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#9931 closed defect (duplicate)

Blast: self.job.model_name is None

Reported by:	chimerax-bug-report@…	Owned by:	Zach Pearson
Priority:	normal	Milestone:
Component:	Sequence	Version:
Keywords:		Cc:
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        macOS-12.6.6-arm64-arm-64bit
ChimeraX Version: 1.6rc202304252053 (2023-04-25 20:53:05 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.6rc202304252053 (2023-04-25)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/Users/diakinmeji-3/Documents/PROPOSALS/2023/14. PEPTAC cooperativity
> design/Figures/Figure 7/AF-CREPT_ligand-1.cxs" format session

Log from Sun Oct 8 11:26:23 2023UCSF ChimeraX version: 1.6rc202304252053
(2023-04-25)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/Users/diakinmeji-3/Documents/Chimera X pdb/BCL9-beta-catenin
> complex.cxs" format session

Log from Wed May 3 00:32:32 2023UCSF ChimeraX version: 1.6rc202304252053
(2023-04-25)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/Users/diakinmeji-3/Documents/Chimera X pdb/CREPT CCT domain.cxs"
> format session

Log from Sat Apr 29 02:32:05 2023You can double click a model's Name or ID in
the model panel to edit those fields  
UCSF ChimeraX version: 1.6rc202304252053 (2023-04-25)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/diakinmeji-3/Documents/Chimera X pdb/Fecto2M_fab77_relion-
> coot-3_real_space_refined_076.pdb" format pdb

Chain information for Fecto2M_fab77_relion-coot-3_real_space_refined_076.pdb
#1  
---  
Chain | Description  
A C E | No description available  
B D F | No description available  
G I K | No description available  
H J L | No description available  
  

> hide atoms

> show cartoons

> set bgColor white

> open 2bbv

2bbv title:  
The refined three-dimensional structure of an insect virus At 2.8 angstroms
resolution [more info...]  
  
Chain information for 2bbv #2  
---  
Chain | Description | UniProt  
A B C | PROTEIN (BLACK BEETLE VIRUS CAPSID PROTEIN) | COAT_BBV 1-363  
D E F | PROTEIN (BLACK BEETLE VIRUS CAPSID PROTEIN) | COAT_BBV 364-407  
N | RNA (5'-R(*UP*CP*UP*UP*AP*UP*AP*UP*CP*U)-3') |  
  
Non-standard residues in 2bbv #2  
---  
CA — calcium ion  
  
2bbv mmCIF Assemblies  
---  
1| complete icosahedral assembly  
2| icosahedral asymmetric unit  
3| icosahedral pentamer  
4| icosahedral 23 hexamer  
5| icosahedral asymmetric unit, std point frame  
6| crystal asymmetric unit, crystal frame  
  

> clear

Unknown command: clear  

> select clear

> close

> open 2bbv

2bbv title:  
The refined three-dimensional structure of an insect virus At 2.8 angstroms
resolution [more info...]  
  
Chain information for 2bbv #1  
---  
Chain | Description | UniProt  
A B C | PROTEIN (BLACK BEETLE VIRUS CAPSID PROTEIN) | COAT_BBV 1-363  
D E F | PROTEIN (BLACK BEETLE VIRUS CAPSID PROTEIN) | COAT_BBV 364-407  
N | RNA (5'-R(*UP*CP*UP*UP*AP*UP*AP*UP*CP*U)-3') |  
  
Non-standard residues in 2bbv #1  
---  
CA — calcium ion  
  
2bbv mmCIF Assemblies  
---  
1| complete icosahedral assembly  
2| icosahedral asymmetric unit  
3| icosahedral pentamer  
4| icosahedral 23 hexamer  
5| icosahedral asymmetric unit, std point frame  
6| crystal asymmetric unit, crystal frame  
  

> close

> open 4NAD

Summary of feedback from opening 4NAD fetched from pdb  
---  
note | Fetching compressed mmCIF 4nad from
http://files.rcsb.org/download/4nad.cif  
  
4nad title:  
Crystal Structure of the C-terminal Domain of CREPT [more info...]  
  
Chain information for 4nad #1  
---  
Chain | Description | UniProt  
A B | Regulation of nuclear pre-mRNA domain-containing protein 1B |
RPR1B_HUMAN 177-326  
  

> lys266

Unknown command: lys266  

> lys 266

Unknown command: lys 266  

> k266

Unknown command: k266  

> lighting simple

> lighting soft

> lighting full

> lighting soft

> rainbow

[Repeated 2 time(s)]

> coulombic

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for 4nad_B SES surface #1.1: minimum, -13.95, mean -1.72,
maximum 12.51  
Coulombic values for 4nad_A SES surface #1.2: minimum, -16.89, mean -1.73,
maximum 12.33  
To also show corresponding color key, enter the above coulombic command and
add key true  

> coulombic

Coulombic values for 4nad_B SES surface #1.1: minimum, -13.95, mean -1.72,
maximum 12.51  
Coulombic values for 4nad_A SES surface #1.2: minimum, -16.89, mean -1.73,
maximum 12.33  
To also show corresponding color key, enter the above coulombic command and
add key true  

