Opened 3 years ago

Closed 3 years ago

#7422 closed defect (can't reproduce)

MatchMaker: 'NoneType' object has no attribute 'setChecked'

Reported by: chimerax-bug-report@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: UI Version:
Keywords: Cc: Tom Goddard
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-10.14.6-x86_64-i386-64bit
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  

> open /Users/vilbert/Desktop/111111111.cxs format session

Log from Tue Aug 9 23:34:19 2022UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  

> open /Users/vilbert/Desktop/111111111.cxs format session

Log from Tue Aug 9 23:13:50 2022 Startup Messages  
---  
warnings | Unable to find icon for toolbar provider 'Dump Bead Data' in bundle
'ChimeraX-GenomeTools'  
Unable to find icon for toolbar provider 'Highlight' in bundle 'ChimeraX-
GenomeTools'  
Unable to find icon for toolbar provider 'Bed Models' in bundle 'ChimeraX-
GenomeTools'  
Unable to find icon for toolbar provider 'Bead Overlap' in bundle 'ChimeraX-
GenomeTools'  
Unable to find icon for toolbar provider 'Genome Distance' in bundle
'ChimeraX-GenomeTools'  
1 messages similar to the above omitted  
  

Window position QRect(2576,160 421x452) outside any known screen, using
primary screen  

UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 4rdn

4rdn title:  
Structure of YTH-YTHDF2 in complex with m6A [more info...]  
  
Chain information for 4rdn #1  
---  
Chain | Description | UniProt  
A B | YTH domain-containing family protein 2 | YTHD2_HUMAN  
  
Non-standard residues in 4rdn #1  
---  
6MD — N-methyladenosine  
SO4 — sulfate ion  
  
4rdn mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  

> set bgColor white

> select /A

1380 atoms, 1273 bonds, 289 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select /B:421

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

> select up

103 atoms, 104 bonds, 12 residues, 1 model selected  

> select up

1203 atoms, 1233 bonds, 148 residues, 1 model selected  

> hide sel target a

> select /B:601@C4'

1 atom, 1 residue, 1 model selected  

> select clear

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

20 atoms, 22 bonds, 1 residue, 1 model selected  

> color sel red

> select clear

> select /B:796@O

1 atom, 1 residue, 1 model selected  

> delete atoms sel

> delete bonds sel

> select clear

[Repeated 1 time(s)]

> select /B:771@O

1 atom, 1 residue, 1 model selected  

> delete atoms sel

> delete bonds sel

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

5 atoms, 4 bonds, 1 residue, 1 model selected  

> delete atoms sel

> delete bonds sel

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

5 atoms, 4 bonds, 1 residue, 1 model selected  

> delete atoms sel

> delete bonds sel

> open 7Z8P

Summary of feedback from opening 7Z8P fetched from pdb  
---  
notes | Fetching compressed mmCIF 7z8p from
http://files.rcsb.org/download/7z8p.cif  
Fetching CCD IFZ from http://ligand-expo.rcsb.org/reports/I/IFZ/IFZ.cif  
Fetching CCD GOL from http://ligand-expo.rcsb.org/reports/G/GOL/GOL.cif  
  
7z8p title:  
Crystal structure of YTHDF2 with compound ZA_166 [more info...]  
  
Chain information for 7z8p #2  
---  
Chain | Description | UniProt  
A B | YTH domain-containing family protein 2 | YTHD2_HUMAN  
  
Non-standard residues in 7z8p #2  
---  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
IFZ — 3-bromanyl-~{N}-methyl-2~{H}-pyrazolo[4,3-d]pyrimidin-7-amine  
SO4 — sulfate ion  
  
7z8p mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
  

> select #2/B:443

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

> select up

125 atoms, 126 bonds, 16 residues, 1 model selected  

> select up

1165 atoms, 1195 bonds, 148 residues, 1 model selected  

> hide sel target a

> select #2/A:415

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

> select up

60 atoms, 60 bonds, 7 residues, 1 model selected  

> select up

640 atoms, 656 bonds, 83 residues, 1 model selected  

> select up

722 atoms, 740 bonds, 93 residues, 1 model selected  

> select up

1152 atoms, 1179 bonds, 147 residues, 1 model selected  

> hide sel target a

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select #2/B:420

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

> select #2/A

1220 atoms, 1204 bonds, 2 pseudobonds, 192 residues, 2 models selected  

> delete atoms (#!2 & sel)

