Error in toolshed error message

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.18362
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Errors  
---  
error | Bundle 'SEQCROW' custom initialization failed  
warnings | Traceback (most recent call last):  
File "D:\program files (x86)\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 342, in initialize  
api._api_caller.initialize(api, session, self)  
File "D:\program files (x86)\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1265, in initialize  
return cls._get_func(api, "initialize")(session, bi)  
File "C:\Users\admin\AppData\Local\UCSF\ChimeraX\1.1\site-
packages\SEQCROW\\__init__.py", line 40, in initialize  
for sub in Substituent.list():  
File "C:\Users\admin\AppData\Local\UCSF\ChimeraX\1.1\site-
packages\AaronTools\substituent.py", line 338, in list  
for f in os.listdir(lib):  
FileNotFoundError: [WinError 3] 系统找不到指定的路径。:
'C:\\\Users\\\admin\\\Aaron_libs\\\Subs'  
  
Your computer has Intel graphics driver 7986 with a known bug that causes all
Qt user interface panels to be blank. ChimeraX can partially fix this but may
make some panel titlebars and edges black. Hopefully newer Intel graphics
drivers will fix this.  
  
Traceback (most recent call last):  
File "D:\program files (x86)\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "C:\Users\admin\AppData\Local\UCSF\ChimeraX\1.1\site-
packages\SEQCROW\\__init__.py", line 28, in <lambda>  
lambda *args, ses=session: _SEQCROW_API.register_selector_menus(ses))  
File "C:\Users\admin\AppData\Local\UCSF\ChimeraX\1.1\site-
packages\SEQCROW\\__init__.py", line 368, in register_selector_menus  
for sub in Substituent.list():  
File "C:\Users\admin\AppData\Local\UCSF\ChimeraX\1.1\site-
packages\AaronTools\substituent.py", line 338, in list  
for f in os.listdir(lib):  
FileNotFoundError: [WinError 3] 系统找不到指定的路径。:
'C:\\\Users\\\admin\\\Aaron_libs\\\Subs'  
  
Error processing trigger "ready":  
FileNotFoundError: [WinError 3] 系统找不到指定的路径。:
'C:\\\Users\\\admin\\\Aaron_libs\\\Subs'  
  
File "C:\Users\admin\AppData\Local\UCSF\ChimeraX\1.1\site-
packages\AaronTools\substituent.py", line 338, in list  
for f in os.listdir(lib):  
  
See log for complete Python traceback.  
  
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 E:/Project/MCR/MC1R_CryoEM/MC1R_Final_PDB/3sn6.cif

3sn6.cif title:  
Crystal structure of the beta2 adrenergic receptor-Gs protein complex [more
info...]  
  
Chain information for 3sn6.cif #1  
---  
Chain | Description  
A | Guanine nucleotide-binding protein G(s) subunit α isoforms short  
B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1  
G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2  
N | Camelid antibody VHH fragment  
R | Endolysin,Beta-2 adrenergic receptor  
  
Non-standard residues in 3sn6.cif #1  
---  
P0G —
8-[(1R)-2-{[1,1-dimethyl-2-(2-methylphenyl)ethyl]amino}-1-hydroxyethyl]-5-hydroxy-2H-1,4-benzoxazin-3(4H)-one  
  

> open E:/Project/MCR/MC1R_CryoEM/MC1R_Final_PDB/6gdg.cif

6gdg.cif title:  
Cryo-EM structure of the adenosine A2A receptor bound to a miniGs heterotrimer
[more info...]  
  
Chain information for 6gdg.cif #2  
---  
Chain | Description  
A | TrxA,Adenosine receptor A2a  
B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1  
C | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2  
D | Guanine nucleotide-binding protein G(s) subunit α isoforms short,Guanine
nucleotide-binding protein G(s) subunit α isoforms short  
E | nanobody Nb35  
  
Non-standard residues in 6gdg.cif #2  
---  
NEC — N-ethyl-5'-carboxamido adenosine  
  

> open E:/Project/MCR/MC1R_CryoEM/MC1R_Final_PDB/6w25.cif

6w25.cif title:  
Crystal structure of the Melanocortin-4 Receptor (MC4R) in complex with
SHU9119 [more info...]  
  
