XMAS session restore: 'NoneType' object has no attribute 'invisibleRootItem'

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19045
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open "N:/Collaborator/20220429_Osnabruck/Paper on crosslinked
> vacuoles/Revision/Materials/7ZU0.cxs"

Log from Wed Nov 15 16:09:08 2023UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open "N:\Collaborator\20220429_Osnabruck\Original
> data\20230322new_results\Structure mapping\7ZU0_structure_mapping.cxs"
> format session

Log from Thu Mar 23 12:49:09 2023 Startup Messages  
---  
warning | Your computer has Intel graphics driver 8190 with a known bug that
causes all Qt user interface panels to be blank. ChimeraX can partially fix
this but may make some panel titlebars and edges black. Hopefully newer Intel
graphics drivers will fix this.  
  
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> ui tool show XMAS

> open "N:/Collaborator/20220429_Osnabruck/Original
> data/20230322new_results/Structure mapping/5dfz.pdb"

5dfz.pdb title:  
Structure of VPS34 complex II from S. Cerevisiae. [more info...]  
  
Chain information for 5dfz.pdb #1  
---  
Chain | Description | UniProt  
A | vacuolar protein sorting-associated protein 38 | VPS38_YEAST  
B | serine/threonine-protein kinase VPS15 | VPS15_YEAST  
C | phosphatidylinositol 3-kinase VPS34 | VPS34_YEAST  
D | autophagy-related protein 6 | BECN1_YEAST  
E | nanobody binding S. cerevisiae VPS34 |  
G | putative N-terminal domain of S. cerevisiae VPS30 |  
  

> show cartoons

> hide atoms

[Repeated 1 time(s)]  
Peptide pair mapping of XlinkX evidence file:
N:/Collaborator/20220429_Osnabruck/Original data/20230322new_results/Structure
mapping/SS_unique_lys_crosslink_targetonly_2FDR_for_ChimeraX.csv  
Unique peptide pairs: 16694 out of 16694  
Unique peptide pairs with pseudobonds: 26  
Pseudobonds are stored in N:/Collaborator/20220429_Osnabruck/Original
data/20230322new_results/Structure
mapping/SS_unique_lys_crosslink_targetonly_2FDR_for_ChimeraX_1.pb  
Mapping information is stored in N:/Collaborator/20220429_Osnabruck/Original
data/20230322new_results/Structure
mapping/SS_unique_lys_crosslink_targetonly_2FDR_for_ChimeraX_1.tsv  

> hide #1.1 models

> show #1.1 models

> hide #1.1 models

> show #1.1 models

> hide #1.1 models

> show #1.1 models

> hide #1.1 models

> Command: split #1 chains

Unknown command: Command: split #1 chains  

> split #1 chains

Split 5dfz.pdb (#1) into 6 models  
Chain information for 5dfz.pdb A #1.1  
---  
Chain | Description  
A | No description available  
  
Chain information for 5dfz.pdb B #1.2  
---  
Chain | Description  
B | No description available  
  
Chain information for 5dfz.pdb C #1.3  
---  
Chain | Description  
C | No description available  
  
Chain information for 5dfz.pdb D #1.4  
---  
Chain | Description  
D | No description available  
  
Chain information for 5dfz.pdb E #1.5  
---  
Chain | Description  
E | No description available  
  
Chain information for 5dfz.pdb G #1.6  
---  
Chain | Description  
G | No description available  
  

> hide #1.6 models

> show #1.6 models

> hide #1.6 models

> show #1.6 models

> color #1 #aaaaff models transparency 0

> hide #1.6 models

> show #1.6 models

> hide #1.6 models

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> color #2 red models transparency 0

  
Peptide pair mapping of XlinkX evidence file:
N:/Collaborator/20220429_Osnabruck/Original data/20230322new_results/Structure
mapping/SS_unique_lys_crosslink_targetonly_2FDR_for_ChimeraX.csv  
Unique peptide pairs: 16694 out of 16694  
Unique peptide pairs with pseudobonds: 26  
Pseudobonds are stored in N:/Collaborator/20220429_Osnabruck/Original
data/20230322new_results/Structure
mapping/SS_unique_lys_crosslink_targetonly_2FDR_for_ChimeraX_1.1,1.2,1.3,1.4,1.5,1.6.pb  
Mapping information is stored in N:/Collaborator/20220429_Osnabruck/Original
data/20230322new_results/Structure
mapping/SS_unique_lys_crosslink_targetonly_2FDR_for_ChimeraX_1.1,1.2,1.3,1.4,1.5,1.6.tsv  