> mlp

Map values for surface "4nad_A SES surface": minimum -26.65, mean -3.922,
maximum 21.98  
Map values for surface "4nad_B SES surface": minimum -26.24, mean -3.865,
maximum 21.31  
To also show corresponding color key, enter the above mlp command and add key
true  

> nucleotides atoms

> style nucleic stick

Changed 0 atom styles  

> show cartoons

[Repeated 1 time(s)]

> rainbow

> show cartoons

> hide cartoons

> show surfaces

> hide surfaces

> show cartoons

Alignment identifier is 1  

> show cartoons

> hide cartoons

> show cartoons

> set bgColor black

> set bgColor white

> style stick

Changed 2104 atom styles  

> show cartoons

> lighting simple

> lighting soft

> select /B,A:176-191,193-203,205-217,219-298

1926 atoms, 1928 bonds, 240 residues, 1 model selected  

> set bgColor black

> color blue

> color gray

> color silver

> set bgColor white

> set bgColor black

> unselect

Unknown command: unselect  

> select /B,A:176-191,193-203,205-217,219-298

1926 atoms, 1928 bonds, 240 residues, 1 model selected  

> select /B,A:176-191,193-203,205-217,219-298

1926 atoms, 1928 bonds, 240 residues, 1 model selected  

> select /B,A:176-191,193-203,205-217,219-298

1926 atoms, 1928 bonds, 240 residues, 1 model selected  

> select /B,A:176-191,193-203,205-217,219-298

1926 atoms, 1928 bonds, 240 residues, 1 model selected  

> select /B,A:176-191,193-203,205-217,219-298

1926 atoms, 1928 bonds, 240 residues, 1 model selected  

> help help:quickstart

> color byattribute chain

No known/registered numeric attribute chain  

> ribbon /c

> select clear

> select /B,A:176-191,193-203,205-217,219-298

1926 atoms, 1928 bonds, 240 residues, 1 model selected  

> select clear

> select /B,A:176-191,193-203,205-217,219-298

1926 atoms, 1928 bonds, 240 residues, 1 model selected  

> select clear

> set bgColor white

> set silhouettes true

> select /A:246

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

> select add /A:245

10 atoms, 8 bonds, 2 residues, 2 models selected  

> select /A:242

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select /A:228

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

> select /A:264

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

> select /A:267

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

> select /A:266

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

> select clear

> select /B,A:176-191,193-203,205-217,219-298

1926 atoms, 1928 bonds, 240 residues, 1 model selected  

> select clear

> select /A:266

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

> select /A:267

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

> select /A:269

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

> select /A:266-269

32 atoms, 31 bonds, 4 residues, 1 model selected  

> select /A:266-286

179 atoms, 179 bonds, 21 residues, 1 model selected  

> color sel blue

> color sel teal

> select clear

> save "/Users/diakinmeji-3/Documents/Chimera X pdb/CREPT CCT domain.cxs"

——— End of log from Sat Apr 29 02:32:05 2023 ———

opened ChimeraX session  

> close

> ui tool show AlphaFold

> alphafold predict
> KHAVVNLINYQDDAELATRAIPELTKLLNDEDQVVVNKAAVMVHQLSKKEASRHAIMRSPQMVSAIVRTMQNTNDVETARCTAGTLHNLSHHREGLLAIFKSGGIPALVKMLGSPVDSVLFYAITTLHNLLLHQEGAKMAVRLAGGLQKMVALLNKTNVKFLAITTDCLQILAYGNQESKLIILASGGPQALVNIMRTYTYEKLLWTTSRVLKVLSVCSSNKPAIVEAGGMQALGLHLTDPSQRLVQNCLWTLRNLSDAATKQEGMEGLLGTLVQLLGSDDINVVTCAAGILSNLTCNNYKNKMMVCQVGGIEALVRTVLRAGDREDITEPAICALRHLTSRHQEAEMAQNAVRLHYGLPVVVKLLHPPSHWPLIKATVGLIRNLALCPANHAPLREQGAIPRLVQLLVRAHQDTQRRTSMGGTQQQFVEGVRMEEIVEGCTGALHILARDVHNRIVIRGLNTIPLFVQLLYSPIENIQRVAAGVLCELAQDKEAAEAIEAEGATAPLTELLHSRNEGVATYAAAVLFRMSE

Running AlphaFold prediction  
AlphaFold prediction finished  
Results in /Users/diakinmeji-3/Downloads/ChimeraX/AlphaFold/prediction_5  

> open
> /Users/diakinmeji-3/Downloads/ChimeraX/AlphaFold/prediction_5/best_model.pdb

Chain information for best_model.pdb #1  
---  
Chain | Description  
A | No description available  
  

> alphafold pae #1 file
> /Users/diakinmeji-3/Downloads/ChimeraX/AlphaFold/prediction_5/best_model_pae.json

