ISOLDE residue validation: No dihedral with that name is registered for this residue type

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/lewisj/Desktop/RecA-initial-models-map/denmod_map_6mer.ccp4

Opened denmod_map_6mer.ccp4 as #1, grid size 324,324,324, pixel 1.09, shown at
level 0.0678, step 2, values float32  

> open /Users/lewisj/Desktop/RecA-initial-models-
> map/Isolde/20220719_isolde_clipped-noh.pdb

Chain information for 20220719_isolde_clipped-noh.pdb #2  
---  
Chain | Description  
A | No description available  
B C | No description available  
D E F | No description available  
X | No description available  
Y | No description available  
  

> volume #1 step 1

> addh

Summary of feedback from adding hydrogens to 20220719_isolde_clipped-noh.pdb
#2  
---  
warnings | Not adding hydrogens to /X DT 1 P because it is missing heavy-atom
bond partners  
Not adding hydrogens to /Y DA 1 P because it is missing heavy-atom bond
partners  
notes | No usable SEQRES records for 20220719_isolde_clipped-noh.pdb (#2)
chain A; guessing termini instead  
No usable SEQRES records for 20220719_isolde_clipped-noh.pdb (#2) chain B;
guessing termini instead  
No usable SEQRES records for 20220719_isolde_clipped-noh.pdb (#2) chain C;
guessing termini instead  
No usable SEQRES records for 20220719_isolde_clipped-noh.pdb (#2) chain D;
guessing termini instead  
No usable SEQRES records for 20220719_isolde_clipped-noh.pdb (#2) chain E;
guessing termini instead  
3 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /A ASN 6, /B ATP 1, /C ATP
1, /D ATP 1, /E ATP 1, /F ATP 1  
Chain-initial residues that are not actual N termini: /B GLU 5, /C GLU 5, /D
ASN 6, /E ASN 6, /F ASN 6  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A ILE 269, /B ILE 269, /B
ATP 1, /C ILE 269, /C ATP 1, /D ILE 269, /D ATP 1, /E ILE 269, /E ATP 1, /F
ILE 269, /F ATP 1  
1447 hydrogen bonds  
Adding 'H' to /B GLU 5  
Adding 'H' to /C GLU 5  
Adding 'H' to /D ASN 6  
Adding 'H' to /E ASN 6  
Adding 'H' to /F ASN 6  
/A ILE 269 is not terminus, removing H atom from 'C'  
/B ILE 269 is not terminus, removing H atom from 'C'  
/C ILE 269 is not terminus, removing H atom from 'C'  
/D ILE 269 is not terminus, removing H atom from 'C'  
/E ILE 269 is not terminus, removing H atom from 'C'  
1 messages similar to the above omitted  
12879 hydrogens added  
  

> ui tool show ISOLDE

> set selectionWidth 4

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
Chain information for 20220719_isolde_clipped-noh.pdb  
---  
Chain | Description  
2.2/A | No description available  
2.2/B 2.2/C | No description available  
2.2/D 2.2/E 2.2/F | No description available  
2.2/X | No description available  
2.2/Y | No description available  
  
Done loading forcefield  
Opened denmod_map_6mer.ccp4 as #2.1.1.1, grid size 324,324,324, pixel 1.09,
shown at step 1, values float32  

> set bgColor white

> clipper spotlight radius 20.00

> select protein

24199 atoms, 24323 bonds, 5 pseudobonds, 1591 residues, 2 models selected  

> select nucleic-acid

1698 atoms, 1828 bonds, 53 residues, 1 model selected  

> select add protein

25897 atoms, 26151 bonds, 5 pseudobonds, 1644 residues, 2 models selected  

> isolde sim start sel

Loading residue template for ATP from internal database  
ISOLDE: stopped sim  
Deleted the following atoms from residue DA Y27: OP1, HO3', H  

> isolde sim start sel

Populating font family aliases took 314 ms. Replace uses of missing font
family "Carlito" with one that exists to avoid this cost.  

ISOLDE: started sim  
reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> select add protein

24231 atoms, 24323 bonds, 5 pseudobonds, 1592 residues, 2 models selected  

> select add nucleic-acid

25929 atoms, 26151 bonds, 5 pseudobonds, 1645 residues, 2 models selected  

> select add ::name="ATP"

25972 atoms, 26196 bonds, 5 pseudobonds, 1646 residues, 2 models selected  

> isolde sim start sel

ISOLDE: started sim  

> volume #2.1.1.1 level 0.1918

reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  
ISOLDE: paused sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 51 residues in model #2.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> select clear

> cview #1/F:61

No objects specified.  

> cview #1/E:61

No objects specified.  

> cview #2/F:61

Traceback (most recent call last):  
File "/Users/lewisj/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/isolde/problem_regions/ui.py", line 81, in update  
clusters, noise = pa.problem_zones(m, restraint_types=restraint_types,  
File "/Users/lewisj/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/isolde/problem_regions/problems.py", line 71, in
problem_zones  
sites.extend(vm(structure, outliers_only=validation_outliers_only))  
File "/Users/lewisj/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/isolde/problem_regions/problems.py", line 140, in
get_protein_backbone_problems  
problems = f(residues)  
File "/Users/lewisj/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/isolde/molobject.py", line 1050, in non_favored  
scores, cases = self.validate(residues)  
File "/Users/lewisj/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/isolde/molobject.py", line 1100, in validate  
return self._validate_by_residue(residues_or_ramas)  
File "/Users/lewisj/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/isolde/molobject.py", line 1117, in _validate_by_residue  
f(self._c_pointer, residues._c_pointers, n, pointer(scores), pointer(cases))  
IndexError: No dihedral with that name is registered for this residue type!  
  
IndexError: No dihedral with that name is registered for this residue type!  
  
File "/Users/lewisj/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/isolde/molobject.py", line 1117, in _validate_by_residue  
f(self._c_pointer, residues._c_pointers, n, pointer(scores), pointer(cases))  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-18.7.4
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 655
OpenGL vendor: Intel Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro15,2
      Processor Name: Quad-Core Intel Core i5
      Processor Speed: 2.4 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 6 MB
      Hyper-Threading Technology: Enabled
      Memory: 8 GB
      System Firmware Version: 1731.120.10.0.0 (iBridge: 19.16.15071.0.0,0)
      OS Loader Version: 540.120.3~6

Software:

    System Software Overview:

      System Version: macOS 12.4 (21F79)
      Kernel Version: Darwin 21.5.0
      Time since boot: 15:52

Graphics/Displays:

    Intel Iris Plus Graphics 655:

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      Type: GPU
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      Vendor: Intel
      Device ID: 0x3ea5
      Revision ID: 0x0001
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        DELL U2415:
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          UI Looks like: 1920 x 1200 @ 59.00Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
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          Rotation: Supported
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Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
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