Chain information for 6w25.cif #3  
---  
Chain | Description  
A | Melanocortin receptor 4,GlgA glycogen synthase,Melanocortin receptor 4  
B | SHU9119  
  
Non-standard residues in 6w25.cif #3  
---  
4J2 — (2R)-2-amino-3-(naphthalen-2-yl)propanoic acid  
ACE — acetyl group  
CA — calcium ion  
NH2 — amino group  
OLA — oleic acid  
  

> open E:/Project/MCR/MC1R_CryoEM/MC1R_Final_PDB/Afa_MC1R_Gs_Nb35_scFv16.pdb

Summary of feedback from opening
E:/Project/MCR/MC1R_CryoEM/MC1R_Final_PDB/Afa_MC1R_Gs_Nb35_scFv16.pdb  
---  
warning | Ignored bad PDB record found on line 10025  
END  
  
Chain information for Afa_MC1R_Gs_Nb35_scFv16.pdb #4  
---  
Chain | Description  
A | No description available  
B | No description available  
F | No description available  
G | No description available  
N | No description available  
R | No description available  
S | No description available  
  

> open E:/Project/MCR/MC1R_CryoEM/MC1R_Final_PDB/Afa_MC1R_Gs_scFv16.pdb

Summary of feedback from opening
E:/Project/MCR/MC1R_CryoEM/MC1R_Final_PDB/Afa_MC1R_Gs_scFv16.pdb  
---  
warning | Ignored bad PDB record found on line 9035  
END  
  
Chain information for Afa_MC1R_Gs_scFv16.pdb #5  
---  
Chain | Description  
A | No description available  
B | No description available  
F | No description available  
G | No description available  
R | No description available  
S | No description available  
  

> open E:/Project/MCR/MC1R_CryoEM/MC1R_Final_PDB/MSH_MC1R_Gs_Nb35.pdb

Summary of feedback from opening
E:/Project/MCR/MC1R_CryoEM/MC1R_Final_PDB/MSH_MC1R_Gs_Nb35.pdb  
---  
warning | Ignored bad PDB record found on line 8184  
END  
  
Chain information for MSH_MC1R_Gs_Nb35.pdb #6  
---  
Chain | Description  
A | No description available  
B | No description available  
G | No description available  
M | No description available  
N | No description available  
R | No description available  
  

> open E:/Project/MCR/MC1R_CryoEM/MC1R_Final_PDB/SHU9119_MC1R_Gs_Nb35.pdb

Summary of feedback from opening
E:/Project/MCR/MC1R_CryoEM/MC1R_Final_PDB/SHU9119_MC1R_Gs_Nb35.pdb  
---  
warning | Ignored bad PDB record found on line 8162  
END  
  
Chain information for SHU9119_MC1R_Gs_Nb35.pdb #7  
---  
Chain | Description  
A | No description available  
B | No description available  
G | No description available  
N | No description available  
R | No description available  
U | No description available  
  
"Other funding source" field cannot be empty when "other" is selected  
Thank you for registering your copy of ChimeraX. By providing the information
requested you will be helping us document the impact this software is having
in the scientific community. The information you supplied will only be used
for reporting summary usage statistics; no individual data will be released.  

> set bgColor white

> hide atoms

> show cartoons

> hide #!1 models

> hide #!2 models

> show #!2 models

> hide #!3 models

> show #!3 models

> hide #!2 models

> hide #!4 models

> hide #!5 models

> hide #!6 models

> hide #!7 models

> hide #!3 models

> show #!3 models

> show #!4 models

> show #!5 models

> show #!6 models

> show #!7 models

> hide #!7 models

> hide #!6 models

> hide #!5 models

> hide #!4 models

> hide #!3 models

> show #!4 models

> select #4/F

108 atoms, 113 bonds, 12 residues, 1 model selected  

> select ::name="CA"