> color #1:17-420 lime

> color #1:433-531 lime

> color #1:13-49 lime

> color #1:449-529 magenta

> color #1:59-121 lime

> color #1:495-526 magenta

> color #1:468-519 lime

> color #1:31-66 magenta

> color #1:476-500 lime

> color #1:21-28 magenta

> color #1:464-524 lime

> color #1:397-532 lime

> color #1:364-364 lime

> color #1:66-66 magenta

> color #1:420-425 lime

> color #1:22-77 magenta

> color #1:4-182 lime

> color #1:418-426 magenta

> color #1:464-526 lime

> color #1:2-6 magenta

> color #1:420-468 lime

> color #1:305-305 lime

> color #1:468-468 magenta

> color bfactor #1 palette alphafold

4061 atoms, 532 residues, atom bfactor range 54.6 to 98.9  

> alphafold pae #1 colorDomains true

[Repeated 1 time(s)]

> color #1:313-313 lime

> color #1:370-370 magenta

> color #1:256-256 lime

> color #1:261-261 magenta

> color #1:249-266 lime

> alphafold contacts #1

> hide #1.1 models

> close #1.1

> color bfactor #1 palette alphafold

4061 atoms, 532 residues, atom bfactor range 54.6 to 98.9  

> alphafold pae #1 colorDomains true

> color bfactor #1 palette alphafold

4061 atoms, 532 residues, atom bfactor range 54.6 to 98.9  

> color #1:163-260 lime

> color #1:278-335 magenta

> color #1:296-353 lime

> color #1:175-240 magenta

> color bfactor #1 palette alphafold

4061 atoms, 532 residues, atom bfactor range 54.6 to 98.9  

> color bfactor

4061 atoms, 532 residues, atom bfactor range 54.6 to 98.9  

> color bfactor #1 palette alphafold

4061 atoms, 532 residues, atom bfactor range 54.6 to 98.9  

> pLDDT

Unknown command: pLDDT  

> help help:user/tools/alphafold.html#pae

> ui tool show "Color Key"

> ui mousemode right "color key"

> key pos 0.798815,0.201661 size 0,0

[Repeated 1 time(s)]

> key pos 0.807292,0.142388 size 0,0

> key labelColor #bfbfbf

> key labelColor default

> ui mousemode right zoom

> ui tool show "Color Key"

> ui mousemode right "color key"

> key pos 0.79729,0.14239

Key is partially or completely offscreen  

> key pos 0.78729,0.14239

Key is partially or completely offscreen  

> key pos 0.77729,0.14239

Key is partially or completely offscreen  

> key pos 0.76729,0.14239

Key is partially or completely offscreen  

> key pos 0.75729,0.14239

Key is partially or completely offscreen  

> key pos 0.74729,0.14239

> key pos 0.73729,0.14239

> key pos 0.72729,0.14239

> key pos 0.71729,0.14239

> color bfactor #1 palette alphafold

4061 atoms, 532 residues, atom bfactor range 54.6 to 98.9  

> key blue-white-red :min : :max white:

> key blue-white-red :min : :max

> key ticks true

> key ticks false

> key pos 0.923918,0.169599 size 0,0

> key pos 0.8089,0.142568 size 0,0

> key pos 0.751868,0.343467 size 8.47139e-05,0

> key labelColor #bfbfbf

> key labelColor default

> key pos 0.549233,0.463005 size 0.0169004,0.120827

> key pos 0.497995,0.168371 size 0.276059,0.0183853

> alphafold pae #1 colorDomains true

> color bfactor #1 palette alphafold

4061 atoms, 532 residues, atom bfactor range 54.6 to 98.9  

> color bypLDDT

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color byattribute pLDDT

No known/registered numeric attribute pLDDT  

> color byPAE

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color bychain

> color bybfactor

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color bfactor

4061 atoms, 532 residues, atom bfactor range 54.6 to 98.9  

> alphafold pae #1 colorDomains true

> key pos 0.516406,0.21966 size 0.271178,0.011018

> color bfactor #1 palette alphafold

4061 atoms, 532 residues, atom bfactor range 54.6 to 98.9  

> alphafold pae #1 colorDomains true

> color bfactor #1 palette alphafold

4061 atoms, 532 residues, atom bfactor range 54.6 to 98.9  

> color bfactor

4061 atoms, 532 residues, atom bfactor range 54.6 to 98.9  

> color bfactor #1 palette alphafold

4061 atoms, 532 residues, atom bfactor range 54.6 to 98.9  

> select /A:5

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

> select /A:6

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

> select /A:7

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

> select /A:8

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

> select /A:9

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

> select /A:10

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

> select /A:11

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

> select /A:12

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

> select /A:13

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

> select /A:12

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

> select /A:11

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

> select /A:10

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

> select /A:9

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

> select /A:8

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

> select /A:7

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

> select /A:6

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

> select /A:5

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

> select /A:4

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

> select /A:2

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

> select clear

> select /A:17

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

> select /A:16

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

> select clear

> select /A:15

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

> select /A:14

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

> save "/Users/diakinmeji-3/Documents/Chimera X pdb/beta-catenin.cxs"

