Opened 15 months ago

Last modified 15 months ago

#15749 assigned defect

SEQCROW error: AttributeError: 'NoneType' object has no attribute 'group'

Reported by: chimerax-bug-report@… Owned by: Tony Schaefer
Priority: normal Milestone:
Component: Third Party Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-6.5.0-45-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> toolshed show

Downloading bundle SEQCROW-1.8.10-py3-none-any.whl  

Errors may have occurred when running pip:  

pip standard error:  
\---  
  
[notice] A new release of pip is available: 23.0 -> 24.2  
[notice] To update, run: chimerax -m pip install --upgrade pip  
\---  

pip standard output:  
\---  
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/  
Processing ./SEQCROW-1.8.10-py3-none-any.whl  
Requirement already satisfied: scipy in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from SEQCROW==1.8.10) (1.9.3)  
Requirement already satisfied: ChimeraX-Core<=1.9,>=1.3 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from SEQCROW==1.8.10) (1.6.1)  
Requirement already satisfied: jinja2 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from SEQCROW==1.8.10) (3.1.2)  
Collecting Send2Trash  
Downloading Send2Trash-1.8.3-py3-none-any.whl (18 kB)  
Requirement already satisfied: psutil in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from SEQCROW==1.8.10) (5.9.4)  
Requirement already satisfied: MarkupSafe>=2.0 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from jinja2->SEQCROW==1.8.10) (2.1.2)  
Requirement already satisfied: numpy<1.26.0,>=1.18.5 in /usr/lib/ucsf-
chimerax/lib/python3.9/site-packages (from scipy->SEQCROW==1.8.10) (1.23.5)  
Installing collected packages: Send2Trash, SEQCROW  
Successfully installed SEQCROW-1.8.10 Send2Trash-1.8.3  
\---  

Successfully installed SEQCROW-1.8.10 Send2Trash-1.8.3  
Installed SEQCROW (1.8.10)  

> ui tool show "2D Builder"

Please register the custom scheme 'editor' via
QWebEngineUrlScheme::registerScheme() before installing the custom scheme
handler.  

Traceback (most recent call last):  
File "/home/chemistrylab/.local/share/ChimeraX/1.6/site-
packages/SEQCROW/tools/mol_builder.py", line 619, in handle_scheme  
tmp_url = re.search(  
AttributeError: 'NoneType' object has no attribute 'group'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/htmlview.py", line 320, in interceptRequest  
self._callback(info)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/htmlview.py", line 93, in _intercept  
return interceptor(request_info, *args)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/htmltool.py", line 112, in _navigate  
self.session.ui.thread_safe(self.handle_scheme, url)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py",
line 368, in thread_safe  
func(*args, **kw)  
File "/home/chemistrylab/.local/share/ChimeraX/1.6/site-
packages/SEQCROW/tools/mol_builder.py", line 630, in handle_scheme  
raise IOError(err)  
OSError: 'NoneType' object has no attribute 'group'  
  
OSError: 'NoneType' object has no attribute 'group'  
  
File "/home/chemistrylab/.local/share/ChimeraX/1.6/site-
packages/SEQCROW/tools/mol_builder.py", line 630, in handle_scheme  
raise IOError(err)  
  
See log for complete Python traceback.  
  

> hide #1 models

Structure could not be generated by the NCI CACTUS web API.Check your
structure for errors:  
Molecule from ChemDoodle Web Components  
  