5 atoms, 5 residues, 5 models selected  

> show sel & #!4 atoms

> select #4/F

108 atoms, 113 bonds, 12 residues, 1 model selected  

> show sel atoms

> style sel stick

Changed 108 atom styles  

> style sel ball

Changed 108 atom styles  

> style sel sphere

Changed 108 atom styles  

> style sel stick

Changed 108 atom styles  

> show sel atoms

> select #4

9863 atoms, 10069 bonds, 6 pseudobonds, 1269 residues, 2 models selected  

> lighting full

> lighting soft

> lighting simple

> lighting soft

> lighting simple

> lighting soft

> lighting simple

> lighting soft

> ~select #4

Nothing selected  

> hide #!4 models

> show #!5 models

> lighting soft

> select #5/F

108 atoms, 113 bonds, 12 residues, 1 model selected  

> style sel stick

Changed 108 atom styles  

> show sel atoms

> select #5/C

1 atom, 1 residue, 1 model selected  

> show sel atoms

> hide #!5 models

> show #!6 models

> select #6/C

1 atom, 1 residue, 1 model selected  

> show sel atoms

> select #6/M

108 atoms, 113 bonds, 12 residues, 1 model selected  

> show sel atoms

> style sel stick

Changed 108 atom styles  

> hide #!6 models

> show #!7 models

> select #7/U

74 atoms, 78 bonds, 7 residues, 1 model selected  

> show sel atoms

> select #7/C

1 atom, 1 residue, 1 model selected  

> show sel atoms

> show #!3 models

> hide #!7 models

> select #7

8030 atoms, 8188 bonds, 4 pseudobonds, 1031 residues, 2 models selected  

> select #3/B

83 atoms, 82 bonds, 14 residues, 1 model selected  

> show sel atoms

> select ::name="CA"

5 atoms, 5 residues, 5 models selected  

> show sel & #!3 atoms

> hide #!3 models

> show #!2 models

> hide #!2 models

> show #!4 models

> hide #!4 models

> select #3

3812 atoms, 3857 bonds, 7 pseudobonds, 507 residues, 3 models selected  

> select #4

9863 atoms, 10069 bonds, 6 pseudobonds, 1269 residues, 2 models selected  

> select #3

3812 atoms, 3857 bonds, 7 pseudobonds, 507 residues, 3 models selected  

> ~select #3

Nothing selected  

> show #!3 models

> show #!3 target m

> view

> ui tool show "Show Sequence Viewer"

> sequence chain #3/B

Alignment identifier is 3/B  

> ui tool show "Show Sequence Viewer"

> sequence chain #3/A

Alignment identifier is 3/A  

> hide #!3 models

> show #!2 models

> select #3

3812 atoms, 3857 bonds, 7 pseudobonds, 507 residues, 3 models selected  

> select #2

7223 atoms, 7381 bonds, 3 pseudobonds, 998 residues, 2 models selected  

> ~select #2

Nothing selected  

> hide #!2 models

> show #!1 models

> show #!2 target m

> ui mousemode right zoom

> hide #!2 models

> select #1

10274 atoms, 10478 bonds, 6 pseudobonds, 1319 residues, 2 models selected  

> ui mousemode right zoom

> hide #!1 models

> show #!6 models

> hide #!6 models

> show #!5 models

> hide #!5 models

> show #!4 models

> hide #!4 models

> show #!3 models

> hide #!3 models

> show #!2 models

> hide #!2 models

> show #!1 models

> ui tool show "Show Sequence Viewer"

> sequence chain #1/R

Alignment identifier is 1/R  

> delete atoms sel

> delete bonds sel

> delete atoms sel

> delete bonds sel

> hide #!1 models

> show #!4 models

> show #!5 models

> mmaker #5/R to #4/R

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker Afa_MC1R_Gs_Nb35_scFv16.pdb, chain R (#4) with
Afa_MC1R_Gs_scFv16.pdb, chain R (#5), sequence alignment score = 1374.1  
RMSD between 267 pruned atom pairs is 0.557 angstroms; (across all 267 pairs:
0.557)  
  

> hide #!5 models

> show #!6 models

> mmaker #6/R to #4/R

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker Afa_MC1R_Gs_Nb35_scFv16.pdb, chain R (#4) with
MSH_MC1R_Gs_Nb35.pdb, chain R (#6), sequence alignment score = 1360.2  
RMSD between 254 pruned atom pairs is 0.428 angstroms; (across all 263 pairs:
0.721)  
  

> hide #!6 models

> show #!7 models

> mmaker #7/R to #4/R

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker Afa_MC1R_Gs_Nb35_scFv16.pdb, chain R (#4) with
SHU9119_MC1R_Gs_Nb35.pdb, chain R (#7), sequence alignment score = 1356.8  
RMSD between 262 pruned atom pairs is 0.631 angstroms; (across all 266 pairs:
0.699)  
  

