ISOLDE residue validation: cannot unpack non-iterable builtin_function_or_method object

[dilipk@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.16299
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 30210 from EMDB

No such database 'EMDB'  

> open 30210 fromDatabase emdb

Summary of feedback from opening 30210 fetched from emdb  
---  
note | Fetching compressed map 30210 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-30210/map/emd_30210.map.gz  
  
Opened emd_30210.map, grid size 192,192,192, pixel 1.01, shown at level
0.0278, step 1, values float32  

> ui tool show ISOLDE

> set selectionWidth 4

Done loading forcefield  

> open 7bv2

Summary of feedback from opening 7bv2 fetched from pdb  
---  
notes | Fetching compressed mmCIF 7bv2 from
http://files.rcsb.org/download/7bv2.cif  
Fetching CCD ZN from http://ligand-expo.rcsb.org/reports/Z/ZN/ZN.cif  
Fetching CCD POP from http://ligand-expo.rcsb.org/reports/P/POP/POP.cif  
Fetching CCD F86 from http://ligand-expo.rcsb.org/reports/F/F86/F86.cif  
  
7bv2 title:  
The nsp12-nsp7-nsp8 complex bound to the template-primer RNA and triphosphate
form of Remdesivir(RTP) [more info...]  
  
Chain information for 7bv2 #2  
---  
Chain | Description  
A | nsp12  
B | nsp8  
C | nsp7  
P | Primer  
T | Templete  
  
Non-standard residues in 7bv2 #2  
---  
F86 —
[(2~{R},3~{S},4~{R},5~{R})-5-(4-azanylpyrrolo[2,1-f][1,2,4]triazin-7-yl)-5-cyano-3,4-bis(oxidanyl)oxolan-2-yl]methyl
dihydrogen phosphate (Remdesivir, bound form)  
MG — magnesium ion  
POP — pyrophosphate 2-  
ZN — zinc ion  
  
7bv2 title:  
The nsp12-nsp7-nsp8 complex bound to the template-primer RNA and triphosphate
form of Remdesivir(RTP) [more info...]  
  
Chain information for 7bv2  
---  
Chain | Description  
2.2/A | nsp12  
2.2/B | nsp8  
2.2/C | nsp7  
2.2/P | Primer  
2.2/T | Templete  
  
Non-standard residues in 7bv2 #2.2  
---  
F86 —
[(2~{R},3~{S},4~{R},5~{R})-5-(4-azanylpyrrolo[2,1-f][1,2,4]triazin-7-yl)-5-cyano-3,4-bis(oxidanyl)oxolan-2-yl]methyl
dihydrogen phosphate (Remdesivir, bound form)  
MG — magnesium ion  
POP — pyrophosphate 2-  
ZN — zinc ion  
  

> volume #1 level 0.1753

> clip assoc #1 to #2

Expected a keyword  

> clipper associate #1 toModel #2

> set bgColor white

> addh

Summary of feedback from adding hydrogens to 7bv2 #2.2  
---  
warnings | Not adding hydrogens to /A LYS 98 CB because it is missing heavy-
atom bond partners  
Not adding hydrogens to /A ASP 100 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A ASP 218 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A ASP 824 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /B ASP 78 CB because it is missing heavy-atom bond
partners  
5 messages similar to the above omitted  
notes | Termini for 7bv2 (#2.2) chain A determined from SEQRES records  
Termini for 7bv2 (#2.2) chain B determined from SEQRES records  
Termini for 7bv2 (#2.2) chain C determined from SEQRES records  
Termini for 7bv2 (#2.2) chain P determined from SEQRES records  
Termini for 7bv2 (#2.2) chain T determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini: /A VAL 31, /A GLU 84, /A
ARG 118, /A ASN 911, /B ASP 78, /C LYS 2, /P G 10, /T U 8  
Chain-final residues that are actual C termini: /P U 20  
Chain-final residues that are not actual C termini: /A LYS 50, /A ASP 100, /A
LEU 895, /A THR 929, /B ALA 191, /C GLY 64, /T C 21  
962 hydrogen bonds  
Adding 'H' to /A VAL 31  
Adding 'H' to /A GLU 84  
Adding 'H' to /A ARG 118  
Adding 'H' to /A ASN 911  
Adding 'H' to /B ASP 78  
1 messages similar to the above omitted  
/A THR 929 is not terminus, removing H atom from 'C'  
/B ALA 191 is not terminus, removing H atom from 'C'  
/C GLY 64 is not terminus, removing H atom from 'C'  
8174 hydrogens added  
  