http://www.ichemlabs.com  
114157 0 0 0 0 999 V2000  
2.5981 1.0000 0.0000 C 0 0 0 0 0 0  
3.4641 0.5000 0.0000 C 0 0 0 0 0 0  
3.4641 -0.5000 0.0000 C 0 0 0 0 0 0  
2.5981 -1.0000 0.0000 C 0 0 0 0 0 0  
1.7321 -0.5000 0.0000 C 0 0 0 0 0 0  
1.7321 0.5000 0.0000 C 0 0 0 0 0 0  
4.3301 1.0000 0.0000 C 0 0 0 0 0 0  
5.1962 0.5000 0.0000 C 0 0 0 0 0 0  
5.1962 -0.5000 0.0000 C 0 0 0 0 0 0  
4.3301 -1.0000 0.0000 C 0 0 0 0 0 0  
6.0622 1.0000 0.0000 C 0 0 0 0 0 0  
6.9282 0.5000 0.0000 C 0 0 0 0 0 0  
6.9282 -0.5000 0.0000 C 0 0 0 0 0 0  
6.0622 -1.0000 0.0000 C 0 0 0 0 0 0  
0.8660 -1.0000 0.0000 C 0 0 0 0 0 0  
0.0000 -0.5000 0.0000 C 0 0 0 0 0 0  
-0.0000 0.5000 0.0000 C 0 0 0 0 0 0  
0.8660 1.0000 0.0000 C 0 0 0 0 0 0  
-0.8660 -1.0000 0.0000 C 0 0 0 0 0 0  
-1.7321 -0.5000 0.0000 C 0 0 0 0 0 0  
-1.7321 0.5000 0.0000 C 0 0 0 0 0 0  
-0.8660 1.0000 0.0000 C 0 0 0 0 0 0  
-2.5981 -1.0000 0.0000 C 0 0 0 0 0 0  
-3.4641 -0.5000 0.0000 C 0 0 0 0 0 0  
-3.4641 0.5000 0.0000 C 0 0 0 0 0 0  
-2.5981 1.0000 0.0000 C 0 0 0 0 0 0  
-4.3301 -1.0000 0.0000 C 0 0 0 0 0 0  
-5.1962 -0.5000 0.0000 C 0 0 0 0 0 0  
-5.1962 0.5000 0.0000 C 0 0 0 0 0 0  
-4.3301 1.0000 0.0000 C 0 0 0 0 0 0  
-6.0622 -1.0000 0.0000 C 0 0 0 0 0 0  
-6.9282 -0.5000 0.0000 C 0 0 0 0 0 0  
-6.9282 0.5000 0.0000 C 0 0 0 0 0 0  
-6.0622 1.0000 0.0000 C 0 0 0 0 0 0  
-7.7942 -1.0000 0.0000 C 0 0 0 0 0 0  
-8.6603 -0.5000 0.0000 N 0 0 0 0 0 0  
-8.6603 0.5000 0.0000 C 0 0 0 0 0 0  
-7.7942 1.0000 0.0000 C 0 0 0 0 0 0  
7.7942 -1.0000 0.0000 C 0 0 0 0 0 0  
7.7942 -2.0000 0.0000 C 0 0 0 0 0 0  
6.9282 -2.5000 0.0000 C 0 0 0 0 0 0  
6.0622 -2.0000 0.0000 C 0 0 0 0 0 0  
5.1962 -2.5000 0.0000 C 0 0 0 0 0 0  
4.3301 -2.0000 0.0000 C 0 0 0 0 0 0  
3.4641 -2.5000 0.0000 C 0 0 0 0 0 0  
2.5981 -2.0000 0.0000 C 0 0 0 0 0 0  
1.7321 -2.5000 0.0000 C 0 0 0 0 0 0  
0.8660 -2.0000 0.0000 C 0 0 0 0 0 0  
-0.0000 -2.5000 0.0000 C 0 0 0 0 0 0  
-0.8660 -2.0000 0.0000 C 0 0 0 0 0 0  
-1.7321 -2.5000 0.0000 C 0 0 0 0 0 0  
-2.5981 -2.0000 0.0000 C 0 0 0 0 0 0  
-3.4641 -2.5000 0.0000 C 0 0 0 0 0 0  
-4.3301 -2.0000 0.0000 C 0 0 0 0 0 0  
-5.1962 -2.5000 0.0000 C 0 0 0 0 0 0  
-6.0622 -2.0000 0.0000 C 0 0 0 0 0 0  
-6.9282 -2.5000 0.0000 C 0 0 0 0 0 0  
-7.7942 -2.0000 0.0000 N 0 0 0 0 0 0  
-7.7942 2.0000 0.0000 N 0 0 0 0 0 0  
-6.9282 2.5000 0.0000 C 0 0 0 0 0 0  
-6.0622 2.0000 0.0000 C 0 0 0 0 0 0  
-5.1962 2.5000 0.0000 C 0 0 0 0 0 0  
-4.3301 2.0000 0.0000 C 0 0 0 0 0 0  
-3.4641 2.5000 0.0000 C 0 0 0 0 0 0  
-2.5981 2.0000 0.0000 C 0 0 0 0 0 0  
-1.7321 2.5000 0.0000 C 0 0 0 0 0 0  
-0.8660 2.0000 0.0000 C 0 0 0 0 0 0  
-0.0000 2.5000 0.0000 C 0 0 0 0 0 0  
0.8660 2.0000 0.0000 C 0 0 0 0 0 0  
1.7321 2.5000 0.0000 C 0 0 0 0 0 0  
2.5981 2.0000 0.0000 C 0 0 0 0 0 0  
3.4641 2.5000 0.0000 C 0 0 0 0 0 0  
4.3301 2.0000 0.0000 C 0 0 0 0 0 0  
5.1962 2.5000 0.0000 C 0 0 0 0 0 0  
6.0622 2.0000 0.0000 C 0 0 0 0 0 0  
6.9282 2.5000 0.0000 C 0 0 0 0 0 0  
7.7942 2.0000 0.0000 C 0 0 0 0 0 0  
7.7942 1.0000 0.0000 C 0 0 0 0 0 0  
8.6603 0.5000 0.0000 N 0 0 0 0 0 0  
8.6603 -0.5000 0.0000 N 0 0 0 0 0 0  
-6.9282 3.5000 0.0000 N 0 0 0 0 0 0  
-6.0622 4.0000 0.0000 C 0 0 0 0 0 0  
-5.1962 3.5000 0.0000 C 0 0 0 0 0 0  
-4.3301 4.0000 0.0000 N 0 0 0 0 0 0  
-3.4641 3.5000 0.0000 C 0 0 0 0 0 0  
-2.5981 4.0000 0.0000 N 0 0 0 0 0 0  
-1.7321 3.5000 0.0000 C 0 0 0 0 0 0  
-0.8660 4.0000 0.0000 N 0 0 0 0 0 0  
-0.0000 3.5000 0.0000 C 0 0 0 0 0 0  
0.8660 4.0000 0.0000 N 0 0 0 0 0 0  
1.7321 3.5000 0.0000 C 0 0 0 0 0 0  
2.5981 4.0000 0.0000 N 0 0 0 0 0 0  
3.4641 3.5000 0.0000 C 0 0 0 0 0 0  
4.3301 4.0000 0.0000 N 0 0 0 0 0 0  
5.1962 3.5000 0.0000 C 0 0 0 0 0 0  
6.0622 4.0000 0.0000 N 0 0 0 0 0 0  
6.9282 3.5000 0.0000 N 0 0 0 0 0 0  
-5.1962 -3.5000 0.0000 C 0 0 0 0 0 0  
-6.0622 -4.0000 0.0000 N 0 0 0 0 0 0  
-6.9282 -3.5000 0.0000 C 0 0 0 0 0 0  
-3.4641 -3.5000 0.0000 C 0 0 0 0 0 0  
-4.3301 -4.0000 0.0000 N 0 0 0 0 0 0  
-1.7321 -3.5000 0.0000 C 0 0 0 0 0 0  
-2.5981 -4.0000 0.0000 N 0 0 0 0 0 0  
-0.0000 -3.5000 0.0000 C 0 0 0 0 0 0  
-0.8660 -4.0000 0.0000 N 0 0 0 0 0 0  
1.7321 -3.5000 0.0000 C 0 0 0 0 0 0  
0.8660 -4.0000 0.0000 N 0 0 0 0 0 0  
3.4641 -3.5000 0.0000 C 0 0 0 0 0 0  
2.5981 -4.0000 0.0000 N 0 0 0 0 0 0  
5.1962 -3.5000 0.0000 C 0 0 0 0 0 0  
4.3301 -4.0000 0.0000 N 0 0 0 0 0 0  
6.9282 -3.5000 0.0000 N 0 0 0 0 0 0  
6.0622 -4.0000 0.0000 C 0 0 0 0 0 0  
1 2 1 0 0 0 0  
2 3 2 0 0 0 0  
3 4 1 0 0 0 0  
4 5 2 0 0 0 0  
5 6 1 0 0 0 0  
6 1 2 0 0 0 0  
2 7 1 0 0 0 0  
7 8 2 0 0 0 0  
8 9 1 0 0 0 0  
9 10 2 0 0 0 0  
10 3 1 0 0 0 0  
8 11 1 0 0 0 0  
11 12 2 0 0 0 0  
12 13 1 0 0 0 0  
13 14 2 0 0 0 0  
14 9 1 0 0 0 0  
5 15 1 0 0 0 0  
15 16 2 0 0 0 0  
16 17 1 0 0 0 0  
17 18 2 0 0 0 0  
18 6 1 0 0 0 0  
16 19 1 0 0 0 0  
19 20 2 0 0 0 0  
20 21 1 0 0 0 0  
21 22 2 0 0 0 0  
22 17 1 0 0 0 0  
20 23 1 0 0 0 0  
23 24 2 0 0 0 0  
24 25 1 0 0 0 0  
25 26 2 0 0 0 0  
26 21 1 0 0 0 0  
24 27 1 0 0 0 0  
27 28 2 0 0 0 0  
28 29 1 0 0 0 0  
29 30 2 0 0 0 0  
30 25 1 0 0 0 0  
28 31 1 0 0 0 0  
31 32 2 0 0 0 0  
32 33 1 0 0 0 0  
33 34 2 0 0 0 0  
34 29 1 0 0 0 0  
32 35 1 0 0 0 0  
35 36 2 0 0 0 0  
36 37 1 0 0 0 0  
37 38 2 0 0 0 0  
38 33 1 0 0 0 0  
13 39 1 0 0 0 0  
39 40 2 0 0 0 0  
40 41 1 0 0 0 0  
41 42 2 0 0 0 0  
42 14 1 0 0 0 0  
42 43 1 0 0 0 0  
43 44 2 0 0 0 0  
44 10 1 0 0 0 0  
44 45 1 0 0 0 0  
45 46 2 0 0 0 0  
46 4 1 0 0 0 0  
46 47 1 0 0 0 0  
47 48 2 0 0 0 0  
48 15 1 0 0 0 0  
48 49 1 0 0 0 0  
49 50 2 0 0 0 0  
50 19 1 0 0 0 0  
50 51 1 0 0 0 0  
51 52 2 0 0 0 0  
52 23 1 0 0 0 0  
52 53 1 0 0 0 0  
53 54 2 0 0 0 0  
54 27 1 0 0 0 0  
54 55 1 0 0 0 0  
55 56 2 0 0 0 0  
56 31 1 0 0 0 0  
56 57 1 0 0 0 0  
57 58 2 0 0 0 0  
58 35 1 0 0 0 0  
38 59 1 0 0 0 0  
59 60 1 0 0 0 0  
60 61 2 0 0 0 0  
61 34 1 0 0 0 0  
61 62 1 0 0 0 0  
62 63 1 0 0 0 0  
63 30 1 0 0 0 0  
63 64 2 0 0 0 0  
64 65 1 0 0 0 0  
65 26 1 0 0 0 0  
65 66 2 0 0 0 0  
66 67 1 0 0 0 0  
67 22 1 0 0 0 0  
67 68 2 0 0 0 0  
68 69 1 0 0 0 0  
69 18 1 0 0 0 0  
69 70 2 0 0 0 0  
70 71 1 0 0 0 0  
71 1 1 0 0 0 0  
71 72 1 0 0 0 0  
72 73 2 0 0 0 0  
73 7 1 0 0 0 0  
73 74 1 0 0 0 0  
74 75 1 0 0 0 0  
75 11 1 0 0 0 0  
75 76 2 0 0 0 0  
76 77 1 0 0 0 0  
77 78 2 0 0 0 0  
78 12 1 0 0 0 0  
78 79 1 0 0 0 0  
79 80 1 0 0 0 0  
80 39 1 0 0 0 0  
60 81 1 0 0 0 0  
81 82 2 0 0 0 0  
82 83 1 0 0 0 0  
83 62 2 0 0 0 0  
83 84 1 0 0 0 0  
84 85 1 0 0 0 0  
85 64 1 0 0 0 0  
85 86 2 0 0 0 0  
86 87 1 0 0 0 0  
87 66 1 0 0 0 0  
87 88 2 0 0 0 0  
88 89 1 0 0 0 0  
89 68 1 0 0 0 0  
89 90 2 0 0 0 0  
90 91 1 0 0 0 0  
91 70 1 0 0 0 0  
91 92 2 0 0 0 0  
92 93 1 0 0 0 0  
93 72 1 0 0 0 0  
93 94 2 0 0 0 0  
94 95 1 0 0 0 0  
95 74 2 0 0 0 0  
95 96 1 0 0 0 0  
96 97 1 0 0 0 0  
97 76 1 0 0 0 0  
55 98 1 0 0 0 0  
98 99 1 0 0 0 0  
99100 2 0 0 0 0  
100 57 1 0 0 0 0  
53101 1 0 0 0 0  
101102 2 0 0 0 0  
102 98 1 0 0 0 0  
51103 1 0 0 0 0  
103104 2 0 0 0 0  
104101 1 0 0 0 0  
49105 1 0 0 0 0  
105106 2 0 0 0 0  
106103 1 0 0 0 0  
47107 1 0 0 0 0  
107108 2 0 0 0 0  
108105 1 0 0 0 0  
45109 1 0 0 0 0  
109110 2 0 0 0 0  
110107 1 0 0 0 0  
43111 1 0 0 0 0  
111112 2 0 0 0 0  
112109 1 0 0 0 0  
41113 1 0 0 0 0  
113114 2 0 0 0 0  
114111 1 0 0 0 0  
M END  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/htmlview.py", line 320, in interceptRequest  
self._callback(info)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/htmlview.py", line 93, in _intercept  
return interceptor(request_info, *args)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/htmltool.py", line 112, in _navigate  
self.session.ui.thread_safe(self.handle_scheme, url)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py",
line 368, in thread_safe  
func(*args, **kw)  
File "/home/chemistrylab/.local/share/ChimeraX/1.6/site-
packages/SEQCROW/tools/mol_builder.py", line 609, in handle_scheme  
msg, status = s_sd_get.msg, s_sd_get.status  
UnboundLocalError: local variable 's_sd_get' referenced before assignment  
  