> close

> ui mousemode right zoom

> alphafold predict
> KHAVVNLINYQDDAELATRAIPELTKLLNDEDQVVVNKAAVMVHQLSKKEASRHAIMRSPQMVSAIVRTMQNTNDVETARCTAGTLHNLSHHREGLLAIFKSGGIPALVKMLGSPVDSVLFYAITTLHNLLLHQEGAKMAVRLAGGLQKMVALLNKTNVKFLAITTDCLQILAYGNQESKLIILASGGPQALVNIMRTYTYEKLLWTTSRVLKVLSVCSSNKPAIVEAGGMQALGLHLTDPSQRLVQNCLWTLRNLSDAATKQEGMEGLLGTLVQLLGSDDINVVTCAAGILSNLTCNNYKNKMMVCQVGGIEALVRTVLRAGDREDITEPAICALRHLTSRHQEAEMAQNAVRLHYGLPVVVKLLHPPSHWPLIKATVGLIRNLALCPANHAPLREQGAIPRLVQLLVRAHQDTQRRTSMGGTQQQFVEGVRMEEIVEGCTGALHILARDVHNRIVIRGLNTIPLFVQLLYSPIENIQRVAAGVLCELAQDKEAAEAIEAEGATAPLTELLHSRNEGVATYAAAVLFRMSE,SQEQLEHRERSLQTLRDIQRMLF

Running AlphaFold prediction  
AlphaFold prediction finished  
Results in /Users/diakinmeji-3/Downloads/ChimeraX/AlphaFold/prediction_6  

> open
> /Users/diakinmeji-3/Downloads/ChimeraX/AlphaFold/prediction_6/best_model.pdb

Chain information for best_model.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> select /b

203 atoms, 204 bonds, 23 residues, 1 model selected  

> color sel red

> select clear

> alphafold pae #1 file
> /Users/diakinmeji-3/Downloads/ChimeraX/AlphaFold/prediction_6/best_model_pae.json

> color #1/A:7-529 lime

> color #1/B:3-20 lime

> color #1/A:7-244 lime

> color #1/B:8-23 magenta

> color #1/A:83-86 lime

> color #1/A:507-507 magenta

> color #1/A:4-530 lime

> color #1/B:5-20 magenta

> color #1/B:4-22 lime

> color #1/A:15-252 magenta

> color bfactor #1 palette alphafold

4264 atoms, 555 residues, atom bfactor range 55.3 to 98.9  

> alphafold pae #1 colorDomains true

[Repeated 1 time(s)]

> select /a

4061 atoms, 4118 bonds, 532 residues, 1 model selected  

> color sel gray

> select clear

> color /a green

> save "/Users/diakinmeji-3/Documents/Chimera X pdb/BCL9-beta-catenin
> complex.cxs"

——— End of log from Wed May 3 00:32:32 2023 ———

opened ChimeraX session  

> select /B:14

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

> select clear

[Repeated 1 time(s)]

> select /B:17

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

> select /B:13

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

> select /B:10

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

> select /B:6

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

> select /B:10

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

> show sel atoms

> select /B:21

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

> select /B:20

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

> select /B:17

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

> select /B:16

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

> select /B:14

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

> select /B:13

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

> select /B:10

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

> select /B:9

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

> select /B:6

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

> select /B:3

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

> select /B:2

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

> select /B:18

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

> select clear

> select /B:21

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

> select /B:20

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

> show sel atoms

> select clear

[Repeated 1 time(s)]

> select /B:23

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

> select /B:1

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

> select /B:17

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

> show sel atoms

> select /B:20

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

> hbonds

587 hydrogen bonds found  

> hbonds delete

> ui tool show Contacts

> ui tool show H-Bonds

> hbonds sel twoColors true intraMol false reveal true

0 hydrogen bonds found  
0 strict hydrogen bonds found  

> hbonds sel twoColors true intraMol false reveal true

0 hydrogen bonds found  
0 strict hydrogen bonds found  

> select A/

Expected an objects specifier or a keyword  

> select A/

Expected an objects specifier or a keyword  

> select clear

> chain a

Unknown command: chain a  

> chain a/

Unknown command: chain a/  

> chain /a

Unknown command: chain /a  

> help help:user

> help help:quickstart

> select /a

4061 atoms, 4118 bonds, 532 residues, 1 model selected  

> select /b

203 atoms, 204 bonds, 23 residues, 1 model selected  

> ui tool show H-Bonds

> hbonds sel twoColors true intraMol false reveal true

7 hydrogen bonds found  
2 strict hydrogen bonds found  

> hbonds sel twoColors true intraMol false reveal true

7 hydrogen bonds found  
2 strict hydrogen bonds found  

> ui tool show Contacts

> contacts sel ignoreHiddenModels true

144 contacts  

> contacts sel ignoreHiddenModels true

144 contacts  

> contacts sel ignoreHiddenModels true

144 contacts  

> contacts sel ignoreHiddenModels true

144 contacts  

> contacts sel intraModel false ignoreHiddenModels true

No contacts  

> contacts sel distanceOnly 4.0 intraModel false ignoreHiddenModels true

No distances  

> contacts sel distanceOnly 4.0 intraModel false ignoreHiddenModels true

No distances  

> contacts sel restrict cross distanceOnly 4.0 intraModel false
> ignoreHiddenModels true

No distances  

> contacts sel restrict cross distanceOnly 4.0 intraModel false
> ignoreHiddenModels true

No distances  

> contacts sel restrict cross distanceOnly 4.0 intraModel false
> ignoreHiddenModels true reveal true

