ISOLDE: UNL template has no bonds

[Tristan Croll]

The following bug report has been submitted:
Platform:        Windows-10-10.0.22621
ChimeraX Version: 1.7.dev202307112022 (2023-07-11 20:22:49 UTC)
Description
(Reporting my own bug so I don't forget - I'm at a conference followed by a few weeks holiday). Residue is named UNL (ChimeraX's default name for a ligand created from SMILES), and my residue-correction code is attempting to match it to the CCD template for UNL which contains no bonds. 

Log:
> isolde shorthand
    
    
    Initialising ISOLDE-specific command aliases:
    Alias	Equivalent full command
    -------------------------------------------------
    st	isolde step {arguments}
    aw	isolde add water {arguments}
    awsf	isolde add water {arguments} sim false
    al	isolde add ligand {arguments}
    aa	isolde add aa $1 sel {arguments}
    ht	isolde mod his sel {arguments}
    so	setattr sel atoms occupancy {arguments}
    ab	isolde adjust bfactors {arguments}
    ss	isolde sim start sel
    rt	isolde release torsions sel {arguments}
    rd	isolde release distances sel {arguments}
    ra	rd; rt
    pf	isolde pepflip sel
    cf	isolde cisflip sel
    cbb	color bfactor {arguments}
    cbo	color byattr occupancy {arguments}
    cbc	color {arguments} bychain; color {arguments} byhet
    cs	clipper set contourSensitivity {arguments}
    

  
UCSF ChimeraX version: 1.7.dev202307112022 (2023-07-11)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> cd "C:/Users/Tristan Croll/Documents/Structures/isolde_users/zhen_gong"

Current working directory is: C:\Users\Tristan
Croll\Documents\Structures\isolde_users\zhen_gong  

> open
> CC[C@H](C)[C@@H]1NC(=O)[C@H](CC(N)=O)NC(=O)[C@@H](N)CC(=O)NCCCC[C@H](NC(=O)[C@H](CC2=CNC3=CC=C(Br)C=C23)NC(=O)[C@@H]2C[C@@H](CN2C1=O)N1C=C(N=N1)C1=CC=C(C=C1)C1=NNC=C1)C(N)=O
> fromDatabase smiles

Translated SMILES to 3D structure via NCI web service (SMILES:
CC[C@H](C)[C@@H]1NC(=O)[C@H](CC(N)=O)NC(=O)[C@@H](N)CC(=O)NCCCC[C@H](NC(=O)[C@H](CC2=CNC3=CC=C(Br)C=C23)NC(=O)[C@@H]2C[C@@H](CN2C1=O)N1C=C(N=N1)C1=CC=C(C=C1)C1=NNC=C1)C(N)=O)  

> save ligand_direct_from_smiles.pdb #1

> open ligand_direct_from_smiles.pdb

> select #2

129 atoms, 135 bonds, 1 residue, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models #2,1,0,0,12.323,0,1,0,-0.075247,0,0,1,-1.1705

> addh #1

Summary of feedback from adding hydrogens to
smiles:CC[C@H](C)[C@@H]1NC(=O)[C@H](CC(N)=O)NC(=O)[C@@H](N)CC(=O)NCCCC[C@H](NC(=O)[C@H](CC2=CNC3=CC=C(Br)C=C23)NC(=O)[C@@H]2C[C@@H](CN2C1=O)N1C=C(N=N1)C1=CC=C(C=C1)C1=NNC=C1)C(N)=O
#1  
---  
notes | Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
1 hydrogens added  
  