> delete bonds (#!2 & sel)

> select clear

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

12 atoms, 13 bonds, 1 residue, 1 model selected  

> color sel magenta

> select #2/B:460

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

> ui tool show Matchmaker

> matchmaker #!2 to #1

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 4rdn, chain B (#1) with 7z8p, chain B (#2), sequence alignment
score = 860.3  
RMSD between 148 pruned atom pairs is 0.277 angstroms; (across all 148 pairs:
0.277)  
  

> matchmaker #!2 to #1

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 4rdn, chain B (#1) with 7z8p, chain B (#2), sequence alignment
score = 860.3  
RMSD between 148 pruned atom pairs is 0.277 angstroms; (across all 148 pairs:
0.277)  
  

> select clear

> select #2/B:602@C06

1 atom, 1 residue, 1 model selected  

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

12 atoms, 13 bonds, 1 residue, 1 model selected  

> select #2/B:412

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

> select up

60 atoms, 60 bonds, 7 residues, 1 model selected  

> select #2/B:401

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

> select up

78 atoms, 81 bonds, 10 residues, 1 model selected  

> select up

1165 atoms, 1195 bonds, 148 residues, 1 model selected  

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

12 atoms, 13 bonds, 1 residue, 1 model selected  

> interfaces select & ~solvent

Missing or invalid "atoms" argument: invalid atoms specifier  

> hbonds sel reveal true

6 hydrogen bonds found  

> select #2/B:432

14 atoms, 15 bonds, 1 residue, 1 model selected  

> select up

22 atoms, 23 bonds, 2 residues, 1 model selected  

> select up

1165 atoms, 1195 bonds, 148 residues, 1 model selected  

> open 7YXE

Summary of feedback from opening 7YXE fetched from pdb  
---  
notes | Fetching compressed mmCIF 7yxe from
http://files.rcsb.org/download/7yxe.cif  
Fetching CCD I82 from http://ligand-expo.rcsb.org/reports/I/I82/I82.cif  
Fetching CCD NA from http://ligand-expo.rcsb.org/reports/N/NA/NA.cif  
  
7yxe title:  
Crystal structure of YTHDF2 with compound ZA_143 [more info...]  
  
Chain information for 7yxe #4  
---  
Chain | Description | UniProt  
A B | YTH domain-containing family protein 2 | YTHD2_HUMAN  
  
Non-standard residues in 7yxe #4  
---  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
I82 — ~{N}-methyl-3-phenyl-2~{H}-pyrazolo[4,3-d]pyrimidin-7-amine  
NA — sodium ion  
SO4 — sulfate ion  
  
7yxe mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
  

> select #4/A

1265 atoms, 1214 bonds, 1 pseudobond, 229 residues, 2 models selected  

> delete atoms (#!4 & sel)

> delete bonds (#!4 & sel)

> select #4/B:421

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

> select up

103 atoms, 104 bonds, 12 residues, 1 model selected  

> select up

1171 atoms, 1201 bonds, 148 residues, 1 model selected  

> select #4/B:605@NA

1 atom, 1 residue, 1 model selected  

> select #4/B:424

10 atoms, 10 bonds, 1 residue, 1 model selected  

> select up

103 atoms, 104 bonds, 12 residues, 1 model selected  

> select up

1171 atoms, 1201 bonds, 148 residues, 1 model selected  

> hide sel target a

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

5 atoms, 4 bonds, 1 residue, 1 model selected  

> delete atoms sel

> delete bonds sel

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

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

> delete atoms sel

> delete bonds sel

> select clear

> select #4/B:605@NA

1 atom, 1 residue, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #4/B:704@O

1 atom, 1 residue, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #4/B:727@O

1 atom, 1 residue, 1 model selected  

> select #4/B:503

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

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

17 atoms, 19 bonds, 1 residue, 1 model selected  

> select ~sel

3806 atoms, 3687 bonds, 6 pseudobonds, 658 residues, 4 models selected  

> select #4/B:420

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

> select clear

> save /Users/vilbert/Desktop/111111111.cxs

——— End of log from Tue Aug 9 23:13:50 2022 ———

opened ChimeraX session  

> ui tool show Matchmaker

> matchmaker #!2 to #4

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 7yxe, chain B (#4) with 7z8p, chain B (#2), sequence alignment
score = 854.3  
RMSD between 148 pruned atom pairs is 0.123 angstroms; (across all 148 pairs:
0.123)  
  