UnboundLocalError: local variable 's_sd_get' referenced before assignment  
  
File "/home/chemistrylab/.local/share/ChimeraX/1.6/site-
packages/SEQCROW/tools/mol_builder.py", line 609, in handle_scheme  
msg, status = s_sd_get.msg, s_sd_get.status  
  
See log for complete Python traceback.  
  
Structure could not be generated by the NCI CACTUS web API.Check your
structure for errors:  
Molecule from ChemDoodle Web Components  
  
http://www.ichemlabs.com  
114157 0 0 0 0 999 V2000  
2.5981 1.0000 0.0000 C 0 0 0 0 0 0  
3.4641 0.5000 0.0000 C 0 0 0 0 0 0  
3.4641 -0.5000 0.0000 C 0 0 0 0 0 0  
2.5981 -1.0000 0.0000 C 0 0 0 0 0 0  
1.7321 -0.5000 0.0000 C 0 0 0 0 0 0  
1.7321 0.5000 0.0000 C 0 0 0 0 0 0  
4.3301 1.0000 0.0000 C 0 0 0 0 0 0  
5.1962 0.5000 0.0000 C 0 0 0 0 0 0  
5.1962 -0.5000 0.0000 C 0 0 0 0 0 0  
4.3301 -1.0000 0.0000 C 0 0 0 0 0 0  
6.0622 1.0000 0.0000 C 0 0 0 0 0 0  
6.9282 0.5000 0.0000 C 0 0 0 0 0 0  
6.9282 -0.5000 0.0000 C 0 0 0 0 0 0  
6.0622 -1.0000 0.0000 C 0 0 0 0 0 0  
0.8660 -1.0000 0.0000 C 0 0 0 0 0 0  
0.0000 -0.5000 0.0000 C 0 0 0 0 0 0  
-0.0000 0.5000 0.0000 C 0 0 0 0 0 0  
0.8660 1.0000 0.0000 C 0 0 0 0 0 0  
-0.8660 -1.0000 0.0000 C 0 0 0 0 0 0  
-1.7321 -0.5000 0.0000 C 0 0 0 0 0 0  
-1.7321 0.5000 0.0000 C 0 0 0 0 0 0  
-0.8660 1.0000 0.0000 C 0 0 0 0 0 0  
-2.5981 -1.0000 0.0000 C 0 0 0 0 0 0  
-3.4641 -0.5000 0.0000 C 0 0 0 0 0 0  
-3.4641 0.5000 0.0000 C 0 0 0 0 0 0  
-2.5981 1.0000 0.0000 C 0 0 0 0 0 0  
-4.3301 -1.0000 0.0000 C 0 0 0 0 0 0  
-5.1962 -0.5000 0.0000 C 0 0 0 0 0 0  
-5.1962 0.5000 0.0000 C 0 0 0 0 0 0  
-4.3301 1.0000 0.0000 C 0 0 0 0 0 0  
-6.0622 -1.0000 0.0000 C 0 0 0 0 0 0  
-6.9282 -0.5000 0.0000 C 0 0 0 0 0 0  
-6.9282 0.5000 0.0000 C 0 0 0 0 0 0  
-6.0622 1.0000 0.0000 C 0 0 0 0 0 0  
-7.7942 -1.0000 0.0000 C 0 0 0 0 0 0  
-8.6603 -0.5000 0.0000 N 0 0 0 0 0 0  
-8.6603 0.5000 0.0000 C 0 0 0 0 0 0  
-7.7942 1.0000 0.0000 C 0 0 0 0 0 0  
7.7942 -1.0000 0.0000 C 0 0 0 0 0 0  
7.7942 -2.0000 0.0000 C 0 0 0 0 0 0  
6.9282 -2.5000 0.0000 C 0 0 0 0 0 0  
6.0622 -2.0000 0.0000 C 0 0 0 0 0 0  
5.1962 -2.5000 0.0000 C 0 0 0 0 0 0  
4.3301 -2.0000 0.0000 C 0 0 0 0 0 0  
3.4641 -2.5000 0.0000 C 0 0 0 0 0 0  
2.5981 -2.0000 0.0000 C 0 0 0 0 0 0  
1.7321 -2.5000 0.0000 C 0 0 0 0 0 0  
0.8660 -2.0000 0.0000 C 0 0 0 0 0 0  
-0.0000 -2.5000 0.0000 C 0 0 0 0 0 0  
-0.8660 -2.0000 0.0000 C 0 0 0 0 0 0  
-1.7321 -2.5000 0.0000 C 0 0 0 0 0 0  
-2.5981 -2.0000 0.0000 C 0 0 0 0 0 0  
-3.4641 -2.5000 0.0000 C 0 0 0 0 0 0  
-4.3301 -2.0000 0.0000 C 0 0 0 0 0 0  
-5.1962 -2.5000 0.0000 C 0 0 0 0 0 0  
-6.0622 -2.0000 0.0000 C 0 0 0 0 0 0  
-6.9282 -2.5000 0.0000 C 0 0 0 0 0 0  
-7.7942 -2.0000 0.0000 N 0 0 0 0 0 0  
-7.7942 2.0000 0.0000 N 0 0 0 0 0 0  
-6.9282 2.5000 0.0000 C 0 0 0 0 0 0  
-6.0622 2.0000 0.0000 C 0 0 0 0 0 0  
-5.1962 2.5000 0.0000 C 0 0 0 0 0 0  
-4.3301 2.0000 0.0000 C 0 0 0 0 0 0  
-3.4641 2.5000 0.0000 C 0 0 0 0 0 0  
-2.5981 2.0000 0.0000 C 0 0 0 0 0 0  
-1.7321 2.5000 0.0000 C 0 0 0 0 0 0  
-0.8660 2.0000 0.0000 C 0 0 0 0 0 0  
-0.0000 2.5000 0.0000 C 0 0 0 0 0 0  
0.8660 2.0000 0.0000 C 0 0 0 0 0 0  
1.7321 2.5000 0.0000 C 0 0 0 0 0 0  
2.5981 2.0000 0.0000 C 0 0 0 0 0 0  
3.4641 2.5000 0.0000 C 0 0 0 0 0 0  
4.3301 2.0000 0.0000 C 0 0 0 0 0 0  
5.1962 2.5000 0.0000 C 0 0 0 0 0 0  
6.0622 2.0000 0.0000 C 0 0 0 0 0 0  
6.9282 2.5000 0.0000 C 0 0 0 0 0 0  
7.7942 2.0000 0.0000 C 0 0 0 0 0 0  
7.7942 1.0000 0.0000 C 0 0 0 0 0 0  
8.6603 0.5000 0.0000 N 0 0 0 0 0 0  
8.6603 -0.5000 0.0000 N 0 0 0 0 0 0  
-6.9282 3.5000 0.0000 N 0 0 0 0 0 0  
-6.0622 4.0000 0.0000 C 0 0 0 0 0 0  
-5.1962 3.5000 0.0000 C 0 0 0 0 0 0  
-4.3301 4.0000 0.0000 N 0 0 0 0 0 0  
-3.4641 3.5000 0.0000 C 0 0 0 0 0 0  
-2.5981 4.0000 0.0000 N 0 0 0 0 0 0  
-1.7321 3.5000 0.0000 C 0 0 0 0 0 0  
-0.8660 4.0000 0.0000 N 0 0 0 0 0 0  
-0.0000 3.5000 0.0000 C 0 0 0 0 0 0  
0.8660 4.0000 0.0000 N 0 0 0 0 0 0  
1.7321 3.5000 0.0000 C 0 0 0 0 0 0  
2.5981 4.0000 0.0000 N 0 0 0 0 0 0  
3.4641 3.5000 0.0000 C 0 0 0 0 0 0  
4.3301 4.0000 0.0000 N 0 0 0 0 0 0  
5.1962 3.5000 0.0000 C 0 0 0 0 0 0  
6.0622 4.0000 0.0000 N 0 0 0 0 0 0  
6.9282 3.5000 0.0000 C 0 0 0 0 0 0  
-5.1962 -3.5000 0.0000 C 0 0 0 0 0 0  
-6.0622 -4.0000 0.0000 N 0 0 0 0 0 0  
-6.9282 -3.5000 0.0000 C 0 0 0 0 0 0  
-3.4641 -3.5000 0.0000 C 0 0 0 0 0 0  
-4.3301 -4.0000 0.0000 N 0 0 0 0 0 0  