> close #2

> isolde parameterise #1

Running ANTECHAMBER command: C:/Program Files/ChimeraX-
daily/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
C:\Users\TRISTA~1\AppData\Local\Temp\tmpu_1gbxi4\ante.in.mol2 -fi mol2 -o
C:\Users\TRISTA~1\AppData\Local\Temp\tmpu_1gbxi4\ante.out.mol2 -fo mol2 -c bcc
-nc 1 -j 5 -s 2 -dr n  
(UNL) ``  
(UNL) `Welcome to antechamber 20.0: molecular input file processor.`  
(UNL) ``  
(UNL) `Info: Finished reading file
(C:\Users\TRISTA~1\AppData\Local\Temp\tmpu_1gbxi4\ante.in.mol2); atoms read
(130), bonds read (136).`  
(UNL) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(UNL) `Running: "C:/Program Files/ChimeraX-daily/bin/amber20/bin/bondtype" -j
part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(UNL) `bash.exe: warning: could not find /tmp, please create!`  
(UNL) ``  
(UNL) ``  
(UNL) `Running: "C:/Program Files/ChimeraX-daily/bin/amber20/bin/atomtype" -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(UNL) `bash.exe: warning: could not find /tmp, please create!`  
(UNL) `Info: Total number of electrons: 544; net charge: 1`  
(UNL) ``  
(UNL) `Running: "C:/Program Files/ChimeraX-daily/bin/amber20/bin/sqm" -O -i
sqm.in -o sqm.out`  
(UNL) `bash.exe: warning: could not find /tmp, please create!`  
(UNL) ``  
(UNL) `Running: "C:/Program Files/ChimeraX-daily/bin/amber20/bin/am1bcc" -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p "C:/Program
Files/ChimeraX-daily/bin/amber20/dat/antechamber/BCCPARM.DAT" -s 2 -j 1`  
(UNL) `bash.exe: warning: could not find /tmp, please create!`  
(UNL) ``  
(UNL) `Running: "C:/Program Files/ChimeraX-daily/bin/amber20/bin/atomtype" -f
ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`  
(UNL) `bash.exe: warning: could not find /tmp, please create!`  
(UNL) ``  
Charges for residue UNL determined  
OpenMM ffXML file UNL written to the current working directory.  

> 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...  

> isolde sim start /*

Launching using CUDA failed with the below message. Falling back to using
OpenCL.  
  
Error loading CUDA module: CUDA_ERROR_UNSUPPORTED_PTX_VERSION (222)  

ISOLDE: started sim  

> select clear

> isolde sim pause

> isolde sim resume

> isolde sim pause

> isolde sim resume

> isolde sim pause

> movie record size 800,600 supersample 3

> isolde sim resume

> isolde sim pause

> movie stop

> movie encode cyclic_peptide_sim.mp4

Movie saved to cyclic_peptide_sim.mp4  
  

> setattr #1 res chain_id A

Assigning chain_id attribute to 1 item  

> save cyclic_peptide.pdb #1

> 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

130 atoms, 136 bonds, 1 residue, 1 model selected  

> show

> delete sel

Traceback (most recent call last):  
File "C:\Users\Tristan Croll\AppData\Local\UCSF\ChimeraX\1.7\site-
packages\chimerax\isolde\ui\validation_tab\unparameterised.py", line 192, in
_fix_button_clicked_cb  
fix_residue_to_match_md_template(self.session, r, template,
cif_template=ccd_template)  
File "C:\Users\Tristan Croll\AppData\Local\UCSF\ChimeraX\1.7\site-
packages\chimerax\isolde\atomic\template_utils.py", line 339, in
fix_residue_to_match_md_template  
template_indices, ccd_indices = match_template_atoms_to_ccd_atoms(session,
md_template, ccd_name)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\Tristan Croll\AppData\Local\UCSF\ChimeraX\1.7\site-
packages\chimerax\isolde\openmm\amberff\template_utils.py", line 61, in
match_template_atoms_to_ccd_atoms  
ccd_graph = make_graph_from_residue_template(ccd_template)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\Tristan Croll\AppData\Local\UCSF\ChimeraX\1.7\site-
packages\chimerax\isolde\graph\\__init__.py", line 46, in
make_graph_from_residue_template  
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 "C:\Users\Tristan Croll\AppData\Local\UCSF\ChimeraX\1.7\site-
packages\chimerax\isolde\graph\\__init__.py", line 46, in
make_graph_from_residue_template  
return Graph(labels, edges)  
^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 518.01
OpenGL renderer: NVIDIA GeForce RTX 3070 Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.2
Locale: en_GB.cp1252
Qt version: PyQt6 6.4.2, Qt 6.4.2
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Qt platform: windows

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