> matchmaker #!2 to #1

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 4rdn, chain B (#1) with 7z8p, chain B (#2), sequence alignment
score = 860.3  
RMSD between 148 pruned atom pairs is 0.277 angstroms; (across all 148 pairs:
0.277)  
  

> matchmaker #!2 & sel to #1 & sel

No 'to' model specified  

> matchmaker #!4 & sel to #1 & sel

No 'to' model specified  

> matchmaker #2/B to #4/B pairing ss

Parameters  
---  
Chain pairing | ss  
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 7yxe, chain B (#4) with 7z8p, chain B (#2), sequence alignment
score = 854.3  
RMSD between 148 pruned atom pairs is 0.123 angstroms; (across all 148 pairs:
0.123)  
  

> matchmaker #1/B#1/B to #4/B#2/B pairing ss

Different number of reference/match chains (2 ref, 1 match)  

> matchmaker #!2,4 to #1/B pairing bs

Parameters  
---  
Chain pairing | bs  
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 4rdn, chain B (#1) with 7z8p, chain B (#2), sequence alignment
score = 860.3  
RMSD between 148 pruned atom pairs is 0.277 angstroms; (across all 148 pairs:
0.277)  
  
Matchmaker 4rdn, chain B (#1) with 7yxe, chain B (#4), sequence alignment
score = 854.3  
RMSD between 148 pruned atom pairs is 0.272 angstroms; (across all 148 pairs:
0.272)  
  

> matchmaker #!2,4 to #1/B pairing bs

Parameters  
---  
Chain pairing | bs  
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 4rdn, chain B (#1) with 7z8p, chain B (#2), sequence alignment
score = 860.3  
RMSD between 148 pruned atom pairs is 0.277 angstroms; (across all 148 pairs:
0.277)  
  
Matchmaker 4rdn, chain B (#1) with 7yxe, chain B (#4), sequence alignment
score = 854.3  
RMSD between 148 pruned atom pairs is 0.272 angstroms; (across all 148 pairs:
0.272)  
  

> select #4/B:735@O

1 atom, 1 residue, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #2/B:727@O

1 atom, 1 residue, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #1/B:705@O

1 atom, 1 residue, 1 model selected  

> delete atoms sel

> delete bonds sel

> select clear

[Repeated 1 time(s)]