> hide #2 models

> ~select #2

Nothing selected  

> select #2

Nothing selected  

> hide target m

> show target m

> hide #2 models

> ~select #2

Nothing selected  

> hide #1.6 models

> show #1.6 models

> hide #1.6 models

> show #1.6 models

> hide #1.6 models

> show #1.6 models

> hide #!1.1 models

> show #!1.1 models

> hide #1.5 models

> show #1.5 models

> hide #1.5 models

> show #1.5 models

> hide #1.5 models

> hide #1.6 models

> show #1.6 models

> hide #1.6 models

> color #3 red models transparency 0

> select #3

26 pseudobonds, 1 model selected  

> ~select #3

Nothing selected  

> set bgColor white

> save "N:/Collaborator/20220429_Osnabruck/Original
> data/20230322new_results/Structure mapping/5dfz.cxs"

> close session

> open "N:/Collaborator/20220429_Osnabruck/Original
> data/20230322new_results/Structure mapping/6jwp.pdb"

6jwp.pdb title:  
Crystal structure of egoc [more info...]  
  
Chain information for 6jwp.pdb #1  
---  
Chain | Description | UniProt  
A | GTP-binding protein GTR1 | GTR1_YEAST  
B | GTP-binding protein GTR2 | GTR2_YEAST  
C | protein MEH1 | MEH1_YEAST  
D | EGO2 | YC075_YEAST  
E | protein SLM4 | SLM4_YEAST  
F | GTP-binding protein GTR1 | GTR1_YEAST  
G | GTP-binding protein GTR2 | GTR2_YEAST  
H | protein MEH1 | MEH1_YEAST  
I | EGO2 | YC075_YEAST  
J | protein SLM4 | SLM4_YEAST  
  
Non-standard residues in 6jwp.pdb #1  
---  
GNP — phosphoaminophosphonic acid-guanylate ester  
MG — magnesium ion  
  

> show cartoons

> hide atoms

> split #1 chains

Split 6jwp.pdb (#1) into 10 models  
Chain information for 6jwp.pdb A #1.1  
---  
Chain | Description  
A | No description available  
  
Chain information for 6jwp.pdb B #1.2  
---  
Chain | Description  
B | No description available  
  
Chain information for 6jwp.pdb C #1.3  
---  
Chain | Description  
C | No description available  
  
Chain information for 6jwp.pdb D #1.4  
---  
Chain | Description  
D | No description available  
  
Chain information for 6jwp.pdb E #1.5  
---  
Chain | Description  
E | No description available  
  
Chain information for 6jwp.pdb F #1.6  
---  
Chain | Description  
F | No description available  
  
Chain information for 6jwp.pdb G #1.7  
---  
Chain | Description  
G | No description available  
  
Chain information for 6jwp.pdb H #1.8  
---  
Chain | Description  
H | No description available  
  
Chain information for 6jwp.pdb I #1.9  
---  
Chain | Description  
I | No description available  
  
Chain information for 6jwp.pdb J #1.10  
---  
Chain | Description  
J | No description available  
  

> color #1 #aaaaff models transparency 0

> color #1.4 black transparency 0

> color #1.4 #cccccc transparency 0

> color #1.9 #cccccc transparency 0

> color #1.3 #cccccc transparency 0

> color #1.8 #cccccc transparency 0

> save "N:/Collaborator/20220429_Osnabruck/Original
> data/20230322new_results/Structure mapping/6jwp_structure_mapping.cxs"