-1.7321 -3.5000 0.0000 C 0 0 0 0 0 0  
-2.5981 -4.0000 0.0000 N 0 0 0 0 0 0  
-0.0000 -3.5000 0.0000 C 0 0 0 0 0 0  
-0.8660 -4.0000 0.0000 N 0 0 0 0 0 0  
1.7321 -3.5000 0.0000 C 0 0 0 0 0 0  
0.8660 -4.0000 0.0000 N 0 0 0 0 0 0  
3.4641 -3.5000 0.0000 C 0 0 0 0 0 0  
2.5981 -4.0000 0.0000 N 0 0 0 0 0 0  
5.1962 -3.5000 0.0000 C 0 0 0 0 0 0  
4.3301 -4.0000 0.0000 N 0 0 0 0 0 0  
6.9282 -3.5000 0.0000 N 0 0 0 0 0 0  
6.0622 -4.0000 0.0000 C 0 0 0 0 0 0  
1 2 1 0 0 0 0  
2 3 2 0 0 0 0  
3 4 1 0 0 0 0  
4 5 2 0 0 0 0  
5 6 1 0 0 0 0  
6 1 2 0 0 0 0  
2 7 1 0 0 0 0  
7 8 2 0 0 0 0  
8 9 1 0 0 0 0  
9 10 2 0 0 0 0  
10 3 1 0 0 0 0  
8 11 1 0 0 0 0  
11 12 2 0 0 0 0  
12 13 1 0 0 0 0  
13 14 2 0 0 0 0  
14 9 1 0 0 0 0  
5 15 1 0 0 0 0  
15 16 2 0 0 0 0  
16 17 1 0 0 0 0  
17 18 2 0 0 0 0  
18 6 1 0 0 0 0  
16 19 1 0 0 0 0  
19 20 2 0 0 0 0  
20 21 1 0 0 0 0  
21 22 2 0 0 0 0  
22 17 1 0 0 0 0  
20 23 1 0 0 0 0  
23 24 2 0 0 0 0  
24 25 1 0 0 0 0  
25 26 2 0 0 0 0  
26 21 1 0 0 0 0  
24 27 1 0 0 0 0  
27 28 2 0 0 0 0  
28 29 1 0 0 0 0  
29 30 2 0 0 0 0  
30 25 1 0 0 0 0  
28 31 1 0 0 0 0  
31 32 2 0 0 0 0  
32 33 1 0 0 0 0  
33 34 2 0 0 0 0  
34 29 1 0 0 0 0  
32 35 1 0 0 0 0  
35 36 2 0 0 0 0  
36 37 1 0 0 0 0  
37 38 2 0 0 0 0  
38 33 1 0 0 0 0  
13 39 1 0 0 0 0  
39 40 2 0 0 0 0  
40 41 1 0 0 0 0  
41 42 2 0 0 0 0  
42 14 1 0 0 0 0  
42 43 1 0 0 0 0  
43 44 2 0 0 0 0  
44 10 1 0 0 0 0  
44 45 1 0 0 0 0  
45 46 2 0 0 0 0  
46 4 1 0 0 0 0  
46 47 1 0 0 0 0  
47 48 2 0 0 0 0  
48 15 1 0 0 0 0  
48 49 1 0 0 0 0  
49 50 2 0 0 0 0  
50 19 1 0 0 0 0  
50 51 1 0 0 0 0  
51 52 2 0 0 0 0  
52 23 1 0 0 0 0  
52 53 1 0 0 0 0  
53 54 2 0 0 0 0  
54 27 1 0 0 0 0  
54 55 1 0 0 0 0  
55 56 2 0 0 0 0  
56 31 1 0 0 0 0  
56 57 1 0 0 0 0  
57 58 2 0 0 0 0  
58 35 1 0 0 0 0  
38 59 1 0 0 0 0  
59 60 1 0 0 0 0  
60 61 2 0 0 0 0  
61 34 1 0 0 0 0  
61 62 1 0 0 0 0  
62 63 1 0 0 0 0  
63 30 1 0 0 0 0  
63 64 2 0 0 0 0  
64 65 1 0 0 0 0  
65 26 1 0 0 0 0  
65 66 2 0 0 0 0  
66 67 1 0 0 0 0  
67 22 1 0 0 0 0  
67 68 2 0 0 0 0  
68 69 1 0 0 0 0  
69 18 1 0 0 0 0  
69 70 2 0 0 0 0  
70 71 1 0 0 0 0  
71 1 1 0 0 0 0  
71 72 1 0 0 0 0  
72 73 2 0 0 0 0  
73 7 1 0 0 0 0  
73 74 1 0 0 0 0  
74 75 1 0 0 0 0  
75 11 1 0 0 0 0  
75 76 2 0 0 0 0  
76 77 1 0 0 0 0  
77 78 2 0 0 0 0  
78 12 1 0 0 0 0  
78 79 1 0 0 0 0  
79 80 1 0 0 0 0  
80 39 1 0 0 0 0  
60 81 1 0 0 0 0  
81 82 2 0 0 0 0  
82 83 1 0 0 0 0  
83 62 2 0 0 0 0  
83 84 1 0 0 0 0  
84 85 1 0 0 0 0  
85 64 1 0 0 0 0  
85 86 2 0 0 0 0  
86 87 1 0 0 0 0  
87 66 1 0 0 0 0  
87 88 2 0 0 0 0  
88 89 1 0 0 0 0  
89 68 1 0 0 0 0  
89 90 2 0 0 0 0  
90 91 1 0 0 0 0  
91 70 1 0 0 0 0  
91 92 2 0 0 0 0  
92 93 1 0 0 0 0  
93 72 1 0 0 0 0  
93 94 2 0 0 0 0  
94 95 1 0 0 0 0  
95 74 2 0 0 0 0  
95 96 1 0 0 0 0  
96 97 1 0 0 0 0  
97 76 1 0 0 0 0  
55 98 1 0 0 0 0  
98 99 1 0 0 0 0  
99100 2 0 0 0 0  
100 57 1 0 0 0 0  
53101 1 0 0 0 0  
101102 2 0 0 0 0  
102 98 1 0 0 0 0  
51103 1 0 0 0 0  
103104 2 0 0 0 0  
104101 1 0 0 0 0  
49105 1 0 0 0 0  
105106 2 0 0 0 0  
106103 1 0 0 0 0  
47107 1 0 0 0 0  
107108 2 0 0 0 0  
108105 1 0 0 0 0  
45109 1 0 0 0 0  
109110 2 0 0 0 0  
110107 1 0 0 0 0  
43111 1 0 0 0 0  
111112 2 0 0 0 0  
112109 1 0 0 0 0  
41113 1 0 0 0 0  
113114 2 0 0 0 0  
114111 1 0 0 0 0  
M END  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/htmlview.py", line 320, in interceptRequest  
self._callback(info)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/htmlview.py", line 93, in _intercept  
return interceptor(request_info, *args)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/htmltool.py", line 112, in _navigate  
self.session.ui.thread_safe(self.handle_scheme, url)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py",
line 368, in thread_safe  
func(*args, **kw)  
File "/home/chemistrylab/.local/share/ChimeraX/1.6/site-
packages/SEQCROW/tools/mol_builder.py", line 609, in handle_scheme  
msg, status = s_sd_get.msg, s_sd_get.status  
UnboundLocalError: local variable 's_sd_get' referenced before assignment  
  
UnboundLocalError: local variable 's_sd_get' referenced before assignment  
  
File "/home/chemistrylab/.local/share/ChimeraX/1.6/site-
packages/SEQCROW/tools/mol_builder.py", line 609, in handle_scheme  
msg, status = s_sd_get.msg, s_sd_get.status  
  
See log for complete Python traceback.  
  