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

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

> delete atoms sel

> delete bonds sel

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

5 atoms, 4 bonds, 1 residue, 1 model selected  

> delete atoms sel

> delete bonds sel

> select clear

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

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

> delete atoms sel

> delete bonds sel

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

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

> select up

1232 atoms, 1217 bonds, 195 residues, 1 model selected  

> select down

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

> delete atoms sel

> delete bonds sel

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

5 atoms, 4 bonds, 1 residue, 1 model selected  

> delete atoms sel

> delete bonds sel

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

20 atoms, 22 bonds, 1 residue, 1 model selected  

> hbonds sel reveal true

24 hydrogen bonds found  

> select #2/B:741@O

1 atom, 1 residue, 1 model selected  

> select #4/B:462@ND2

1 atom, 1 residue, 1 model selected  

> select up

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

> hide sel target a

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

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

> hide sel target a

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

17 atoms, 19 bonds, 1 residue, 1 model selected  

> hbonds sel reveal true

6 hydrogen bonds found  

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

20 atoms, 22 bonds, 1 residue, 1 model selected  

> hbonds sel reveal true

24 hydrogen bonds found  

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

17 atoms, 19 bonds, 1 residue, 1 model selected  

> hbonds sel reveal true

6 hydrogen bonds found  

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

17 atoms, 19 bonds, 1 residue, 1 model selected  

> hbonds sel reveal true

6 hydrogen bonds found  

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

20 atoms, 22 bonds, 1 residue, 1 model selected  

> hbonds sel reveal true

24 hydrogen bonds found  

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

17 atoms, 19 bonds, 1 residue, 1 model selected  

> color sel orange

> hbonds sel reveal true

6 hydrogen bonds found  

> hbonds sel reveal true

6 hydrogen bonds found  

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

12 atoms, 13 bonds, 1 residue, 1 model selected  

> hbonds sel reveal true

6 hydrogen bonds found  

> select up

1221 atoms, 1208 bonds, 193 residues, 1 model selected  

> select down

12 atoms, 13 bonds, 1 residue, 1 model selected  

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

20 atoms, 22 bonds, 1 residue, 1 model selected  

> open 7Z7B

Summary of feedback from opening 7Z7B fetched from pdb  
---  
notes | Fetching compressed mmCIF 7z7b from
http://files.rcsb.org/download/7z7b.cif  
Fetching CCD CL from http://ligand-expo.rcsb.org/reports/C/CL/CL.cif  
Fetching CCD OYK from http://ligand-expo.rcsb.org/reports/O/OYK/OYK.cif  
  
7z7b title:  
Crystal structure of YTHDF2 with compound YLI_DC1_003 [more info...]  
  
Chain information for 7z7b #5  
---  
Chain | Description | UniProt  
A B | YTH domain-containing family protein 2 | YTHD2_HUMAN  
  
Non-standard residues in 7z7b #5  
---  
CL — chloride ion  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
OYK — ~{N},9-dimethylpurin-6-amine  
SO4 — sulfate ion  
  
7z7b mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
  

> select #5/B:472

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

> select #5/A

1332 atoms, 1243 bonds, 269 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #5/B:534

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

> select up

116 atoms, 117 bonds, 15 residues, 1 model selected  

> select up

1167 atoms, 1196 bonds, 148 residues, 1 model selected  

> hide sel target a

> ui tool show Matchmaker

> matchmaker #5#!2,4 to #1/B pairing bs

Parameters  
---  
Chain pairing | bs  
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 4rdn, chain B (#1) with 7z7b, chain B (#5), sequence alignment
score = 860.3  
RMSD between 148 pruned atom pairs is 0.306 angstroms; (across all 148 pairs:
0.306)  
  
Matchmaker 4rdn, chain B (#1) with 7z8p, chain B (#2), sequence alignment
score = 860.3  
RMSD between 148 pruned atom pairs is 0.277 angstroms; (across all 148 pairs:
0.277)  
  
Matchmaker 4rdn, chain B (#1) with 7yxe, chain B (#4), sequence alignment
score = 854.3  
RMSD between 148 pruned atom pairs is 0.272 angstroms; (across all 148 pairs:
0.272)  
  

> matchmaker #5#!2,4 to #1/B pairing bs

Parameters  
---  
Chain pairing | bs  
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 4rdn, chain B (#1) with 7z7b, chain B (#5), sequence alignment
score = 860.3  
RMSD between 148 pruned atom pairs is 0.306 angstroms; (across all 148 pairs:
0.306)  
  
Matchmaker 4rdn, chain B (#1) with 7z8p, chain B (#2), sequence alignment
score = 860.3  
RMSD between 148 pruned atom pairs is 0.277 angstroms; (across all 148 pairs:
0.277)  
  
Matchmaker 4rdn, chain B (#1) with 7yxe, chain B (#4), sequence alignment
score = 854.3  
RMSD between 148 pruned atom pairs is 0.272 angstroms; (across all 148 pairs:
0.272)  
  

> select #5/B:602@C01

1 atom, 1 residue, 1 model selected  

> select up

12 atoms, 13 bonds, 1 residue, 1 model selected  

> select up

1271 atoms, 1218 bonds, 232 residues, 1 model selected  

> select down

12 atoms, 13 bonds, 1 residue, 1 model selected  

> color sel blue

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

20 atoms, 22 bonds, 1 residue, 1 model selected  

> ui tool show "Color Actions"

> color sel navajo white

> color sel burly wood

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

12 atoms, 13 bonds, 1 residue, 1 model selected  

> color sel red

> select #4/B:525

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

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

17 atoms, 19 bonds, 1 residue, 1 model selected  

> ui tool show "Color Actions"