  
Peptide pair mapping of XlinkX evidence file:
N:/Collaborator/20220429_Osnabruck/Original data/20230322new_results/Structure
mapping/SS_unique_lys_crosslink_targetonly_2FDR_for_ChimeraX.csv  
Unique peptide pairs: 16694 out of 16694  
Unique peptide pairs with pseudobonds: 3  
Pseudobonds are stored in N:/Collaborator/20220429_Osnabruck/Original
data/20230322new_results/Structure
mapping/SS_unique_lys_crosslink_targetonly_2FDR_for_ChimeraX_1.1,1.2,1.3,1.4,1.5,1.6,1.7,1.8,1.9,1.10.pb  
Mapping information is stored in N:/Collaborator/20220429_Osnabruck/Original
data/20230322new_results/Structure
mapping/SS_unique_lys_crosslink_targetonly_2FDR_for_ChimeraX_1.1,1.2,1.3,1.4,1.5,1.6,1.7,1.8,1.9,1.10.tsv  
Please select pseudobonds  
Distances updated in N:/Collaborator/20220429_Osnabruck/Original
data/20230322new_results/Structure
mapping/SS_unique_lys_crosslink_targetonly_2FDR_for_ChimeraX_1.1,1.2,1.3,1.4,1.5,1.6,1.7,1.8,1.9,1.10.tsv  

> hide #2 models

> hide #3 models

> show #3 models

> color #3 red models transparency 0

Pseudobonds are stored in N:/Collaborator/20220429_Osnabruck/Original
data/20230322new_results/Structure mapping/1.pb  
Opened Pseudobonds 1.pb, 6 bonds  

> hide #3 models

> show #3 models

> ~select #3

Nothing selected  

> hide #4 models

> save "N:/Collaborator/20220429_Osnabruck/Original
> data/20230322new_results/Structure mapping/6jwp_structure_mapping.cxs"

[Repeated 1 time(s)]

> close session

> open "N:/Collaborator/20220429_Osnabruck/Original
> data/20230322new_results/Structure mapping/7p3y.pdb"

7p3y.pdb title:  
Homology model of the full-length ap-3 complex In an intermediate open
conformation [more info...]  
  
Chain information for 7p3y.pdb #1  
---  
Chain | Description | UniProt  
A | ap-3 complex subunit δ |  
B | Y55_G0035830.MRNA.1.CDS.1 |  
M | ap-3 complex subunit μ | AP3M_YEAST  
S | ap complex subunit σ |  
  

> split #1 chains

Split 7p3y.pdb (#1) into 4 models  
Chain information for 7p3y.pdb A #1.1  
---  
Chain | Description  
A | No description available  
  
Chain information for 7p3y.pdb B #1.2  
---  
Chain | Description  
B | No description available  
  
Chain information for 7p3y.pdb M #1.3  
---  
Chain | Description  
M | No description available  
  
Chain information for 7p3y.pdb S #1.4  
---  
Chain | Description  
S | No description available  
  

> color #1 #aaaaff models transparency 0

  
Peptide pair mapping of XlinkX evidence file:
N:/Collaborator/20220429_Osnabruck/Original data/20230322new_results/Structure
mapping/SS_unique_lys_crosslink_targetonly_2FDR_for_ChimeraX.csv  
Unique peptide pairs: 16694 out of 16694  
Unique peptide pairs with pseudobonds: 5  
Pseudobonds are stored in N:/Collaborator/20220429_Osnabruck/Original
data/20230322new_results/Structure
mapping/SS_unique_lys_crosslink_targetonly_2FDR_for_ChimeraX_1.1,1.2,1.3,1.4.pb  
Mapping information is stored in N:/Collaborator/20220429_Osnabruck/Original
data/20230322new_results/Structure
mapping/SS_unique_lys_crosslink_targetonly_2FDR_for_ChimeraX_1.1,1.2,1.3,1.4.tsv  

> color #2 red models transparency 0

> save "N:/Collaborator/20220429_Osnabruck/Original
> data/20230322new_results/Structure mapping/7p3y_structure_mapping.cxs"

> close session

> open "N:/Collaborator/20220429_Osnabruck/Original
> data/20230322new_results/Structure mapping/7pqh.cif"

7pqh.cif title:  
Cryo-EM structure of Saccharomyces cerevisiae TOROID (TORC1 Organized in
Inhibited Domains). [more info...]  
  