No distances  

> contacts sel restrict cross distanceOnly 4.0 intraModel false
> ignoreHiddenModels true reveal true

No distances  

> select clear

> select /B:17

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

> hide sel atoms

> select clear

> save "/Users/diakinmeji-3/Documents/PROPOSALS/2023/14. PEPTAC cooperativity
> design/Figures/Figure 7/Beta-Cat ligand_ARM-1.tif" width 936 height 739
> supersample 3 transparentBackground true

> save "/Users/diakinmeji-3/Documents/PROPOSALS/2023/14. PEPTAC cooperativity
> design/Figures/Figure 7/Beta-Cat ligand_ARM-2.tif" width 936 height 739
> supersample 3 transparentBackground true

> close

> open
> /Users/diakinmeji-3/Downloads/ChimeraX/AlphaFold/prediction_32/best_model.pdb
> format pdb

Chain information for best_model.pdb #1  
---  
Chain | Description  
A | No description available  
  

> ui tool show "Show Sequence Viewer"

> sequence chain /A

Alignment identifier is 1/A  

> select /A:154

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

> select /A

1195 atoms, 1204 bonds, 154 residues, 1 model selected  

> close

> toolshed show

[Repeated 1 time(s)]

> ui tool show AlphaFold

> alphafold predict
> AMGSTEELIKALQDLENAASGDATVRQKIASLPQEVQDVSLLEKITDKEAAERLSKTVDEACLLLAEYNGRLAAELEDRRQLARMLVEYTQNQKDVLSEKEKKLEEYKQKLARVTQVRKELKSHIQSLPDLSLLPNVTGGLAPLPSAGDLFSTD,AMGSTEELIKALQDLENAASGDATVRQKIASLPQEVQDVSLLEKITDKEAAERLSKTVDEACLLLAEYNGRLAAELEDRRQLARMLVEYTQNQKDVLSEKEKKLEEYKQKLARVTQVRKELKSHIQSLPDLSLLPNVTGGLAPLPSAGDLFSTD,KDVLSEKEKKLEEYKQKLARV

Running AlphaFold prediction  
AlphaFold prediction finished  
Results in /Users/diakinmeji-3/Downloads/ChimeraX/AlphaFold/prediction_35  

Downloaded prediction file not found:
/Users/diakinmeji-3/Downloads/ChimeraX/AlphaFold/prediction_35/best_model.pdb  

> alphafold predict
> AMGSTEELIKALQDLENAASGDATVRQKIASLPQEVQDVSLLEKITDKEAAERLSKTVDEACLLLAEYNGRLAAELEDRRQLARMLVEYTQNQKDVLSEKEKKLEEYKQKLARVTQVRKELKSHIQSLPDLSLLPNVTGGLAPLPSAGDLFSTD,AMGSTEELIKALQDLENAASGDATVRQKIASLPQEVQDVSLLEKITDKEAAERLSKTVDEACLLLAEYNGRLAAELEDRRQLARMLVEYTQNQKDVLSEKEKKLEEYKQKLARVTQVRKELKSHIQSLPDLSLLPNVTGGLAPLPSAGDLFSTD,KDVLSEKEKKLEEYKQKLARV
> templates true

Running AlphaFold prediction  

> open /Users/diakinmeji-3/Downloads/ChimeraX/AlphaFold/prediction_35/log.txt

Unrecognized file suffix '.txt'  

> open 4NAD

4nad title:  
Crystal Structure of the C-terminal Domain of CREPT [more info...]  
  
Chain information for 4nad #1  
---  
Chain | Description | UniProt  
A B | Regulation of nuclear pre-mRNA domain-containing protein 1B |
RPR1B_HUMAN 177-326  
  

> alphafold predict 4NAD,KDVLSEKEKKLEEYKQKLARV

Missing or invalid "sequences" argument: Sequences argument "4NAD" is not a
chain specifier, alignment id, UniProt id, or sequence characters  

Populating font family aliases took 126 ms. Replace uses of missing font
family "Lato" with one that exists to avoid this cost.  

> alphafold predict UP00000,KDVLSEKEKKLEEYKQKLARV

Missing or invalid "sequences" argument: Sequences argument "UP00000" is not a
chain specifier, alignment id, UniProt id, or sequence characters  
Fetching compressed Q9NQG5 UniProt info from
https://www.uniprot.org/uniprot/Q9NQG5.xml  

> alphafold predict Q9NQG5,KDVLSEKEKKLEEYKQKLARV

Running AlphaFold prediction  
AlphaFold prediction finished  
Results in /Users/diakinmeji-3/Downloads/ChimeraX/AlphaFold/prediction_36  

> open
> /Users/diakinmeji-3/Downloads/ChimeraX/AlphaFold/prediction_36/best_model.pdb

Chain information for best_model.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> close

> open
> /Users/diakinmeji-3/Downloads/ChimeraX/AlphaFold/prediction_36/best_model.pdb
> format pdb

Chain information for best_model.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> ui tool show "AlphaFold Error Plot"

> alphafold pae #1 file
> /Users/diakinmeji-3/Downloads/ChimeraX/AlphaFold/prediction_36/best_model_pae.json