> color sel lawn green

> color sel medium spring green

> color sel chartreuse

> color sel spring green

> color sel lime green

> color sel medium sea green

> color sel sea green

> color sel yellow green

> color sel green yellow

> color sel green

> color sel lime green

> color sel spring green

> color sel medium aquamarine

> color sel medium spring green

> color sel spring green

> color sel lime green

> color sel lawn green

> color sel chartreuse

> color sel green

> color sel lime green

> select clear

> select #2/B:459

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

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

12 atoms, 13 bonds, 1 residue, 1 model selected  

> color sel cornflower blue

> open 7Z7F

Summary of feedback from opening 7Z7F fetched from pdb  
---  
notes | Fetching compressed mmCIF 7z7f from
http://files.rcsb.org/download/7z7f.cif  
Fetching CCD IF3 from http://ligand-expo.rcsb.org/reports/I/IF3/IF3.cif  
  
7z7f title:  
Crystal structure of YTHDF2 with compound YLI_DC1_005 [more info...]  
  
Chain information for 7z7f #6  
---  
Chain | Description | UniProt  
A B | YTH domain-containing family protein 2 | YTHD2_HUMAN  
  
Non-standard residues in 7z7f #6  
---  
CL — chloride ion  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
IF3 — ~{N}2,~{N}6,9-trimethylpurine-2,6-diamine  
SO4 — sulfate ion  
  
7z7f mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
  

> select #6/A

1285 atoms, 1230 bonds, 236 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #6/B:535

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

> select up

115 atoms, 116 bonds, 15 residues, 1 model selected  

> select up

1170 atoms, 1198 bonds, 149 residues, 1 model selected  

> hide sel target a

> undo

[Repeated 1 time(s)]

> select #6/B:472

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

> select up

60 atoms, 61 bonds, 8 residues, 1 model selected  

> select up

1170 atoms, 1198 bonds, 149 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select up

79 atoms, 13 bonds, 66 residues, 1 model selected  

> select down

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select up

79 atoms, 13 bonds, 66 residues, 1 model selected  

> select up

5142 atoms, 4914 bonds, 6 pseudobonds, 949 residues, 6 models selected  

> select down

79 atoms, 13 bonds, 66 residues, 1 model selected  

> hide sel target a

> undo

> select #6/B:602@O4

1 atom, 1 residue, 1 model selected  

> select up

5 atoms, 4 bonds, 1 residue, 1 model selected  

> delete atoms sel

> delete bonds sel

> select clear

[Repeated 2 time(s)]

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

5 atoms, 4 bonds, 1 residue, 1 model selected  

> delete atoms sel

> delete bonds sel

> select clear

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

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

> delete atoms sel

> delete bonds sel

> open 7Z7F

7z7f title:  
Crystal structure of YTHDF2 with compound YLI_DC1_005 [more info...]  
  
Chain information for 7z7f #7  
---  
Chain | Description | UniProt  
A B | YTH domain-containing family protein 2 | YTHD2_HUMAN  
  
Non-standard residues in 7z7f #7  
---  
CL — chloride ion  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
IF3 — ~{N}2,~{N}6,9-trimethylpurine-2,6-diamine  
SO4 — sulfate ion  
  
7z7f mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
  

> select #7/B

1249 atoms, 1211 bonds, 215 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #7/A:422

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

> select #7/A:422

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

> select up

103 atoms, 104 bonds, 12 residues, 1 model selected  

> select up

1169 atoms, 1199 bonds, 149 residues, 1 model selected  

> hide sel target a

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

14 atoms, 15 bonds, 1 residue, 1 model selected  

> color sel magenta

> ui tool show Matchmaker

> matchmaker #5-7#!2,4 to #1/B pairing bs

Reference and/or match model contains no nucleic or amino acid chains.  
Use the command-line 'align' command to superimpose small molecules/ligands.  

> matchmaker #5-6#!2,4 to #1/B pairing bs

Reference and/or match model contains no nucleic or amino acid chains.  
Use the command-line 'align' command to superimpose small molecules/ligands.  

> matchmaker #5-7#!2,4 to #1/B pairing bs

Reference and/or match model contains no nucleic or amino acid chains.  
Use the command-line 'align' command to superimpose small molecules/ligands.  