Structure could not be generated by the NCI CACTUS web API.Check your
structure for errors:  
Molecule from ChemDoodle Web Components  
  
http://www.ichemlabs.com  
114157 0 0 0 0 999 V2000  
2.5981 1.0000 0.0000 C 0 0 0 0 0 0  
3.4641 0.5000 0.0000 C 0 0 0 0 0 0  
3.4641 -0.5000 0.0000 C 0 0 0 0 0 0  
2.5981 -1.0000 0.0000 C 0 0 0 0 0 0  
1.7321 -0.5000 0.0000 C 0 0 0 0 0 0  
1.7321 0.5000 0.0000 C 0 0 0 0 0 0  
4.3301 1.0000 0.0000 C 0 0 0 0 0 0  
5.1962 0.5000 0.0000 C 0 0 0 0 0 0  
5.1962 -0.5000 0.0000 C 0 0 0 0 0 0  
4.3301 -1.0000 0.0000 C 0 0 0 0 0 0  
6.0622 1.0000 0.0000 C 0 0 0 0 0 0  
6.9282 0.5000 0.0000 C 0 0 0 0 0 0  
6.9282 -0.5000 0.0000 C 0 0 0 0 0 0  
6.0622 -1.0000 0.0000 C 0 0 0 0 0 0  
0.8660 -1.0000 0.0000 C 0 0 0 0 0 0  
0.0000 -0.5000 0.0000 C 0 0 0 0 0 0  
-0.0000 0.5000 0.0000 C 0 0 0 0 0 0  
0.8660 1.0000 0.0000 C 0 0 0 0 0 0  
-0.8660 -1.0000 0.0000 C 0 0 0 0 0 0  
-1.7321 -0.5000 0.0000 C 0 0 0 0 0 0  
-1.7321 0.5000 0.0000 C 0 0 0 0 0 0  
-0.8660 1.0000 0.0000 C 0 0 0 0 0 0  
-2.5981 -1.0000 0.0000 C 0 0 0 0 0 0  
-3.4641 -0.5000 0.0000 C 0 0 0 0 0 0  
-3.4641 0.5000 0.0000 C 0 0 0 0 0 0  
-2.5981 1.0000 0.0000 C 0 0 0 0 0 0  
-4.3301 -1.0000 0.0000 C 0 0 0 0 0 0  
-5.1962 -0.5000 0.0000 C 0 0 0 0 0 0  
-5.1962 0.5000 0.0000 C 0 0 0 0 0 0  
-4.3301 1.0000 0.0000 C 0 0 0 0 0 0  
-6.0622 -1.0000 0.0000 C 0 0 0 0 0 0  
-6.9282 -0.5000 0.0000 C 0 0 0 0 0 0  
-6.9282 0.5000 0.0000 C 0 0 0 0 0 0  
-6.0622 1.0000 0.0000 C 0 0 0 0 0 0  
-7.7942 -1.0000 0.0000 C 0 0 0 0 0 0  
-8.6603 -0.5000 0.0000 N 0 0 0 0 0 0  
-8.6603 0.5000 0.0000 C 0 0 0 0 0 0  
-7.7942 1.0000 0.0000 C 0 0 0 0 0 0  
7.7942 -1.0000 0.0000 C 0 0 0 0 0 0  
7.7942 -2.0000 0.0000 C 0 0 0 0 0 0  
6.9282 -2.5000 0.0000 C 0 0 0 0 0 0  
6.0622 -2.0000 0.0000 C 0 0 0 0 0 0  
5.1962 -2.5000 0.0000 C 0 0 0 0 0 0  
4.3301 -2.0000 0.0000 C 0 0 0 0 0 0  
3.4641 -2.5000 0.0000 C 0 0 0 0 0 0  
2.5981 -2.0000 0.0000 C 0 0 0 0 0 0  
1.7321 -2.5000 0.0000 C 0 0 0 0 0 0  
0.8660 -2.0000 0.0000 C 0 0 0 0 0 0  
-0.0000 -2.5000 0.0000 C 0 0 0 0 0 0  
-0.8660 -2.0000 0.0000 C 0 0 0 0 0 0  
-1.7321 -2.5000 0.0000 C 0 0 0 0 0 0  
-2.5981 -2.0000 0.0000 C 0 0 0 0 0 0  
-3.4641 -2.5000 0.0000 C 0 0 0 0 0 0  
-4.3301 -2.0000 0.0000 C 0 0 0 0 0 0  
-5.1962 -2.5000 0.0000 C 0 0 0 0 0 0  
-6.0622 -2.0000 0.0000 C 0 0 0 0 0 0  
-6.9282 -2.5000 0.0000 C 0 0 0 0 0 0  
-7.7942 -2.0000 0.0000 N 0 0 0 0 0 0  
-7.7942 2.0000 0.0000 N 0 0 0 0 0 0  
-6.9282 2.5000 0.0000 C 0 0 0 0 0 0  
-6.0622 2.0000 0.0000 C 0 0 0 0 0 0  
-5.1962 2.5000 0.0000 C 0 0 0 0 0 0  
-4.3301 2.0000 0.0000 C 0 0 0 0 0 0  
-3.4641 2.5000 0.0000 C 0 0 0 0 0 0  
-2.5981 2.0000 0.0000 C 0 0 0 0 0 0  
-1.7321 2.5000 0.0000 C 0 0 0 0 0 0  
-0.8660 2.0000 0.0000 C 0 0 0 0 0 0  
-0.0000 2.5000 0.0000 C 0 0 0 0 0 0  
0.8660 2.0000 0.0000 C 0 0 0 0 0 0  
1.7321 2.5000 0.0000 C 0 0 0 0 0 0  
2.5981 2.0000 0.0000 C 0 0 0 0 0 0  
3.4641 2.5000 0.0000 C 0 0 0 0 0 0  
4.3301 2.0000 0.0000 C 0 0 0 0 0 0  
5.1962 2.5000 0.0000 C 0 0 0 0 0 0  
6.0622 2.0000 0.0000 C 0 0 0 0 0 0  
6.9282 2.5000 0.0000 C 0 0 0 0 0 0  
7.7942 2.0000 0.0000 C 0 0 0 0 0 0  
7.7942 1.0000 0.0000 C 0 0 0 0 0 0  
8.6603 0.5000 0.0000 N 0 0 0 0 0 0  
8.6603 -0.5000 0.0000 C 0 0 0 0 0 0  
-6.9282 3.5000 0.0000 N 0 0 0 0 0 0  
-6.0622 4.0000 0.0000 C 0 0 0 0 0 0  
-5.1962 3.5000 0.0000 C 0 0 0 0 0 0  
-4.3301 4.0000 0.0000 N 0 0 0 0 0 0  
-3.4641 3.5000 0.0000 C 0 0 0 0 0 0  
-2.5981 4.0000 0.0000 N 0 0 0 0 0 0  
-1.7321 3.5000 0.0000 C 0 0 0 0 0 0  
-0.8660 4.0000 0.0000 N 0 0 0 0 0 0  
-0.0000 3.5000 0.0000 C 0 0 0 0 0 0  
0.8660 4.0000 0.0000 N 0 0 0 0 0 0  
1.7321 3.5000 0.0000 C 0 0 0 0 0 0  
2.5981 4.0000 0.0000 N 0 0 0 0 0 0  
3.4641 3.5000 0.0000 C 0 0 0 0 0 0  
4.3301 4.0000 0.0000 N 0 0 0 0 0 0  
5.1962 3.5000 0.0000 C 0 0 0 0 0 0  
6.0622 4.0000 0.0000 N 0 0 0 0 0 0  
6.9282 3.5000 0.0000 C 0 0 0 0 0 0  
-5.1962 -3.5000 0.0000 C 0 0 0 0 0 0  
-6.0622 -4.0000 0.0000 N 0 0 0 0 0 0  
-6.9282 -3.5000 0.0000 C 0 0 0 0 0 0  
-3.4641 -3.5000 0.0000 C 0 0 0 0 0 0  
-4.3301 -4.0000 0.0000 N 0 0 0 0 0 0  
-1.7321 -3.5000 0.0000 C 0 0 0 0 0 0  
-2.5981 -4.0000 0.0000 N 0 0 0 0 0 0  
-0.0000 -3.5000 0.0000 C 0 0 0 0 0 0  
-0.8660 -4.0000 0.0000 N 0 0 0 0 0 0  
1.7321 -3.5000 0.0000 C 0 0 0 0 0 0  
0.8660 -4.0000 0.0000 N 0 0 0 0 0 0  
3.4641 -3.5000 0.0000 C 0 0 0 0 0 0  
2.5981 -4.0000 0.0000 N 0 0 0 0 0 0  
5.1962 -3.5000 0.0000 C 0 0 0 0 0 0  
4.3301 -4.0000 0.0000 N 0 0 0 0 0 0  
6.9282 -3.5000 0.0000 N 0 0 0 0 0 0  
6.0622 -4.0000 0.0000 C 0 0 0 0 0 0  
1 2 1 0 0 0 0  
2 3 2 0 0 0 0  
3 4 1 0 0 0 0  
4 5 2 0 0 0 0  
5 6 1 0 0 0 0  
6 1 2 0 0 0 0  
2 7 1 0 0 0 0  
7 8 2 0 0 0 0  
8 9 1 0 0 0 0  
9 10 2 0 0 0 0  
10 3 1 0 0 0 0  
8 11 1 0 0 0 0  
11 12 2 0 0 0 0  
12 13 1 0 0 0 0  
13 14 2 0 0 0 0  
14 9 1 0 0 0 0  
5 15 1 0 0 0 0  
15 16 2 0 0 0 0  
16 17 1 0 0 0 0  
17 18 2 0 0 0 0  
18 6 1 0 0 0 0  
16 19 1 0 0 0 0  
19 20 2 0 0 0 0  
20 21 1 0 0 0 0  
21 22 2 0 0 0 0  
22 17 1 0 0 0 0  
20 23 1 0 0 0 0  
23 24 2 0 0 0 0  
24 25 1 0 0 0 0  
25 26 2 0 0 0 0  
26 21 1 0 0 0 0  
24 27 1 0 0 0 0  
27 28 2 0 0 0 0  
28 29 1 0 0 0 0  
29 30 2 0 0 0 0  
30 25 1 0 0 0 0  
28 31 1 0 0 0 0  
31 32 2 0 0 0 0  
32 33 1 0 0 0 0  
33 34 2 0 0 0 0  
34 29 1 0 0 0 0  
32 35 1 0 0 0 0  
35 36 2 0 0 0 0  
36 37 1 0 0 0 0  
37 38 2 0 0 0 0  
38 33 1 0 0 0 0  
13 39 1 0 0 0 0  
39 40 2 0 0 0 0  
40 41 1 0 0 0 0  
41 42 2 0 0 0 0  
42 14 1 0 0 0 0  
42 43 1 0 0 0 0  
43 44 2 0 0 0 0  
44 10 1 0 0 0 0  
44 45 1 0 0 0 0  
45 46 2 0 0 0 0  
46 4 1 0 0 0 0  
46 47 1 0 0 0 0  
47 48 2 0 0 0 0  
48 15 1 0 0 0 0  
48 49 1 0 0 0 0  
49 50 2 0 0 0 0  
50 19 1 0 0 0 0  
50 51 1 0 0 0 0  
51 52 2 0 0 0 0  
52 23 1 0 0 0 0  
52 53 1 0 0 0 0  
53 54 2 0 0 0 0  
54 27 1 0 0 0 0  
54 55 1 0 0 0 0  
55 56 2 0 0 0 0  
56 31 1 0 0 0 0  
56 57 1 0 0 0 0  
57 58 2 0 0 0 0  
58 35 1 0 0 0 0  
38 59 1 0 0 0 0  
59 60 1 0 0 0 0  
60 61 2 0 0 0 0  
61 34 1 0 0 0 0  
61 62 1 0 0 0 0  
62 63 1 0 0 0 0  
63 30 1 0 0 0 0  
63 64 2 0 0 0 0  
64 65 1 0 0 0 0  
65 26 1 0 0 0 0  
65 66 2 0 0 0 0  
66 67 1 0 0 0 0  
67 22 1 0 0 0 0  
67 68 2 0 0 0 0  
68 69 1 0 0 0 0  
69 18 1 0 0 0 0  
69 70 2 0 0 0 0  
70 71 1 0 0 0 0  
71 1 1 0 0 0 0  
71 72 1 0 0 0 0  
72 73 2 0 0 0 0  
73 7 1 0 0 0 0  
73 74 1 0 0 0 0  
74 75 1 0 0 0 0  
75 11 1 0 0 0 0  
75 76 2 0 0 0 0  
76 77 1 0 0 0 0  
77 78 2 0 0 0 0  
78 12 1 0 0 0 0  
78 79 1 0 0 0 0  
79 80 1 0 0 0 0  
80 39 1 0 0 0 0  
60 81 1 0 0 0 0  
81 82 2 0 0 0 0  
82 83 1 0 0 0 0  
83 62 2 0 0 0 0  
83 84 1 0 0 0 0  
84 85 1 0 0 0 0  
85 64 1 0 0 0 0  
85 86 2 0 0 0 0  
86 87 1 0 0 0 0  
87 66 1 0 0 0 0  
87 88 2 0 0 0 0  
88 89 1 0 0 0 0  
89 68 1 0 0 0 0  
89 90 2 0 0 0 0  
90 91 1 0 0 0 0  
91 70 1 0 0 0 0  
91 92 2 0 0 0 0  
92 93 1 0 0 0 0  
93 72 1 0 0 0 0  
93 94 2 0 0 0 0  
94 95 1 0 0 0 0  
95 74 2 0 0 0 0  
95 96 1 0 0 0 0  
96 97 1 0 0 0 0  
97 76 1 0 0 0 0  
55 98 1 0 0 0 0  
98 99 1 0 0 0 0  
99100 2 0 0 0 0  
100 57 1 0 0 0 0  
53101 1 0 0 0 0  
101102 2 0 0 0 0  
102 98 1 0 0 0 0  
51103 1 0 0 0 0  
103104 2 0 0 0 0  
104101 1 0 0 0 0  
49105 1 0 0 0 0  
105106 2 0 0 0 0  
106103 1 0 0 0 0  
47107 1 0 0 0 0  
107108 2 0 0 0 0  
108105 1 0 0 0 0  
45109 1 0 0 0 0  
109110 2 0 0 0 0  
110107 1 0 0 0 0  
43111 1 0 0 0 0  
111112 2 0 0 0 0  
112109 1 0 0 0 0  
41113 1 0 0 0 0  
113114 2 0 0 0 0  
114111 1 0 0 0 0  
M END  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/htmlview.py", line 320, in interceptRequest  
self._callback(info)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/htmlview.py", line 93, in _intercept  
return interceptor(request_info, *args)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/htmltool.py", line 112, in _navigate  
self.session.ui.thread_safe(self.handle_scheme, url)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py",
line 368, in thread_safe  
func(*args, **kw)  
File "/home/chemistrylab/.local/share/ChimeraX/1.6/site-
packages/SEQCROW/tools/mol_builder.py", line 609, in handle_scheme  
msg, status = s_sd_get.msg, s_sd_get.status  
UnboundLocalError: local variable 's_sd_get' referenced before assignment  
  