> hide #!7 models

> show #!3 models

> mmaker #3/A to #4/R

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker Afa_MC1R_Gs_Nb35_scFv16.pdb, chain R (#4) with 6w25.cif, chain A
(#3), sequence alignment score = 714.7  
RMSD between 185 pruned atom pairs is 1.101 angstroms; (across all 263 pairs:
6.724)  
  

> hide #!3 models

> show #!2 models

> mmaker #2/A to #4/R

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker Afa_MC1R_Gs_Nb35_scFv16.pdb, chain R (#4) with 6gdg.cif, chain A
(#2), sequence alignment score = 416.6  
RMSD between 128 pruned atom pairs is 1.204 angstroms; (across all 248 pairs:
5.141)  
  

> hide #!2 models

> show #!1 models

> mmaker #1/R to #4/R

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker Afa_MC1R_Gs_Nb35_scFv16.pdb, chain R (#4) with 3sn6.cif, chain R
(#1), sequence alignment score = 449.2  
RMSD between 153 pruned atom pairs is 1.062 angstroms; (across all 255 pairs:
3.612)  
  

> hide #!1 models

> hide #!4 models

> show #!6 models

> show #!7 models

> mmaker #6/R :F45

> matchmaker #6/R :F45

Missing required "to" argument  

> select #6/R :F45

Nothing selected  

> select #6/R:45

11 atoms, 11 bonds, 1 residue, 1 model selected  

> style sel stick

Changed 11 atom styles  

> hide #!7 models

> show sel atoms

> hide #!6 models

> show #!7 models

> show #!6 models

> select #7/A:51

6 atoms, 5 bonds, 1 residue, 1 model selected  

> show sel atoms

> hide #!6 models

> hide #!7 models

> show #!3 models

> select #3/A:51

11 atoms, 11 bonds, 1 residue, 1 model selected  

> show sel atoms

> show #!7 models

> select #7

8030 atoms, 8188 bonds, 4 pseudobonds, 1031 residues, 2 models selected  

> ~select #7

Nothing selected  

> select #7/R:45

11 atoms, 11 bonds, 1 residue, 1 model selected  

> show sel atoms

> style sel stick

Changed 11 atom styles  

> ui mousemode right "tape measure"

> ui mousemode right "tape measure"

> select #7/R:45ca

Nothing selected  

> select #7/R:45@ca

1 atom, 1 residue, 1 model selected  

> ui mousemode right "tape measure"

> select #3/A:51@ca

1 atom, 1 residue, 1 model selected  

> ui mousemode right "tape measure"

> ui mousemode right distance

> select #3/A:51@ca #7/R:45@ca

2 atoms, 2 residues, 2 models selected  

> ui mousemode right distance

> ui mousemode right "tape measure"

> ui mousemode right distance

> distance #3/A:51@ca #7/R:45@ca

Distance between 6w25.cif #3/A PHE 51 CA and SHU9119_MC1R_Gs_Nb35.pdb #7/R PHE
45 CA: 1.768Å  

> define plane #3/A:51-70

Plane plane' placed at [156.78031293 11.7097483 99.48863265] with normal
[0.3190852 0.80424068 0.50137966]  

> define plane #3/A:47-70 4

Expected a keyword  

> define plane #3/A:47-70 plane4

Expected a keyword  

> define plane #3/A:47-70 name plane4

Plane plane4' placed at [154.35868966 12.83686782 99.27197701] with normal
[0.35709759 0.85985814 0.36486338]  

> delete plane

Missing or invalid "atoms" argument: invalid atoms specifier  

> delete plane4

Missing or invalid "atoms" argument: invalid atoms specifier  

> ~plane #3/A:51-70

Unknown command: define ~plane #3/A:51-70  

> ~plane #3/A:51-70

Unknown command: ~plane #3/A:51-70  

> delete plane #3/A:51-70

Missing or invalid "atoms" argument: invalid atoms specifier  

> hide plane #3/A:51-70

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> hide #!8 models

> hide #8.1 models

> show #!8 models

> hide #!3 models

> show #!3 models

> close #3

> close #8

> open E:/Project/MCR/MC1R_CryoEM/MC1R_Final_PDB/6w25.cif

6w25.cif title:  
Crystal structure of the Melanocortin-4 Receptor (MC4R) in complex with
SHU9119 [more info...]  
  
