ISOLDE: Unparameterised residue detected

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Darwin-19.6.0-x86_64-i386-64bit
ChimeraX Version: 1.0 (2020-06-04 23:15:07 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.0 (2020-06-04)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/zhouxiaoting/Documents/homo-complex2/RealSpaceRefine_70/homosdh-
> new1-coot-1.pdb

Chain information for homosdh-new1-coot-1.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
  

> set bgColor white

> open /Users/zhouxiaoting/Documents/homo-complex2/22-8-29/new-
> cryosparc_P16_J1207_006_volume_map_sharp.mrc

Opened new-cryosparc_P16_J1207_006_volume_map_sharp.mrc, grid size
384,384,384, pixel 0.73, shown at level 0.0634, step 2, values float32  

> volume #2 step 1

> volume #2 level 0.1478

> ui tool show ISOLDE

> set selectionWidth 4

Chain information for homosdh-new1-coot-1.pdb  
---  
Chain | Description  
1.2/A | No description available  
1.2/B | No description available  
1.2/C | No description available  
1.2/D | No description available  
  
Done loading forcefield  

> select

8637 atoms, 8819 bonds, 47 pseudobonds, 13 models selected  
Loading residue template for FAD from internal database  
Loading residue template for PEV from internal database  
Loading residue template for UQ1 from internal database  

> addh

Summary of feedback from adding hydrogens to homosdh-new1-coot-1.pdb #1.2  
---  
warnings | Unknown hybridization for atoms (S2, S4, S1, S3) of residue type
SF4; not adding hydrogens to them  
Unknown hybridization for atoms (S2, S4, S1, S3) of residue type F3S; not
adding hydrogens to them  
notes | No usable SEQRES records for homosdh-new1-coot-1.pdb (#1.2) chain A;
guessing termini instead  
No usable SEQRES records for homosdh-new1-coot-1.pdb (#1.2) chain B; guessing
termini instead  
No usable SEQRES records for homosdh-new1-coot-1.pdb (#1.2) chain C; guessing
termini instead  
No usable SEQRES records for homosdh-new1-coot-1.pdb (#1.2) chain D; guessing
termini instead  
Chain-initial residues that are actual N termini: /A ILE 51, /B THR 35, /C ALA
34, /D SER 59  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A TYR 664, /C MET 169, /D LEU
159  
Chain-final residues that are not actual C termini: /B TYR 273  
1052 hydrogen bonds  
/B TYR 273 is not terminus, removing H atom from 'C'  
8553 hydrogens added  
  
Traceback (most recent call last):  
File "/Users/zhouxiaoting/Library/Application Support/ChimeraX/1.0/site-
packages/chimerax/isolde/isolde.py", line 2727, in start_sim  
self.params, self.sim_params, excluded_residues = self.ignored_residues)  
File "/Users/zhouxiaoting/Library/Application Support/ChimeraX/1.0/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 612, in __init__  
raise e  
File "/Users/zhouxiaoting/Library/Application Support/ChimeraX/1.0/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__  
isolde.forcefield_mgr)  
File "/Users/zhouxiaoting/Library/Application Support/ChimeraX/1.0/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1344, in __init__  
sim_params, residue_templates)  
File "/Users/zhouxiaoting/Library/Application Support/ChimeraX/1.0/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1426, in
_create_openmm_system  
raise RuntimeError('Unparameterised residue detected')  
RuntimeError: Unparameterised residue detected  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/Users/zhouxiaoting/Library/Application Support/ChimeraX/1.0/site-
packages/chimerax/isolde/isolde.py", line 2707, in _start_sim_or_toggle_pause  
self.start_sim()  
File "/Users/zhouxiaoting/Library/Application Support/ChimeraX/1.0/site-
packages/chimerax/isolde/isolde.py", line 2740, in start_sim  
self._unparam_mgr._sim_unparam_res_cb()  
File "/Users/zhouxiaoting/Library/Application Support/ChimeraX/1.0/site-
packages/chimerax/isolde/validation/unparameterised.py", line 205, in
_sim_unparam_res_cb  
self._show_main_frame()  
File "/Users/zhouxiaoting/Library/Application Support/ChimeraX/1.0/site-
packages/chimerax/isolde/validation/unparameterised.py", line 48, in
_show_main_frame  
self._update_unparameterised_residues_list()  
File "/Users/zhouxiaoting/Library/Application Support/ChimeraX/1.0/site-
packages/chimerax/isolde/validation/unparameterised.py", line 87, in
_update_unparameterised_residues_list  
by_name, by_comp = ff.find_possible_templates(r)  
File "/Users/zhouxiaoting/Library/Application Support/ChimeraX/1.0/site-
packages/chimerax/isolde/openmm/forcefields.py", line 319, in
find_possible_templates  
rgraph = self.residue_graph(res)  
File "/Users/zhouxiaoting/Library/Application Support/ChimeraX/1.0/site-
packages/chimerax/isolde/openmm/forcefields.py", line 270, in residue_graph  
return Graph(labels, edges)  
RuntimeError: edges should be a n x 2 array of unsigned ints!  
  
RuntimeError: edges should be a n x 2 array of unsigned ints!  
  
File "/Users/zhouxiaoting/Library/Application Support/ChimeraX/1.0/site-
packages/chimerax/isolde/openmm/forcefields.py", line 270, in residue_graph  
return Graph(labels, edges)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-3.10.23
OpenGL renderer: AMD Radeon Pro 5300M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro16,1
      Processor Name: 6-Core Intel Core i7
      Processor Speed: 2.6 GHz
      Number of Processors: 1
      Total Number of Cores: 6
      L2 Cache (per Core): 256 KB
      L3 Cache: 12 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      Boot ROM Version: 1731.140.2.0.0 (iBridge: 19.16.16067.0.0,0)

Software:

    System Software Overview:

      System Version: macOS 10.15.7 (19H2026)
      Kernel Version: Darwin 19.6.0
      Time since boot: 1:08

Graphics/Displays:

    Intel UHD Graphics 630:

      Chipset Model: Intel UHD Graphics 630
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3e9b
      Revision ID: 0x0000
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal: Supported, feature set macOS GPUFamily2 v1

    AMD Radeon Pro 5300M:

      Chipset Model: AMD Radeon Pro 5300M
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x8
      VRAM (Total): 4 GB
      Vendor: AMD (0x1002)
      Device ID: 0x7340
      Revision ID: 0x0043
      ROM Revision: 113-D3220E-190
      VBIOS Version: 113-D32207P1-019
      Option ROM Version: 113-D32207P1-019
      EFI Driver Version: 01.A1.190
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal: Supported, feature set macOS GPUFamily2 v1
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 3072 x 1920 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal

PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.8

[Eric Pettersen]

ChimeraX 1.0!

[Tristan Croll]

Ancient - ChimeraX 1.0.