B SER 106 to ALA  

> isolde sim start /B:106

ISOLDE: started sim  

> isolde sim stop discardTo start

Sim termination reason: None  
reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> select up

10 atoms, 9 bonds, 1 residue, 2 models selected  

> swapaa sel SER

Using Dunbrack library  
/B ALA 106: phi -76.0, psi -18.8 trans  
Applying SER rotamer (chi angles: 67.5) to /B SER 106  
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  
[Repeated 1 time(s)]




OpenGL version: 3.3.0 NVIDIA 560.35.03
OpenGL renderer: NVIDIA RTX A2000 12GB/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=gnome
XDG_SESSION_DESKTOP=gnome
XDG_CURRENT_DESKTOP=GNOME
DISPLAY=:1
Manufacturer: HP
Model: HP Z2 Mini G9 Workstation Desktop PC
OS: Rocky Linux 9.4 Blue Onyx
Architecture: 64bit ELF
Virtual Machine: none
CPU: 20 12th Gen Intel(R) Core(TM) i7-12700K
Cache Size: 25600 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            30Gi       7.8Gi       8.7Gi        64Mi        14Gi        22Gi
	Swap:           32Gi          0B        32Gi

Graphics:
	02:00.0 VGA compatible controller [0300]: NVIDIA Corporation GA106 [RTX A2000 12GB] [10de:2571] (rev a1)	
	Subsystem: Hewlett-Packard Company Device [103c:1611]	
	Kernel driver in use: nvidia

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