Chain information for 6w25.cif #3  
---  
Chain | Description  
A | Melanocortin receptor 4,GlgA glycogen synthase,Melanocortin receptor 4  
B | SHU9119  
  
Non-standard residues in 6w25.cif #3  
---  
4J2 — (2R)-2-amino-3-(naphthalen-2-yl)propanoic acid  
ACE — acetyl group  
CA — calcium ion  
NH2 — amino group  
OLA — oleic acid  
  

> mmaker #3/A to #4/R

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker Afa_MC1R_Gs_Nb35_scFv16.pdb, chain R (#4) with 6w25.cif, chain A
(#3), sequence alignment score = 714.7  
RMSD between 185 pruned atom pairs is 1.101 angstroms; (across all 263 pairs:
6.724)  
  

> select #3/A:51

11 atoms, 11 bonds, 1 residue, 1 model selected  

> show sel atoms

> distance #3/A:51@ca #7/R:45@ca

Distance between 6w25.cif #3/A PHE 51 CA and SHU9119_MC1R_Gs_Nb35.pdb #7/R PHE
45 CA: 1.768Å  

> hide #!3 models

> show #!3 models

> select #3/A:106@ca

1 atom, 1 residue, 1 model selected  

> select #3/A:106 #7/R:100

16 atoms, 14 bonds, 2 residues, 2 models selected  

> show sel atoms

> style sel stick

Changed 16 atom styles  

> distance #3/A:106@ca #7/R:100@ca

Distance between 6w25.cif #3/A LEU 106 CA and SHU9119_MC1R_Gs_Nb35.pdb #7/R
LEU 100 CA: 1.933Å  

> select #3/A:241 #7/R:237

16 atoms, 14 bonds, 2 residues, 2 models selected  

> show sel atoms

> select #7/R:237

8 atoms, 7 bonds, 1 residue, 1 model selected  

> style sel stick

Changed 8 atom styles  

> distance #3/A:1241@ca #7/R:237@ca

Expected exactly two atoms and/or measurable objects (e.g. axes, planes), got
1  

> distance #3/A:241@ca #7/R:237@ca

Distance between 6w25.cif #3/A MET 241 CA and SHU9119_MC1R_Gs_Nb35.pdb #7/R
LEU 237 CA: 13.877Å  

> select #3/A:258 #7/R:254

28 atoms, 30 bonds, 2 residues, 2 models selected  

> show sel atoms

> style sel stick

Changed 28 atom styles  

> angle #3/A:241@ca #7/R:237@ca #7/R:254@ca

angle is provided by the uninstalled bundle SEQCROW  
Downloading bundle SEQCROW-0.24.1-py3-none-any.whl  
Successfully installed SEQCROW-0.24.1  
Installed SEQCROW (0.24.1)  
resumed SEQCROW queue  
Replacing data format 'Gaussian input file' as defined by SEQCROW bundle with
definition from SEQCROW bundle  
Replacing data format 'Gaussian output file' as defined by SEQCROW bundle with
definition from SEQCROW bundle  
Replacing data format 'ORCA output file' as defined by SEQCROW bundle with
definition from SEQCROW bundle  
Replacing data format 'Psi4 output file' as defined by SEQCROW bundle with
definition from SEQCROW bundle  
Replacing data format 'XYZ file' as defined by SEQCROW bundle with definition
from SEQCROW bundle  
Replacing data format 'FCHK file' as defined by SEQCROW bundle with definition
from SEQCROW bundle  

Traceback (most recent call last):  
File "D:\program files (x86)\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 342, in initialize  
api._api_caller.initialize(api, session, self)  
File "D:\program files (x86)\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1265, in initialize  
return cls._get_func(api, "initialize")(session, bi)  
File "C:\Users\admin\AppData\Local\UCSF\ChimeraX\1.1\site-
packages\SEQCROW\\__init__.py", line 40, in initialize  
for sub in Substituent.list():  
File "C:\Users\admin\AppData\Local\UCSF\ChimeraX\1.1\site-
packages\AaronTools\substituent.py", line 338, in list  
for f in os.listdir(lib):  
FileNotFoundError: [WinError 3] 系统找不到指定的路径。:
'C:\\\Users\\\admin\\\Aaron_libs\\\Subs'  
  