> select clear

> ui tool show Matchmaker

> matchmaker #5-7#!2,4 to #1/B pairing bs

Reference and/or match model contains no nucleic or amino acid chains.  
Use the command-line 'align' command to superimpose small molecules/ligands.  
Traceback (most recent call last):  
File
"/private/var/folders/c2/q_28hscx3cx6z7xdv52dsp_40000gn/T/AppTranslocation/CF483CE0-67D2-4EE2-A3AB-C063D26BB562/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File
"/private/var/folders/c2/q_28hscx3cx6z7xdv52dsp_40000gn/T/AppTranslocation/CF483CE0-67D2-4EE2-A3AB-C063D26BB562/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in <lambda>  
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())  
File
"/private/var/folders/c2/q_28hscx3cx6z7xdv52dsp_40000gn/T/AppTranslocation/CF483CE0-67D2-4EE2-A3AB-C063D26BB562/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 341, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  

Populating font family aliases took 881 ms. Replace uses of missing font
family ".SF NS Text" with one that exists to avoid this cost.  

Error processing trigger "setting changed":  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
File
"/private/var/folders/c2/q_28hscx3cx6z7xdv52dsp_40000gn/T/AppTranslocation/CF483CE0-67D2-4EE2-A3AB-C063D26BB562/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 341, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/private/var/folders/c2/q_28hscx3cx6z7xdv52dsp_40000gn/T/AppTranslocation/CF483CE0-67D2-4EE2-A3AB-C063D26BB562/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File
"/private/var/folders/c2/q_28hscx3cx6z7xdv52dsp_40000gn/T/AppTranslocation/CF483CE0-67D2-4EE2-A3AB-C063D26BB562/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in <lambda>  
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())  
File
"/private/var/folders/c2/q_28hscx3cx6z7xdv52dsp_40000gn/T/AppTranslocation/CF483CE0-67D2-4EE2-A3AB-C063D26BB562/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 341, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
Error processing trigger "setting changed":  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
File
"/private/var/folders/c2/q_28hscx3cx6z7xdv52dsp_40000gn/T/AppTranslocation/CF483CE0-67D2-4EE2-A3AB-C063D26BB562/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 341, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/private/var/folders/c2/q_28hscx3cx6z7xdv52dsp_40000gn/T/AppTranslocation/CF483CE0-67D2-4EE2-A3AB-C063D26BB562/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File
"/private/var/folders/c2/q_28hscx3cx6z7xdv52dsp_40000gn/T/AppTranslocation/CF483CE0-67D2-4EE2-A3AB-C063D26BB562/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in <lambda>  
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())  
File
"/private/var/folders/c2/q_28hscx3cx6z7xdv52dsp_40000gn/T/AppTranslocation/CF483CE0-67D2-4EE2-A3AB-C063D26BB562/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 341, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
Error processing trigger "setting changed":  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
File
"/private/var/folders/c2/q_28hscx3cx6z7xdv52dsp_40000gn/T/AppTranslocation/CF483CE0-67D2-4EE2-A3AB-C063D26BB562/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 341, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
  
See log for complete Python traceback.  
  

> save /Users/vilbert/Desktop/111111111.cxs

——— End of log from Tue Aug 9 23:34:19 2022 ———

opened ChimeraX session  

> ui tool show Matchmaker

Traceback (most recent call last):  
File
"/private/var/folders/c2/q_28hscx3cx6z7xdv52dsp_40000gn/T/AppTranslocation/CF483CE0-67D2-4EE2-A3AB-C063D26BB562/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File
"/private/var/folders/c2/q_28hscx3cx6z7xdv52dsp_40000gn/T/AppTranslocation/CF483CE0-67D2-4EE2-A3AB-C063D26BB562/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in <lambda>  
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())  
File
"/private/var/folders/c2/q_28hscx3cx6z7xdv52dsp_40000gn/T/AppTranslocation/CF483CE0-67D2-4EE2-A3AB-C063D26BB562/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 341, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
Error processing trigger "setting changed":  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
File
"/private/var/folders/c2/q_28hscx3cx6z7xdv52dsp_40000gn/T/AppTranslocation/CF483CE0-67D2-4EE2-A3AB-C063D26BB562/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 341, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-12.10.12
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 640
OpenGL vendor: Intel Inc.