UnboundLocalError: local variable 's_sd_get' referenced before assignment  
  
File "/home/chemistrylab/.local/share/ChimeraX/1.6/site-
packages/SEQCROW/tools/mol_builder.py", line 609, in handle_scheme  
msg, status = s_sd_get.msg, s_sd_get.status  
  
See log for complete Python traceback.  
  

> undo

Structure could not be generated by the NCI CACTUS web API.Check your
structure for errors:  
Molecule from ChemDoodle Web Components  
  
http://www.ichemlabs.com  
114157 0 0 0 0 999 V2000  
2.5981 1.0000 0.0000 C 0 0 0 0 0 0  
3.4641 0.5000 0.0000 C 0 0 0 0 0 0  
3.4641 -0.5000 0.0000 C 0 0 0 0 0 0  
2.5981 -1.0000 0.0000 C 0 0 0 0 0 0  
1.7321 -0.5000 0.0000 C 0 0 0 0 0 0  
1.7321 0.5000 0.0000 C 0 0 0 0 0 0  
4.3301 1.0000 0.0000 C 0 0 0 0 0 0  
5.1962 0.5000 0.0000 C 0 0 0 0 0 0  
5.1962 -0.5000 0.0000 C 0 0 0 0 0 0  
4.3301 -1.0000 0.0000 C 0 0 0 0 0 0  
6.0622 1.0000 0.0000 C 0 0 0 0 0 0  
6.9282 0.5000 0.0000 C 0 0 0 0 0 0  
6.9282 -0.5000 0.0000 C 0 0 0 0 0 0  
6.0622 -1.0000 0.0000 C 0 0 0 0 0 0  
0.8660 -1.0000 0.0000 C 0 0 0 0 0 0  
0.0000 -0.5000 0.0000 C 0 0 0 0 0 0  
-0.0000 0.5000 0.0000 C 0 0 0 0 0 0  
0.8660 1.0000 0.0000 C 0 0 0 0 0 0  
-0.8660 -1.0000 0.0000 C 0 0 0 0 0 0  
-1.7321 -0.5000 0.0000 C 0 0 0 0 0 0  
-1.7321 0.5000 0.0000 C 0 0 0 0 0 0  
-0.8660 1.0000 0.0000 C 0 0 0 0 0 0  
-2.5981 -1.0000 0.0000 C 0 0 0 0 0 0  
-3.4641 -0.5000 0.0000 C 0 0 0 0 0 0  
-3.4641 0.5000 0.0000 C 0 0 0 0 0 0  
-2.5981 1.0000 0.0000 C 0 0 0 0 0 0  
-4.3301 -1.0000 0.0000 C 0 0 0 0 0 0  
-5.1962 -0.5000 0.0000 C 0 0 0 0 0 0  
-5.1962 0.5000 0.0000 C 0 0 0 0 0 0  
-4.3301 1.0000 0.0000 C 0 0 0 0 0 0  
-6.0622 -1.0000 0.0000 C 0 0 0 0 0 0  
-6.9282 -0.5000 0.0000 C 0 0 0 0 0 0  
-6.9282 0.5000 0.0000 C 0 0 0 0 0 0  
-6.0622 1.0000 0.0000 C 0 0 0 0 0 0  
-7.7942 -1.0000 0.0000 C 0 0 0 0 0 0  
-8.6603 -0.5000 0.0000 C 0 0 0 0 0 0  
-8.6603 0.5000 0.0000 C 0 0 0 0 0 0  
-7.7942 1.0000 0.0000 C 0 0 0 0 0 0  
7.7942 -1.0000 0.0000 C 0 0 0 0 0 0  
7.7942 -2.0000 0.0000 C 0 0 0 0 0 0  
6.9282 -2.5000 0.0000 C 0 0 0 0 0 0  
6.0622 -2.0000 0.0000 C 0 0 0 0 0 0  
5.1962 -2.5000 0.0000 C 0 0 0 0 0 0  
4.3301 -2.0000 0.0000 C 0 0 0 0 0 0  
3.4641 -2.5000 0.0000 C 0 0 0 0 0 0  
2.5981 -2.0000 0.0000 C 0 0 0 0 0 0  
1.7321 -2.5000 0.0000 C 0 0 0 0 0 0  
0.8660 -2.0000 0.0000 C 0 0 0 0 0 0  
-0.0000 -2.5000 0.0000 C 0 0 0 0 0 0  
-0.8660 -2.0000 0.0000 C 0 0 0 0 0 0  
-1.7321 -2.5000 0.0000 C 0 0 0 0 0 0  
-2.5981 -2.0000 0.0000 C 0 0 0 0 0 0  
-3.4641 -2.5000 0.0000 C 0 0 0 0 0 0  
-4.3301 -2.0000 0.0000 C 0 0 0 0 0 0  
-5.1962 -2.5000 0.0000 C 0 0 0 0 0 0  
-6.0622 -2.0000 0.0000 C 0 0 0 0 0 0  
-6.9282 -2.5000 0.0000 C 0 0 0 0 0 0  
-7.7942 -2.0000 0.0000 C 0 0 0 0 0 0  
-7.7942 2.0000 0.0000 C 0 0 0 0 0 0  
-6.9282 2.5000 0.0000 C 0 0 0 0 0 0  
-6.0622 2.0000 0.0000 C 0 0 0 0 0 0  
-5.1962 2.5000 0.0000 C 0 0 0 0 0 0  
-4.3301 2.0000 0.0000 C 0 0 0 0 0 0  
-3.4641 2.5000 0.0000 C 0 0 0 0 0 0  
-2.5981 2.0000 0.0000 C 0 0 0 0 0 0  
-1.7321 2.5000 0.0000 C 0 0 0 0 0 0  
-0.8660 2.0000 0.0000 C 0 0 0 0 0 0  
-0.0000 2.5000 0.0000 C 0 0 0 0 0 0  
0.8660 2.0000 0.0000 C 0 0 0 0 0 0  
1.7321 2.5000 0.0000 C 0 0 0 0 0 0  
2.5981 2.0000 0.0000 C 0 0 0 0 0 0  
3.4641 2.5000 0.0000 C 0 0 0 0 0 0  
4.3301 2.0000 0.0000 C 0 0 0 0 0 0  
5.1962 2.5000 0.0000 C 0 0 0 0 0 0  
6.0622 2.0000 0.0000 C 0 0 0 0 0 0  
6.9282 2.5000 0.0000 C 0 0 0 0 0 0  
7.7942 2.0000 0.0000 C 0 0 0 0 0 0  
7.7942 1.0000 0.0000 C 0 0 0 0 0 0  
8.6603 0.5000 0.0000 C 0 0 0 0 0 0  
8.6603 -0.5000 0.0000 C 0 0 0 0 0 0  
-6.9282 3.5000 0.0000 C 0 0 0 0 0 0  
-6.0622 4.0000 0.0000 C 0 0 0 0 0 0  
-5.1962 3.5000 0.0000 C 0 0 0 0 0 0  
-4.3301 4.0000 0.0000 C 0 0 0 0 0 0  
-3.4641 3.5000 0.0000 C 0 0 0 0 0 0  
-2.5981 4.0000 0.0000 C 0 0 0 0 0 0  
-1.7321 3.5000 0.0000 C 0 0 0 0 0 0  
-0.8660 4.0000 0.0000 C 0 0 0 0 0 0  
-0.0000 3.5000 0.0000 C 0 0 0 0 0 0  
0.8660 4.0000 0.0000 C 0 0 0 0 0 0  
1.7321 3.5000 0.0000 C 0 0 0 0 0 0  
2.5981 4.0000 0.0000 C 0 0 0 0 0 0  
3.4641 3.5000 0.0000 C 0 0 0 0 0 0  
4.3301 4.0000 0.0000 C 0 0 0 0 0 0  
5.1962 3.5000 0.0000 C 0 0 0 0 0 0  
6.0622 4.0000 0.0000 C 0 0 0 0 0 0  
6.9282 3.5000 0.0000 C 0 0 0 0 0 0  
-5.1962 -3.5000 0.0000 C 0 0 0 0 0 0  