> alphafold pae #1 colorDomains true

> color bfactor #1 palette alphafold

2775 atoms, 347 residues, atom bfactor range 18.1 to 98.1  

> select /B:9

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

> select /B:17

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

> show sel atoms

> select clear

[Repeated 2 time(s)]

> select /B:9

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

> show sel atoms

> close

> open
> /Users/diakinmeji-3/Downloads/ChimeraX/AlphaFold/prediction_36/best_model.pdb
> format pdb

Chain information for best_model.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> save "/Users/diakinmeji-3/Documents/PROPOSALS/2023/14. PEPTAC cooperativity
> design/Figures/Figure 7/AF-CREPT_ligand-1.cxs" includeMaps true

——— End of log from Sun Oct 8 11:26:23 2023 ———

opened ChimeraX session  

> ui tool show "AlphaFold Error Plot"

> alphafold pae #1 file
> /Users/diakinmeji-3/Downloads/ChimeraX/AlphaFold/prediction_36/best_model_pae.json

> color bfactor #1 palette alphafold

2775 atoms, 347 residues, atom bfactor range 18.1 to 98.1  

> color #1/A:87-87 lime

> color #1/B:7-7 magenta

> color #1/A:2-139 lime

> color #1/A:173-309 lime

> color #1/B:4-21 lime

> color #1/A:166-314 lime

> color #1/A:10-159 magenta

> color #1/A:8-315 lime

> color #1/B:7-18 lime

> color #1/A:7-171 magenta

> color #1/A:8-156 lime

> color #1/B:5-21 magenta

> color #1/A:8-126 lime

> color #1/A:142-314 magenta

> color #1/A:159-316 lime

> color #1/A:8-138 magenta

> color #1/B:3-20 lime

> color #1/A:176-294 magenta

> color #1/A:156-313 lime

> color #1/A:5-154 magenta

> color #1/A:256-257 lime

> color #1/A:45-45 magenta

> color #1/A:173-321 lime

> color #1/A:12-158 magenta

> color #1/A:14-133 lime

> color #1/A:150-311 magenta

> color #1/A:191-292 lime

> color #1/A:306-323 magenta

> color #1/B:5-17 lime

> color #1/A:3-165 magenta

> color #1/A:307-324 lime

> color #1/B:4-17 magenta

> color #1/B:4-21 lime

> color #1/A:177-295 magenta

> alphafold pae #1 colorDomains true

> close

> ui tool show AlphaFold

> alphafold match 4FLA

Missing or invalid "sequences" argument: Sequences argument "4FLA" is not a
chain specifier, alignment id, UniProt id, or sequence characters  

> alphafold match 4NAD

Missing or invalid "sequences" argument: Sequences argument "4NAD" is not a
chain specifier, alignment id, UniProt id, or sequence characters  

> open 4NAD format mmcif fromDatabase pdb

4nad title:  
Crystal Structure of the C-terminal Domain of CREPT [more info...]  
  
Chain information for 4nad #1  
---  
Chain | Description | UniProt  
A B | Regulation of nuclear pre-mRNA domain-containing protein 1B |
RPR1B_HUMAN 177-326  
  

No sequence chosen for AlphaFold search  

> alphafold match #1/B

Fetching AlphaFold database settings from
https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database3.json  
Fetching compressed AlphaFold Q9NQG5 from
https://alphafold.ebi.ac.uk/files/AF-Q9NQG5-F1-model_v4.cif  
1 AlphaFold model found using UniProt identifier: Q9NQG5 (chain B)  
AlphaFold prediction matching 4nad  
---  
Chain| UniProt Id| UniProt Name| RMSD| Length| Seen| % Id  
B | Q9NQG5 | RPR1B_HUMAN | 2.43 | 150 | 133 | 100  
  
Opened 1 AlphaFold model  

> alphafold match #2.1

Fetching compressed AlphaFold A0A6D2WQS4 from
https://alphafold.ebi.ac.uk/files/AF-A0A6D2WQS4-F1-model_v4.cif  
1 AlphaFold model found using sequence similarity searches: A0A6D2WQS4 (chain
B)  
AlphaFold prediction matching AlphaFold RPR1B_HUMAN chain B  
---  
Chain| UniProt Id| UniProt Name| RMSD| Length| Seen| % Id  
B | A0A6D2WQS4 | A0A6D2WQS4_PANTR | 4.57 | 326 | 150 | 100  
  
Opened 1 AlphaFold model  

> alphafold match #3.1

1 AlphaFold model found using sequence similarity searches: A0A6D2WQS4 (chain
B)  
AlphaFold prediction matching AlphaFold A0A6D2WQS4_PANTR chain B  
---  
Chain| UniProt Id| UniProt Name| RMSD| Length| Seen| % Id  
B | A0A6D2WQS4 | A0A6D2WQS4_PANTR | 0.00 | 326 | 326 | 100  
  
Opened 1 AlphaFold model  

> alphafold search #3.1

Webservices job id: LA722F94TO7R4H7F  

> close

> open 4NAD format mmcif fromDatabase pdb

4nad title:  
Crystal Structure of the C-terminal Domain of CREPT [more info...]  
  
