ISOLDE: fix unparameterized residue: cannot unpack non-iterable builtin_function_or_method object

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Linux-5.4.0-74-generic-x86_64-with-debian-buster-sid
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 /home/zhanglab/Desktop/Phenix2/nopsite_phenix_Zhongliang_ribosmoe_coot-
> coot-1.pdb

Summary of feedback from opening
/home/zhanglab/Desktop/Phenix2/nopsite_phenix_Zhongliang_ribosmoe_coot-
coot-1.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
{\rtf1\ansi\ansicpg1252\cocoartf2578  
  
Ignored bad PDB record found on line 2  
\cocoatextscaling0\cocoaplatform0{\fonttbl\f0\fswiss\fcharset0 Helvetica;}  
  
Ignored bad PDB record found on line 3  
{\colortbl;\red255\green255\blue255;}  
  
Ignored bad PDB record found on line 4  
{\\*\expandedcolortbl;;}  
  
Ignored bad PDB record found on line 5  
\margl1440\margr1440\vieww36400\viewh23440\viewkind0  
  
718 messages similar to the above omitted  
  
Chain information for nopsite_phenix_Zhongliang_ribosmoe_coot-coot-1.pdb #1  
---  
Chain | Description  
0 | No description available  
1 | No description available  
2 | No description available  
3 | No description available  
4 | No description available  
6 | No description available  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
V | No description available  
W | No description available  
X | No description available  
Y | No description available  
Z | No description available  
a | No description available  
c | No description available  
d | No description available  
e | No description available  
f | No description available  
g | No description available  
h | No description available  
i | No description available  
j | No description available  
k | No description available  
l | No description available  
m | No description available  
n | No description available  
o | No description available  
p | No description available  
q | No description available  
r | No description available  
s | No description available  
t | No description available  
v | No description available  
  

> open /home/zhanglab/Desktop/Phenix2/P10_J61_rescaled.mrc

Opened P10_J61_rescaled.mrc, grid size 320,320,320, pixel 1.06, shown at level
0.23, step 2, values float32  

> hide atoms

> show cartoons

> volume #2 step 1

> transparency 50

> ui tool show "Fit in Map"

Fit molecule nopsite_phenix_Zhongliang_ribosmoe_coot-coot-1.pdb (#1) to map
P10_J61_rescaled.mrc (#2) using 143674 atoms  
average map value = 0.318, steps = 60  
shifted from previous position = 0.0131  
rotated from previous position = 0.00893 degrees  
atoms outside contour = 64274, contour level = 0.23041  
  
Position of nopsite_phenix_Zhongliang_ribosmoe_coot-coot-1.pdb (#1) relative
to P10_J61_rescaled.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99999999 0.00008386 0.00012220 -0.02339288  
-0.00008385 1.00000000 -0.00004833 0.02015898  
-0.00012220 0.00004832 0.99999999 0.01375248  
Axis 0.31002260 0.78391758 -0.53792119  
Axis point 117.59913407 0.00000000 194.36817826  
Rotation angle (degrees) 0.00893156  
Shift along axis 0.00115291  
  

> ui tool show ISOLDE

> set selectionWidth 4

Chain information for nopsite_phenix_Zhongliang_ribosmoe_coot-coot-1.pdb  
---  
Chain | Description  
1.2/0 | No description available  
1.2/1 | No description available  
1.2/2 | No description available  
1.2/3 | No description available  
1.2/4 | No description available  
1.2/6 | No description available  
1.2/A | No description available  
1.2/B | No description available  
1.2/C | No description available  
1.2/D | No description available  
1.2/E | No description available  
1.2/F | No description available  
1.2/G | No description available  
1.2/H | No description available  
1.2/J | No description available  
1.2/K | No description available  
1.2/L | No description available  
1.2/M | No description available  
1.2/N | No description available  
1.2/O | No description available  
1.2/P | No description available  
1.2/Q | No description available  
1.2/R | No description available  
1.2/S | No description available  
1.2/T | No description available  
1.2/U | No description available  
1.2/V | No description available  
1.2/W | No description available  
1.2/X | No description available  
1.2/Y | No description available  
1.2/Z | No description available  
1.2/a | No description available  
1.2/c | No description available  
1.2/d | No description available  
1.2/e | No description available  
1.2/f | No description available  
1.2/g | No description available  
1.2/h | No description available  
1.2/i | No description available  
1.2/j | No description available  
1.2/k | No description available  
1.2/l | No description available  
1.2/m | No description available  
1.2/n | No description available  
1.2/o | No description available  
1.2/p | No description available  
1.2/q | No description available  
1.2/r | No description available  
1.2/s | No description available  
1.2/t | No description available  
1.2/v | No description available  
  