SEQCROW (installed) [version: 0.24.1] [api package: SEQCROW] [category:
General, Input/Output, External Program] [tool: Build QM Input [categories:
AaronTools] [synopsis: Create Gaussian, ORCA, or Psi4 input file]] [tool:
Structure Modification [categories: AaronTools] [synopsis: Modify
substituents, swap ligands, and fuse rings]] [tool: Change Substituents
[categories: Structure Editing] [synopsis: Modify substituents, swap ligands,
and fuse rings]] [tool: Swap Transition Metal Ligands [categories: Structure
Editing] [synopsis: Modify substituents, swap ligands, and fuse rings]] [tool:
Fuse Ring [categories: Structure Editing] [synopsis: Modify substituents, swap
ligands, and fuse rings]] [tool: Browse AaronTools Libraries [categories:
AaronTools] [synopsis: Browse the AaronTools ligand, substituent, and ring
libraries]] [tool: Process QM Thermochemistry [categories: AaronTools]
[synopsis: Compute the free energy of a molecule with frequency data]] [tool:
Managed Models [categories: SEQCROW] [synopsis: see models managed by
SEQCROW]] [tool: Add to Personal Library [categories: AaronTools] [synopsis:
Add to your personal ligand, substituent, and ring libraries]] [tool:
Visualize Normal Modes [categories: AaronTools] [synopsis: Visualize normal
modes from a frequency output file as displacement vectors or as an
animation]] [tool: Job Queue [categories: SEQCROW] [synopsis: View status of
jobs]] [tool: Substituent Sterimol [categories: Structure Analysis] [synopsis:
Calculate L, B1, and B5 Sterimol parameters for a substituent]] [tool: Bond
Editor [categories: Structure Editing] [synopsis: Draw or erase bonds]] [tool:
Change Element [categories: Structure Editing] [synopsis: Modify substituents,
swap ligands, and fuse rings]] [tool: Rotate Atoms [categories: Structure
Editing] [synopsis: Rotate all or part of a molecular structure]] [tool:
Buried Volume [categories: Structure Analysis] [synopsis: Calculate percent
buried volume]] [tool: File Info [categories: AaronTools] [synopsis:
Miscellaneous file data]] [command: rmsdAlign [categories: Structure Analysis]
[synopsis: Calculate RMSD between structures]] [command: substitute
[categories: Structure Editing] [synopsis: change substiuents]] [command:
fuseRing [categories: Structure Editing] [synopsis: fuse a ring]] [command:
tsbond [categories: Structure Editing] [synopsis: display a forming/breaking
bond as semi-transparent]] [command: ~tsbond [categories: Structure Editing]
[synopsis: remove a forming/breaking bond]] [command: sterimol [categories:
Structure Analysis] [synopsis: calculate L, B1, and B5 Sterimol parameters]]
[command: percentVolumeBuried [categories: Structure Analysis] [synopsis:
calculate percent volume buried by ligands around a metal center]]: custom
initialization failed  

> toolshed show

Downloading bundle SEQCROW-0.24.1-py3-none-any.whl  
Traceback (most recent call last):  
File "D:\program files (x86)\ChimeraX 1.1\bin\lib\site-
packages\chimerax\help_viewer\tool.py", line 389, in download_finished  
session=self.session)  
File "D:\program files (x86)\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 903, in install_bundle  
_install_bundle(self, bundle, logger, per_user=per_user, reinstall=reinstall,
session=session, no_deps=no_deps)  
File "D:\program files (x86)\ChimeraX 1.1\bin\lib\site-
packages\chimerax\toolshed_utils\\__init__.py", line 213, in _install_bundle  
raise ToolshedInstalledError("bundle %r already installed" % bundle.name)  
AttributeError: 'str' object has no attribute 'name'  
  
AttributeError: 'str' object has no attribute 'name'  
  
File "D:\program files (x86)\ChimeraX 1.1\bin\lib\site-
packages\chimerax\toolshed_utils\\__init__.py", line 213, in _install_bundle  
raise ToolshedInstalledError("bundle %r already installed" % bundle.name)  
  
See log for complete Python traceback.  
  