> hide HC

> restraint ligands #2

Unknown command: isolde restraint ligands #2  

> isolde restrain ligands #2

> select #2

16804 atoms, 17042 bonds, 36 pseudobonds, 1047 residues, 17 models selected  
Loading residue template for POP from internal database  
Traceback (most recent call last):  
File "C:\Users\dilipk\AppData\Local\UCSF\ChimeraX\1.1\site-
packages\chimerax\isolde\validation\unparameterised.py", line 174, in
_fix_selected_unparameterised_residue  
residue, template_name, ccd_template = item.data  
TypeError: cannot unpack non-iterable builtin_function_or_method object  
  
TypeError: cannot unpack non-iterable builtin_function_or_method object  
  
File "C:\Users\dilipk\AppData\Local\UCSF\ChimeraX\1.1\site-
packages\chimerax\isolde\validation\unparameterised.py", line 174, in
_fix_selected_unparameterised_residue  
residue, template_name, ccd_template = item.data  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Users\dilipk\AppData\Local\UCSF\ChimeraX\1.1\site-
packages\chimerax\isolde\validation\unparameterised.py", line 174, in
_fix_selected_unparameterised_residue  
residue, template_name, ccd_template = item.data  
TypeError: cannot unpack non-iterable builtin_function_or_method object  
  
TypeError: cannot unpack non-iterable builtin_function_or_method object  
  
File "C:\Users\dilipk\AppData\Local\UCSF\ChimeraX\1.1\site-
packages\chimerax\isolde\validation\unparameterised.py", line 174, in
_fix_selected_unparameterised_residue  
residue, template_name, ccd_template = item.data  
  
See log for complete Python traceback.  
  

File C:/Users/dilipk/Downloads/f86.pdb.cif does not appear to contain any
valid residue templates.  

Traceback (most recent call last):  
File "C:\Users\dilipk\AppData\Local\UCSF\ChimeraX\1.1\site-
packages\chimerax\isolde\isolde.py", line 1204, in _add_cif_template_files_gui  
load_cif_templates(self.session, files)  
File "C:\Users\dilipk\AppData\Local\UCSF\ChimeraX\1.1\site-
packages\chimerax\isolde\atomic\template_utils.py", line 601, in
load_cif_templates  
raise RuntimeError('No files successfully loaded.')  
RuntimeError: No files successfully loaded.  
  
RuntimeError: No files successfully loaded.  
  
File "C:\Users\dilipk\AppData\Local\UCSF\ChimeraX\1.1\site-
packages\chimerax\isolde\atomic\template_utils.py", line 601, in
load_cif_templates  
raise RuntimeError('No files successfully loaded.')  
  
See log for complete Python traceback.  
  

File C:/Users/dilipk/Downloads/f86.cif does not appear to contain any valid
residue templates.  

Traceback (most recent call last):  
File "C:\Users\dilipk\AppData\Local\UCSF\ChimeraX\1.1\site-
packages\chimerax\isolde\isolde.py", line 1204, in _add_cif_template_files_gui  
load_cif_templates(self.session, files)  
File "C:\Users\dilipk\AppData\Local\UCSF\ChimeraX\1.1\site-
packages\chimerax\isolde\atomic\template_utils.py", line 601, in
load_cif_templates  
raise RuntimeError('No files successfully loaded.')  
RuntimeError: No files successfully loaded.  
  
RuntimeError: No files successfully loaded.  
  
File "C:\Users\dilipk\AppData\Local\UCSF\ChimeraX\1.1\site-
packages\chimerax\isolde\atomic\template_utils.py", line 601, in
load_cif_templates  
raise RuntimeError('No files successfully loaded.')  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.13399 Core Profile Forward-Compatible Context 15.201.1151.1008
OpenGL renderer: AMD Radeon HD 6700 Series
OpenGL vendor: ATI Technologies Inc.
Manufacturer: System manufacturer
Model: System Product Name
OS: Microsoft Windows 10 Enterprise (Build 16299)
Memory: 17,160,163,328
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-2600K CPU @ 3.40GHz"
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
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[Eric Pettersen]

Reported by Dilip Kumar

[Tristan Croll]

OK, the traceback here is due to a boneheaded oversight on my part - I either didn't notice or forgot that QListWidgetItem already has setData() and data() methods, and was simply adding data as a Python property. Will fix that.

More important to your situation, though: unusual residues/ligands that are covalently bonded to other residues are not currently supported by ISOLDE. That means you won't be able to actually simulate the Remdesivir (F86) in 7bv2 - but what you can do is use the command isolde ignore :F86 to exclude that residue from simulations. It'll still be present in the model, but when running simulations surrounding atoms will pass straight through it. The residue directly bonded to it will be rigidly fixed in space. As long as you take some care in the vicinity there's still a lot that you can do with the rest of the model.

Also, for what it's worth I think the pyrophosphate (POP) and magnesium ions associated with it are rubbish and should be removed from the model - there's next to no density to support them and the geometry is all wrong.

[Tristan Croll]

Long since fixed, but forgot to close the ticket. Sorry!