Done loading forcefield  

> volume #1.1.1.1 level 0.2011

> addh

Summary of feedback from adding hydrogens to
nopsite_phenix_Zhongliang_ribosmoe_coot-coot-1.pdb #1.2  
---  
notes | No usable SEQRES records for nopsite_phenix_Zhongliang_ribosmoe_coot-
coot-1.pdb (#1.2) chain 0; guessing termini instead  
No usable SEQRES records for nopsite_phenix_Zhongliang_ribosmoe_coot-
coot-1.pdb (#1.2) chain 1; guessing termini instead  
No usable SEQRES records for nopsite_phenix_Zhongliang_ribosmoe_coot-
coot-1.pdb (#1.2) chain 2; guessing termini instead  
No usable SEQRES records for nopsite_phenix_Zhongliang_ribosmoe_coot-
coot-1.pdb (#1.2) chain 3; guessing termini instead  
No usable SEQRES records for nopsite_phenix_Zhongliang_ribosmoe_coot-
coot-1.pdb (#1.2) chain 4; guessing termini instead  
46 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /0 ALA 2, /1 VAL 7, /2 GLY
4, /3 PRO 2, /4 VAL 1, /6 MET 1, /A A 5, /B U 1, /C ALA 2, /D ALA 2, /E LEU 9,
/F GLN 8, /G ARG 3, /H MET 1, /J PRO 2, /K ILE 2, /L LEU 3, /M LEU 2, /N PRO
2, /O ALA 7, /P MET 1, /Q ALA 2, /R THR 4, /S GLU 9, /T THR 3, /U MET 1, /V
SER 6, /W ASN 12, /X MET 1, /Y GLY 4, /Z SER 2, /a U 8, /c GLY 2, /d ALA 2, /e
ASN 41, /f MET 1, /g PRO 2, /h MET 3, /i ARG 25, /j GLY 3, /k LYS 23, /l PRO
2, /m ALA 2, /n ALA 2, /o ALA 2, /p ALA 2, /q LYS 43, /r CYS 20, /s PRO 2, /t
LYS 5, /v ALA 2  
Chain-initial residues that are not actual N termini: /6 GLY 56, /A U 1023, /U
THR 61  
Chain-final residues that are actual C termini: /4 GLY 37, /A U 3132, /B A
115, /T ALA 100, /a C 1526, /d LYS 201, /i ARG 151, /j GLN 101, /k VAL 139, /n
TRP 61, /q LYS 136, /t LEU 86  
Chain-final residues that are not actual C termini: /0 ASP 55, /1 THR 54, /2
LEU 45, /3 ASN 63, /6 TYR 65, /6 GLY 47, /A G 1012, /C ARG 273, /D ARG 214, /E
THR 215, /F LYS 185, /G LYS 176, /H ALA 47, /J GLN 147, /K LEU 122, /L GLU
145, /M GLU 135, /N ARG 117, /O PHE 122, /P LYS 112, /Q ALA 123, /R ILE 103,
/S PRO 121, /U ASP 104, /U ALA 46, /V ARG 100, /W GLY 82, /X ARG 63, /Y LEU
68, /Z GLN 60, /c VAL 208, /e MET 200, /f LYS 95, /g HIS 153, /h TRP 132, /l
LYS 123, /m ILE 117, /o ARG 88, /p ARG 92, /r SER 82, /s ILE 84, /v ASN 23  
15112 hydrogen bonds  
Adding 'H' to /6 GLY 56  
Adding 'H' to /U THR 61  
/0 ASP 55 is not terminus, removing H atom from 'C'  
/1 THR 54 is not terminus, removing H atom from 'C'  
/2 LEU 45 is not terminus, removing H atom from 'C'  
/3 ASN 63 is not terminus, removing H atom from 'C'  
/6 TYR 65 is not terminus, removing H atom from 'C'  
36 messages similar to the above omitted  
94549 hydrogens added  
  
Loading residue template for LIG from internal database  

> volume #1.1.1.1 level 0.1579

> volume #1.1.1.1 level 0.1808

> select ligand

189 atoms, 193 bonds, 1 model selected  

> view sel

> volume #1.1.1.1 level 0.1125

> volume #1.1.1.1 level 0.06921

Fetching CCD GMP from http://ligand-expo.rcsb.org/reports/G/GMP/GMP.cif  

> volume #1.1.1.1 level 0.08959

Traceback (most recent call last):  
File "/home/zhanglab/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/validation/unparameterised.py", line 172, 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 "/home/zhanglab/.local/share/ChimeraX/1.0/site-
packages/chimerax/isolde/validation/unparameterised.py", line 172, in
_fix_selected_unparameterised_residue  
residue, template_name, ccd_template = item.data  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/ui/gui.py",
line 2016, in <lambda>  
dw.closeEvent = lambda e, tw=tool_window, mw=mw: mw.close_request(tw, e)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/ui/gui.py",
line 576, in close_request  
all_windows = self.tool_instance_to_windows[tool_instance]  
KeyError: <chimerax.isolde.tool.ISOLDE_ToolUI object at 0x7fc6cfef2750>  
  
KeyError:  
  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-packages/chimerax/ui/gui.py",
line 576, in close_request  
all_windows = self.tool_instance_to_windows[tool_instance]  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 455.45.01
OpenGL renderer: GeForce RTX 2080 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: System manufacturer
Model: System Product Name
OS: Ubuntu 18.04 bionic
Architecture: 64bit ELF
CPU: 28 Intel(R) Core(TM) i9-9940X CPU @ 3.30GHz
Cache Size: 19712 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:           125G         30G        4.9G        377M         90G         93G
	Swap:          2.0G        1.2G        805M

Graphics:
	19:00.0 VGA compatible controller [0300]: NVIDIA Corporation GV102 [10de:1e07] (rev a1)	
	Subsystem: Device [196e:134e]	
	Kernel driver in use: nvidia
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.8

[Tristan Croll]

Fixed. Now properly uses the setData() and data() methods.