Downloading bundle SEQCROW-0.24.1-py3-none-any.whl  
Traceback (most recent call last):  
File "D:\program files (x86)\ChimeraX 1.1\bin\lib\site-
packages\chimerax\help_viewer\tool.py", line 389, in download_finished  
session=self.session)  
File "D:\program files (x86)\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 903, in install_bundle  
_install_bundle(self, bundle, logger, per_user=per_user, reinstall=reinstall,
session=session, no_deps=no_deps)  
File "D:\program files (x86)\ChimeraX 1.1\bin\lib\site-
packages\chimerax\toolshed_utils\\__init__.py", line 213, in _install_bundle  
raise ToolshedInstalledError("bundle %r already installed" % bundle.name)  
AttributeError: 'str' object has no attribute 'name'  
  
AttributeError: 'str' object has no attribute 'name'  
  
File "D:\program files (x86)\ChimeraX 1.1\bin\lib\site-
packages\chimerax\toolshed_utils\\__init__.py", line 213, in _install_bundle  
raise ToolshedInstalledError("bundle %r already installed" % bundle.name)  
  
See log for complete Python traceback.  
  
Downloading bundle SEQCROW-0.24.1-py3-none-any.whl  
Traceback (most recent call last):  
File "D:\program files (x86)\ChimeraX 1.1\bin\lib\site-
packages\chimerax\help_viewer\tool.py", line 389, in download_finished  
session=self.session)  
File "D:\program files (x86)\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 903, in install_bundle  
_install_bundle(self, bundle, logger, per_user=per_user, reinstall=reinstall,
session=session, no_deps=no_deps)  
File "D:\program files (x86)\ChimeraX 1.1\bin\lib\site-
packages\chimerax\toolshed_utils\\__init__.py", line 213, in _install_bundle  
raise ToolshedInstalledError("bundle %r already installed" % bundle.name)  
AttributeError: 'str' object has no attribute 'name'  
  
AttributeError: 'str' object has no attribute 'name'  
  
File "D:\program files (x86)\ChimeraX 1.1\bin\lib\site-
packages\chimerax\toolshed_utils\\__init__.py", line 213, in _install_bundle  
raise ToolshedInstalledError("bundle %r already installed" % bundle.name)  
  
See log for complete Python traceback.  
  

> toolshed show

Downloading bundle SEQCROW-0.12-py3-none-any.whl  
Traceback (most recent call last):  
File "D:\program files (x86)\ChimeraX 1.1\bin\lib\site-
packages\chimerax\help_viewer\tool.py", line 389, in download_finished  
session=self.session)  
File "D:\program files (x86)\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 903, in install_bundle  
_install_bundle(self, bundle, logger, per_user=per_user, reinstall=reinstall,
session=session, no_deps=no_deps)  
File "D:\program files (x86)\ChimeraX 1.1\bin\lib\site-
packages\chimerax\toolshed_utils\\__init__.py", line 213, in _install_bundle  
raise ToolshedInstalledError("bundle %r already installed" % bundle.name)  
AttributeError: 'str' object has no attribute 'name'  
  
AttributeError: 'str' object has no attribute 'name'  
  
File "D:\program files (x86)\ChimeraX 1.1\bin\lib\site-
packages\chimerax\toolshed_utils\\__init__.py", line 213, in _install_bundle  
raise ToolshedInstalledError("bundle %r already installed" % bundle.name)  
  
See log for complete Python traceback.  
  
Downloading bundle SEQCROW-0.16-py3-none-any.whl  
Traceback (most recent call last):  
File "D:\program files (x86)\ChimeraX 1.1\bin\lib\site-
packages\chimerax\help_viewer\tool.py", line 389, in download_finished  
session=self.session)  
File "D:\program files (x86)\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 903, in install_bundle  
_install_bundle(self, bundle, logger, per_user=per_user, reinstall=reinstall,
session=session, no_deps=no_deps)  
File "D:\program files (x86)\ChimeraX 1.1\bin\lib\site-
packages\chimerax\toolshed_utils\\__init__.py", line 213, in _install_bundle  
raise ToolshedInstalledError("bundle %r already installed" % bundle.name)  
AttributeError: 'str' object has no attribute 'name'  
  
AttributeError: 'str' object has no attribute 'name'  
  
File "D:\program files (x86)\ChimeraX 1.1\bin\lib\site-
packages\chimerax\toolshed_utils\\__init__.py", line 213, in _install_bundle  
raise ToolshedInstalledError("bundle %r already installed" % bundle.name)  
  
See log for complete Python traceback.  
  