-6.0622 -4.0000 0.0000 C 0 0 0 0 0 0  
-6.9282 -3.5000 0.0000 C 0 0 0 0 0 0  
-3.4641 -3.5000 0.0000 C 0 0 0 0 0 0  
-4.3301 -4.0000 0.0000 C 0 0 0 0 0 0  
-1.7321 -3.5000 0.0000 C 0 0 0 0 0 0  
-2.5981 -4.0000 0.0000 C 0 0 0 0 0 0  
-0.0000 -3.5000 0.0000 C 0 0 0 0 0 0  
-0.8660 -4.0000 0.0000 C 0 0 0 0 0 0  
1.7321 -3.5000 0.0000 C 0 0 0 0 0 0  
0.8660 -4.0000 0.0000 C 0 0 0 0 0 0  
3.4641 -3.5000 0.0000 C 0 0 0 0 0 0  
2.5981 -4.0000 0.0000 C 0 0 0 0 0 0  
5.1962 -3.5000 0.0000 C 0 0 0 0 0 0  
4.3301 -4.0000 0.0000 C 0 0 0 0 0 0  
6.9282 -3.5000 0.0000 C 0 0 0 0 0 0  
6.0622 -4.0000 0.0000 C 0 0 0 0 0 0  
1 2 1 0 0 0 0  
2 3 2 0 0 0 0  
3 4 1 0 0 0 0  
4 5 2 0 0 0 0  
5 6 1 0 0 0 0  
6 1 2 0 0 0 0  
2 7 1 0 0 0 0  
7 8 2 0 0 0 0  
8 9 1 0 0 0 0  
9 10 2 0 0 0 0  
10 3 1 0 0 0 0  
8 11 1 0 0 0 0  
11 12 2 0 0 0 0  
12 13 1 0 0 0 0  
13 14 2 0 0 0 0  
14 9 1 0 0 0 0  
5 15 1 0 0 0 0  
15 16 2 0 0 0 0  
16 17 1 0 0 0 0  
17 18 2 0 0 0 0  
18 6 1 0 0 0 0  
16 19 1 0 0 0 0  
19 20 2 0 0 0 0  
20 21 1 0 0 0 0  
21 22 2 0 0 0 0  
22 17 1 0 0 0 0  
20 23 1 0 0 0 0  
23 24 2 0 0 0 0  
24 25 1 0 0 0 0  
25 26 2 0 0 0 0  
26 21 1 0 0 0 0  
24 27 1 0 0 0 0  
27 28 2 0 0 0 0  
28 29 1 0 0 0 0  
29 30 2 0 0 0 0  
30 25 1 0 0 0 0  
28 31 1 0 0 0 0  
31 32 2 0 0 0 0  
32 33 1 0 0 0 0  
33 34 2 0 0 0 0  
34 29 1 0 0 0 0  
32 35 1 0 0 0 0  
35 36 2 0 0 0 0  
36 37 1 0 0 0 0  
37 38 2 0 0 0 0  
38 33 1 0 0 0 0  
13 39 1 0 0 0 0  
39 40 2 0 0 0 0  
40 41 1 0 0 0 0  
41 42 2 0 0 0 0  
42 14 1 0 0 0 0  
42 43 1 0 0 0 0  
43 44 2 0 0 0 0  
44 10 1 0 0 0 0  
44 45 1 0 0 0 0  
45 46 2 0 0 0 0  
46 4 1 0 0 0 0  
46 47 1 0 0 0 0  
47 48 2 0 0 0 0  
48 15 1 0 0 0 0  
48 49 1 0 0 0 0  
49 50 2 0 0 0 0  
50 19 1 0 0 0 0  
50 51 1 0 0 0 0  
51 52 2 0 0 0 0  
52 23 1 0 0 0 0  
52 53 1 0 0 0 0  
53 54 2 0 0 0 0  
54 27 1 0 0 0 0  
54 55 1 0 0 0 0  
55 56 2 0 0 0 0  
56 31 1 0 0 0 0  
56 57 1 0 0 0 0  
57 58 2 0 0 0 0  
58 35 1 0 0 0 0  
38 59 1 0 0 0 0  
59 60 1 0 0 0 0  
60 61 2 0 0 0 0  
61 34 1 0 0 0 0  
61 62 1 0 0 0 0  
62 63 1 0 0 0 0  
63 30 1 0 0 0 0  
63 64 2 0 0 0 0  
64 65 1 0 0 0 0  
65 26 1 0 0 0 0  
65 66 2 0 0 0 0  
66 67 1 0 0 0 0  
67 22 1 0 0 0 0  
67 68 2 0 0 0 0  
68 69 1 0 0 0 0  
69 18 1 0 0 0 0  
69 70 2 0 0 0 0  
70 71 1 0 0 0 0  
71 1 1 0 0 0 0  
71 72 1 0 0 0 0  
72 73 2 0 0 0 0  
73 7 1 0 0 0 0  
73 74 1 0 0 0 0  
74 75 1 0 0 0 0  
75 11 1 0 0 0 0  
75 76 2 0 0 0 0  
76 77 1 0 0 0 0  
77 78 2 0 0 0 0  
78 12 1 0 0 0 0  
78 79 1 0 0 0 0  
79 80 1 0 0 0 0  
80 39 1 0 0 0 0  
60 81 1 0 0 0 0  
81 82 2 0 0 0 0  
82 83 1 0 0 0 0  
83 62 2 0 0 0 0  
83 84 1 0 0 0 0  
84 85 1 0 0 0 0  
85 64 1 0 0 0 0  
85 86 2 0 0 0 0  
86 87 1 0 0 0 0  
87 66 1 0 0 0 0  
87 88 2 0 0 0 0  
88 89 1 0 0 0 0  
89 68 1 0 0 0 0  
89 90 2 0 0 0 0  
90 91 1 0 0 0 0  
91 70 1 0 0 0 0  
91 92 2 0 0 0 0  
92 93 1 0 0 0 0  
93 72 1 0 0 0 0  
93 94 2 0 0 0 0  
94 95 1 0 0 0 0  
95 74 2 0 0 0 0  
95 96 1 0 0 0 0  
96 97 1 0 0 0 0  
97 76 1 0 0 0 0  
55 98 1 0 0 0 0  
98 99 1 0 0 0 0  
99100 2 0 0 0 0  
100 57 1 0 0 0 0  
53101 1 0 0 0 0  
101102 2 0 0 0 0  
102 98 1 0 0 0 0  
51103 1 0 0 0 0  
103104 2 0 0 0 0  
104101 1 0 0 0 0  
49105 1 0 0 0 0  
105106 2 0 0 0 0  
106103 1 0 0 0 0  
47107 1 0 0 0 0  
107108 2 0 0 0 0  
108105 1 0 0 0 0  
45109 1 0 0 0 0  
109110 2 0 0 0 0  
110107 1 0 0 0 0  
43111 1 0 0 0 0  
111112 2 0 0 0 0  
112109 1 0 0 0 0  
41113 1 0 0 0 0  
113114 2 0 0 0 0  
114111 1 0 0 0 0  
M END  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/htmlview.py", line 320, in interceptRequest  
self._callback(info)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/widgets/htmlview.py", line 93, in _intercept  
return interceptor(request_info, *args)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/htmltool.py", line 112, in _navigate  
self.session.ui.thread_safe(self.handle_scheme, url)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py",
line 368, in thread_safe  
func(*args, **kw)  
File "/home/chemistrylab/.local/share/ChimeraX/1.6/site-
packages/SEQCROW/tools/mol_builder.py", line 609, in handle_scheme  
msg, status = s_sd_get.msg, s_sd_get.status  
UnboundLocalError: local variable 's_sd_get' referenced before assignment  
  