Chain information for 4nad #1  
---  
Chain | Description | UniProt  
A B | Regulation of nuclear pre-mRNA domain-containing protein 1B |
RPR1B_HUMAN 177-326  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 665, in customEvent  
func(*args, **kw)  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/blastprotein/job.py", line 97, in on_finish  
BlastProteinResults.from_job(  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/blastprotein/ui/results.py", line 90, in from_job  
return cls(  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/blastprotein/ui/results.py", line 86, in __init__  
self._build_ui()  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/blastprotein/ui/results.py", line 229, in _build_ui  
param_str = self._format_param_str()  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/blastprotein/ui/results.py", line 201, in _format_param_str  
model_formatted = ''.join([self.job.model_name, chain])  
TypeError: sequence item 0: expected str instance, NoneType found  
  
TypeError: sequence item 0: expected str instance, NoneType found  
  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/blastprotein/ui/results.py", line 201, in _format_param_str  
model_formatted = ''.join([self.job.model_name, chain])  
  
See log for complete Python traceback.  
  

> close

> ui tool show AlphaFold

> help help:user/tools/alphafold.html

[Repeated 1 time(s)]

> alphafold predict
> TEELIKALQDLENAASGDATVRQKIASLPQEVQDVSLLEKITDKEAAERLSKTVDEACLLLAEYNGRLAAELEDRRQLARMLVEYTQNQKDVLSEKEKKLEEYKQKLARVTQVRKELKSHIQSLPDLSLLPNVTGGLAPLPSAGDLFSTD,TEELIKALQDLENAASGDATVRQKIASLPQEVQDVSLLEKITDKEAAERLSKTVDEACLLLAEYNGRLAAELEDRRQLARMLVEYTQNQKDVLSEKEKKLEEYKQKLARVTQVRKELKSHIQSLPDLSLLPNVTGGLAPLPSAGDLFSTD,KDVLSEKEKKLEEYKQKLARV

Running AlphaFold prediction  
AlphaFold prediction finished  
Results in /Users/diakinmeji-3/Downloads/ChimeraX/AlphaFold/prediction_37  

> open
> /Users/diakinmeji-3/Downloads/ChimeraX/AlphaFold/prediction_37/best_model.pdb

Chain information for best_model.pdb #1  
---  
Chain | Description  
A B | No description available  
C | No description available  
  

> ui tool show "Show Sequence Viewer"

> sequence chain /C

Alignment identifier is 1/C  

> select clear

Drag select of 1 residues  
Drag select of 2 residues  
[Repeated 1 time(s)]

> select /C:6

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

> select /C:5

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

> select /C:4

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

> select clear

[Repeated 5 time(s)]Drag select of 5 residues  

> select clear

> select /C:10

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

> select /C:9

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

> save "/Users/diakinmeji-3/Documents/PROPOSALS/2023/14. PEPTAC cooperativity
> design/Figures/Figure 7/AF-CREPT_ligand-2.cxs"

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 285, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/blastprotein/ui/results.py", line 157, in take_snapshot  
, 'table_session': self.table.session_info()  
AttributeError: 'BlastProteinResults' object has no attribute 'table'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 290, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x126fb6220> ->
<chimerax.blastprotein.ui.results.BlastProteinResults object at 0x16d75a9d0>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 899, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save  
mgr.discovery(self._state_containers)  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x126fb6220> -> <chimerax.blastprotein.ui.results.BlastProteinResults object
at 0x16d75a9d0>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x126fb6220> ->
<chimerax.blastprotein.ui.results.BlastProteinResults object at 0x16d75a9d0>  
  
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->  
  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 285, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/blastprotein/ui/results.py", line 157, in take_snapshot  
, 'table_session': self.table.session_info()  
AttributeError: 'BlastProteinResults' object has no attribute 'table'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 290, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x126fb6220> ->
<chimerax.blastprotein.ui.results.BlastProteinResults object at 0x16d75a9d0>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 116, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 51, in display  
run(session, cmd)  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 90, in provider_save  
saver_info.save(session, path, **provider_kw)  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core_formats/__init__.py", line 84, in save  
return cxs_save(session, path, **kw)  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 899, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save  
mgr.discovery(self._state_containers)  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x126fb6220> -> <chimerax.blastprotein.ui.results.BlastProteinResults object
at 0x16d75a9d0>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x126fb6220> ->
<chimerax.blastprotein.ui.results.BlastProteinResults object at 0x16d75a9d0>  
  
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->  
  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  

> select clear

> save "/Users/diakinmeji-3/Documents/PROPOSALS/2023/14. PEPTAC cooperativity
> design/Figures/Figure 7/AF-CREPT_ligand-2.cxs"

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 285, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/blastprotein/ui/results.py", line 157, in take_snapshot  
, 'table_session': self.table.session_info()  
AttributeError: 'BlastProteinResults' object has no attribute 'table'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 290, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x126fb6220> ->
<chimerax.blastprotein.ui.results.BlastProteinResults object at 0x16d75a9d0>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 899, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save  
mgr.discovery(self._state_containers)  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x126fb6220> -> <chimerax.blastprotein.ui.results.BlastProteinResults object
at 0x16d75a9d0>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x126fb6220> ->
<chimerax.blastprotein.ui.results.BlastProteinResults object at 0x16d75a9d0>  
  