Downloading bundle SEQCROW-0.16-py3-none-any.whl  
Traceback (most recent call last):  
File "D:\program files (x86)\ChimeraX 1.1\bin\lib\site-
packages\chimerax\help_viewer\tool.py", line 389, in download_finished  
session=self.session)  
File "D:\program files (x86)\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 903, in install_bundle  
_install_bundle(self, bundle, logger, per_user=per_user, reinstall=reinstall,
session=session, no_deps=no_deps)  
File "D:\program files (x86)\ChimeraX 1.1\bin\lib\site-
packages\chimerax\toolshed_utils\\__init__.py", line 213, in _install_bundle  
AttributeError: 'str' object has no attribute 'name'  
  
AttributeError: 'str' object has no attribute 'name'  
  
File "D:\program files (x86)\ChimeraX 1.1\bin\lib\site-
packages\chimerax\toolshed_utils\\__init__.py", line 213, in _install_bundle  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 26.20.100.7986
OpenGL renderer: Intel(R) HD Graphics 620
OpenGL vendor: Intel
Manufacturer: Dell Inc.
Model: XPS 13 9360
OS: Microsoft Windows 10 专业版 (Build 18363)
Memory: 8,301,887,488
MaxProcessMemory: 137,438,953,344
CPU: 4 Intel(R) Core(TM) i5-7200U CPU @ 2.50GHz"
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.8.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.6.20
    chardet: 3.0.4
    ChimeraX-AddH: 2.1.3
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.6.1
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.0.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.0
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.0
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.0
    ChimeraX-Clipper: 0.15.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.1
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.0.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-DataFormats: 1.0
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.0
    ChimeraX-Hbonds: 2.0
    ChimeraX-Help: 1.0
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.0
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0
    ChimeraX-ISOLDE: 1.1.0
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.0
    ChimeraX-Log: 1.1.1
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Map: 1.0.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.1
    ChimeraX-MDcrds: 2.0
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.0
    ChimeraX-mmCIF: 2.2
    ChimeraX-MMTF: 2.0
    ChimeraX-Modeller: 1.0
    ChimeraX-ModelPanel: 1.0
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.0
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0
    ChimeraX-OpenCommand: 1.2.1
    ChimeraX-PDB: 2.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0
    ChimeraX-PubChem: 2.0
    ChimeraX-Read-Pbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.0
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.2
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.0.4
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.0
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0
    ChimeraX-ToolshedUtils: 1.0
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.2.3
    ChimeraX-uniprot: 2.0
    ChimeraX-ViewDockX: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.20
    decorator: 4.4.2
    distlib: 0.3.1
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    gdcm: 2.8.8
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.16
    imagecodecs: 2020.5.30
    imagecodecs-lite: 2020.1.31
    imagesize: 1.2.0
    ipykernel: 5.3.0
    ipython: 7.15.0
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.3
    jupyter-core: 4.6.3
    kiwisolver: 1.2.0
    line-profiler: 2.1.2
    lxml: 4.5.1
    MarkupSafe: 1.1.1
    matplotlib: 3.2.1
    msgpack: 1.0.0
    netifaces: 0.10.9
    networkx: 2.4
    numexpr: 2.7.1
    numpy: 1.18.5+mkl
    numpydoc: 1.0.0
    openvr: 1.12.501
    packaging: 20.4
    parso: 0.7.1
    pickleshare: 0.7.5
    Pillow: 7.1.2
    pip: 20.2.2
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.7
    psutil: 5.7.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.6.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.12.3
    PyQt5-sip: 4.19.19
    PyQtWebEngine-commercial: 5.12.1
    python-dateutil: 2.8.1
    pytz: 2020.1
    pywin32: 228
    pyzmq: 19.0.2
    qtconsole: 4.7.4
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.4.1
    Send2Trash: 1.5.0
    SEQCROW: 0.24.1
    setuptools: 49.4.0
    sfftk-rw: 0.6.6.dev0
    six: 1.15.0
    snowballstemmer: 2.0.0
    sortedcontainers: 2.2.2
    Sphinx: 3.1.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 1.0.3
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.4
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.6.3
    tinyarray: 1.2.2
    tornado: 6.0.4
    traitlets: 5.0.4
    urllib3: 1.25.10
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.34.2
    WMI: 1.5.1