UnboundLocalError: local variable 's_sd_get' referenced before assignment  
  
File "/home/chemistrylab/.local/share/ChimeraX/1.6/site-
packages/SEQCROW/tools/mol_builder.py", line 609, in handle_scheme  
msg, status = s_sd_get.msg, s_sd_get.status  
  
See log for complete Python traceback.  
  

> hide #1 models




OpenGL version: 4.5 (Core Profile) Mesa 23.2.1-1ubuntu3.1~22.04.2
OpenGL renderer: llvmpipe (LLVM 15.0.7, 256 bits)
OpenGL vendor: Mesa

Python: 3.9.11
Locale: en_IN.ISO8859-1
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: xcb

XDG_SESSION_TYPE=wayland
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
WAYLAND_DISPLAY=wayland-0
GNOME_SETUP_DISPLAY=:1
DISPLAY=:0
Manufacturer: innotek GmbH
Model: VirtualBox
OS: Ubuntu 22.04 Jammy Jellyfish
Architecture: 64bit ELF
Virtual Machine: oracle
CPU: 1 Intel(R) Core(TM) i5-7500T CPU @ 2.70GHz
Cache Size: 6144 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:           8.1Gi       1.6Gi       2.1Gi       125Mi       4.4Gi       6.1Gi
	Swap:          2.0Gi          0B       2.0Gi

Graphics:
	00:02.0 VGA compatible controller [0300]: VMware SVGA II Adapter [15ad:0405]	
	Subsystem: VMware SVGA II Adapter [15ad:0405]	
	Kernel driver in use: vmwgfx

Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2023.5.7
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9.1
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.10
    ChimeraX-AtomicLibrary: 10.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.8
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6.1
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.1
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-LinuxSupport: 1.0.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.0.12
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.3.7
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.1
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.28.4
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    distro: 1.7.0
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.39.3
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.9.26
    imagesize: 1.4.1
    importlib-metadata: 6.6.0
    ipykernel: 6.21.1
    ipython: 8.10.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.6
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.0.2
    jupyter-core: 5.3.0
    jupyterlab-widgets: 3.0.7
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.2
    matplotlib: 3.6.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 2.8.8
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.23.5
    openvr: 1.23.701
    packaging: 23.1
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.3.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.5.0
    prompt-toolkit: 3.0.38
    psutil: 5.9.4
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.4.2
    PyQt6-Qt6: 6.4.3
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.3
    python-dateutil: 2.8.2
    pytz: 2023.3
    pyzmq: 25.0.2
    qtconsole: 5.4.0
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.28.2
    scipy: 1.9.3
    Send2Trash: 1.8.3
    SEQCROW: 1.8.10
    setuptools: 67.4.0
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.4.1
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tcia-utils: 1.2.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.1
    traitlets: 5.9.0
    typing-extensions: 4.5.0
    tzdata: 2023.3
    urllib3: 1.26.15
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7
    zipp: 3.15.0

Change History (2)

comment:1 by Tom Goddard, 15 months ago

Component: Unassigned → Third Party
Owner: set to Tony Schaefer
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → SEQCROW error: AttributeError: 'NoneType' object has no attribute 'group'

comment:2 by Tony Schaefer, 15 months ago 

I don't think I have many options for fixing this. The structure has >100
atoms and bonds, and I don't think cactus can parse v2000 files with that
many atoms/bonds. It doesn't seem to be able to parse v3000 files either. I
will probably add a more clear error message though.

Tony

On Fri, Aug 9, 2024 at 12:28 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

>
>
>
Note: See TracTickets for help on using tickets.