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro14,1
      Processor Name: Intel Core i5
      Processor Speed: 2,3 GHz
      Number of Processors: 1
      Total Number of Cores: 2
      L2 Cache (per Core): 256 KB
      L3 Cache: 4 MB
      Hyper-Threading Technology: Enabled
      Memory: 8 GB
      Boot ROM Version: 198.0.0.0.0
      SMC Version (system): 2.43f6

Software:

    System Software Overview:

      System Version: macOS 10.14.6 (18G103)
      Kernel Version: Darwin 18.7.0
      Time since boot: 7 days 9:05

Graphics/Displays:

    Intel Iris Plus Graphics 640:

      Chipset Model: Intel Iris Plus Graphics 640
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x5926
      Revision ID: 0x0006
      Metal: Supported, feature set macOS GPUFamily2 v1
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: No


Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.3
    Babel: 2.10.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2021.10.8
    cftime: 1.6.0
    charset-normalizer: 2.0.12
    ChimeraX-AddCharge: 1.2.3
    ChimeraX-AddH: 2.1.3
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.4.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.39.1
    ChimeraX-AtomicLibrary: 7.0
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.7
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.17.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.1
    ChimeraX-CommandLine: 1.2.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-Cytoscape: 0.1
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-DevelExtras: 0.4.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-GenomeTools: 0.9
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    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
    ChimeraX-Label: 1.1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.6
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.7
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.5
    ChimeraX-ModelPanel: 1.3.2
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-NIHPresets: 1.0.6
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.9
    ChimeraX-PDB: 2.6.6
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBImages: 1.1
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-Phenix: 0.3
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RMF: 0.11
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    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
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.8
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-TestManager: 0.3
    ChimeraX-Toolbar: 1.1.1
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.2.1
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.1.0
    ChimeraX-XMAS: 1.1.2
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.26
    debugpy: 1.6.0
    decorator: 5.1.1
    docutils: 0.17.1
    entrypoints: 0.4
    filelock: 3.4.2
    fonttools: 4.33.3
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.27
    imagecodecs: 2021.11.20
    imagesize: 1.3.0
    ipykernel: 6.6.1
    ipython: 7.31.1
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.0.3
    jupyter-client: 7.1.0
    jupyter-core: 4.10.0
    kiwisolver: 1.4.2
    line-profiler: 3.4.0
    lxml: 4.7.1
    lz4: 3.1.10
    MarkupSafe: 2.1.1
    matplotlib: 3.5.1
    matplotlib-inline: 0.1.3
    MolecularDynamicsViewer: 1.4
    msgpack: 1.0.3
    nest-asyncio: 1.5.5
    netCDF4: 1.5.8
    networkx: 2.6.3
    numexpr: 2.8.1
    numpy: 1.22.1
    openvr: 1.16.802
    packaging: 21.0
    ParmEd: 3.4.3
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.0.1
    pip: 21.3.1
    pkginfo: 1.8.2
    prompt-toolkit: 3.0.29
    psutil: 5.9.0
    ptyprocess: 0.7.0
    pycollada: 0.7.2
    pydicom: 2.2.2
    Pygments: 2.11.2
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.0
    PyQt6-Qt6: 6.3.0
    PyQt6-sip: 13.3.1
    PyQt6-WebEngine-commercial: 6.3.0
    PyQt6-WebEngine-Qt6: 6.3.0
    python-dateutil: 2.8.2
    pytz: 2022.1
    pyzmq: 23.1.0
    qtconsole: 5.3.0
    QtPy: 2.1.0
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    SEQCROW: 1.4.4
    setuptools: 59.8.0
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.3.2
    sphinx-autodoc-typehints: 1.15.2
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-community: 1.0.0
    tables: 3.7.0
    tifffile: 2021.11.2
    tinyarray: 1.2.4
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.9
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.1
    wheel-filename: 1.3.0

Change History (2)

comment:1 by Eric Pettersen, 3 years ago

Cc: Tom Goddard added
Component: Unassigned → UI
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → MatchMaker: 'NoneType' object has no attribute 'setChecked'

comment:2 by Eric Pettersen, 3 years ago

Resolution: → can't reproduce
Status: accepted → closed

I'm not sure how this is possible. The user restores a session and then just brings up MatchMaker which immediately throws this error. I guess I would need the session (which also has these errors), though MatchMaker is not saved/restored in sessions so I'm mystified how the session could be relevant. At any rate, I was unable to reproduce this.

Note: See TracTickets for help on using tickets.