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->  
  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 285, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/blastprotein/ui/results.py", line 157, in take_snapshot  
, 'table_session': self.table.session_info()  
AttributeError: 'BlastProteinResults' object has no attribute 'table'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 290, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x126fb6220> ->
<chimerax.blastprotein.ui.results.BlastProteinResults object at 0x16d75a9d0>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/tool.py", line 165, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 386, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/__init__.py", line 1289, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/__init__.py", line 37, in run_provider  
providers.run_provider(session, name)  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/providers.py", line 45, in run_provider  
what(session)  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/providers.py", line 27, in _file_save  
show_save_file_dialog(session)  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 51, in display  
run(session, cmd)  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 90, in provider_save  
saver_info.save(session, path, **provider_kw)  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core_formats/__init__.py", line 84, in save  
return cxs_save(session, path, **kw)  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 899, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save  
mgr.discovery(self._state_containers)  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x126fb6220> -> <chimerax.blastprotein.ui.results.BlastProteinResults object
at 0x16d75a9d0>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x126fb6220> ->
<chimerax.blastprotein.ui.results.BlastProteinResults object at 0x16d75a9d0>  
  
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->  
  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  

> close

> open
> /Users/diakinmeji-3/Downloads/ChimeraX/AlphaFold/prediction_37/best_model.pdb
> format pdb

Chain information for best_model.pdb #1  
---  
Chain | Description  
A B | No description available  
C | No description available  
  

> close

> open
> /Users/diakinmeji-3/Downloads/ChimeraX/AlphaFold/prediction_37/best_model.pdb

Chain information for best_model.pdb #1  
---  
Chain | Description  
A B | No description available  
C | No description available  
  

> alphafold pae #1 file
> /Users/diakinmeji-3/Downloads/ChimeraX/AlphaFold/prediction_37/best_model_pae.json

> color bfactor #1 palette alphafold

2523 atoms, 321 residues, atom bfactor range 26 to 98.5  

> save "/Users/diakinmeji-3/Documents/PROPOSALS/2023/14. PEPTAC cooperativity
> design/Figures/Figure 7/AF-CREPT_ligand-2.cxs"

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 285, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/blastprotein/ui/results.py", line 157, in take_snapshot  
, 'table_session': self.table.session_info()  
AttributeError: 'BlastProteinResults' object has no attribute 'table'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 290, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x126fb6220> ->
<chimerax.blastprotein.ui.results.BlastProteinResults object at 0x16d75a9d0>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 899, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save  
mgr.discovery(self._state_containers)  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x126fb6220> -> <chimerax.blastprotein.ui.results.BlastProteinResults object
at 0x16d75a9d0>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x126fb6220> ->
<chimerax.blastprotein.ui.results.BlastProteinResults object at 0x16d75a9d0>  
  
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->  
  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 285, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/blastprotein/ui/results.py", line 157, in take_snapshot  
, 'table_session': self.table.session_info()  
AttributeError: 'BlastProteinResults' object has no attribute 'table'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 290, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x126fb6220> ->
<chimerax.blastprotein.ui.results.BlastProteinResults object at 0x16d75a9d0>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 116, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 51, in display  
run(session, cmd)  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 90, in provider_save  
saver_info.save(session, path, **provider_kw)  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core_formats/__init__.py", line 84, in save  
return cxs_save(session, path, **kw)  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 899, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save  
mgr.discovery(self._state_containers)  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x126fb6220> -> <chimerax.blastprotein.ui.results.BlastProteinResults object
at 0x16d75a9d0>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x126fb6220> ->
<chimerax.blastprotein.ui.results.BlastProteinResults object at 0x16d75a9d0>  
  
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->  
  
File
"/Applications/ChimeraX-1.6-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,3
      Chip: Apple M1 Pro
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 16 GB
      System Firmware Version: 8422.121.1
      OS Loader Version: 7459.141.1

Software:

    System Software Overview:

      System Version: macOS 12.6.6 (21G646)
      Kernel Version: Darwin 21.6.0
      Time since boot: 2 days 10:04

Graphics/Displays:

    Apple M1 Pro:

      Chipset Model: Apple M1 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 16
      Vendor: Apple (0x106b)
      Metal Family: Supported, Metal GPUFamily Apple 7
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3024 x 1964 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        LG ULTRAFINE:
          Resolution: 4608 x 2592
          UI Looks like: 2304 x 1296 @ 60.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported


Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    appnope: 0.1.3
    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: 2021.10.8
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9.1
    ChimeraX-AddH: 2.2.4
    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: 1.6rc202304252053
    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-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
    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: 2022.2.22
    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: 21.3
    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
    setuptools: 67.4.0
    setuptools-scm: 7.0.5
    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 Eric Pettersen, 2 years ago

Component:	Unassigned → Sequence
Owner:	set to Zach Pearson
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → Blast: self.job.model_name is None

comment:2 by Eric Pettersen, 2 years ago

Resolution:	→ duplicate
Status:	assigned → closed

Duplicate of #9070

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