Chain information for 7pqh.cif #1  
---  
Chain | Description | UniProt  
A B G J | Target of rapamycin complex 1 subunit KOG1,Target of rapamycin
complex 1 subunit Kog1 | KOG1_YEAST  
C D I L | Target of rapamycin complex subunit LST8 | LST8_YEAST  
E F H K | Serine/threonine-protein kinase TOR2 | TOR2_YEAST  
  

> show cartoons

> hide atoms

> split #1 chains

Split 7pqh.cif (#1) into 12 models  
Chain information for 7pqh.cif A #1.1  
---  
Chain | Description  
A | No description available  
  
Chain information for 7pqh.cif B #1.2  
---  
Chain | Description  
B | No description available  
  
Chain information for 7pqh.cif C #1.3  
---  
Chain | Description  
C | No description available  
  
Chain information for 7pqh.cif D #1.4  
---  
Chain | Description  
D | No description available  
  
Chain information for 7pqh.cif E #1.5  
---  
Chain | Description  
E | No description available  
  
Chain information for 7pqh.cif F #1.6  
---  
Chain | Description  
F | No description available  
  
Chain information for 7pqh.cif G #1.7  
---  
Chain | Description  
G | No description available  
  
Chain information for 7pqh.cif H #1.8  
---  
Chain | Description  
H | No description available  
  
Chain information for 7pqh.cif I #1.9  
---  
Chain | Description  
I | No description available  
  
Chain information for 7pqh.cif J #1.10  
---  
Chain | Description  
J | No description available  
  
Chain information for 7pqh.cif K #1.11  
---  
Chain | Description  
K | No description available  
  
Chain information for 7pqh.cif L #1.12  
---  
Chain | Description  
L | No description available  
  

> color #1 #aaaaff models transparency 0

> color #1.5 #cccccc transparency 0

> color #1.6 #cccccc transparency 0

> color #1.8 #cccccc transparency 0

> color #1.11 #cccccc transparency 0

> select #1.5

17910 atoms, 18271 bonds, 8 pseudobonds, 2238 residues, 2 models selected  

> ~select #1.5

Nothing selected  

> select #1.6

17904 atoms, 18265 bonds, 8 pseudobonds, 2238 residues, 2 models selected  

> ~select #1.6

Nothing selected  

> select #1.10

9711 atoms, 9930 bonds, 9 pseudobonds, 1213 residues, 2 models selected  

> ~select #1.10

Nothing selected  

> select #1.10

9711 atoms, 9930 bonds, 9 pseudobonds, 1213 residues, 2 models selected  

> ~select #1.10

Nothing selected  

> select #1.8

9299 atoms, 9509 bonds, 4 pseudobonds, 1157 residues, 2 models selected  

> ~select #1.8

Nothing selected  

> select #1.11

9299 atoms, 9509 bonds, 4 pseudobonds, 1157 residues, 2 models selected  

> ~select #1.11

Nothing selected  

> save "N:/Collaborator/20220429_Osnabruck/Original
> data/20230322new_results/Structure mapping/7pqh_structure_mapping.cxs"

  
Peptide pair mapping of XlinkX evidence file:
N:/Collaborator/20220429_Osnabruck/Original data/20230322new_results/Structure
mapping/SS_unique_lys_crosslink_targetonly_2FDR_for_ChimeraX.csv  
Unique peptide pairs: 16694 out of 16694  
Unique peptide pairs with pseudobonds: 6  
Pseudobonds are stored in N:/Collaborator/20220429_Osnabruck/Original
data/20230322new_results/Structure
mapping/SS_unique_lys_crosslink_targetonly_2FDR_for_ChimeraX_1.1,1.2,1.3,1.4,1.5,1.6,1.7,1.8,1.9,1.10,1.11,1.12.pb  
Mapping information is stored in N:/Collaborator/20220429_Osnabruck/Original
data/20230322new_results/Structure
mapping/SS_unique_lys_crosslink_targetonly_2FDR_for_ChimeraX_1.1,1.2,1.3,1.4,1.5,1.6,1.7,1.8,1.9,1.10,1.11,1.12.tsv  

> hide #2 models

> ~select #2

22 pseudobonds, 1 model selected  

> hide #3 models

> show #3 models

> show #2 models

> hide #2 models

> color #3 red models transparency 0

> ~select #3

Nothing selected  

> select #1.1

9693 atoms, 9912 bonds, 17 pseudobonds, 1209 residues, 4 models selected  

> select #1.3

2366 atoms, 2422 bonds, 300 residues, 1 model selected  

> select #1.2

9686 atoms, 9905 bonds, 17 pseudobonds, 1208 residues, 4 models selected  

> ~select #1.2

Nothing selected  

> select #1.2

9686 atoms, 9905 bonds, 17 pseudobonds, 1208 residues, 4 models selected  

> ~select #1.2

Nothing selected  

> close session

> open "N:/Collaborator/20220429_Osnabruck/Original
> data/20230322new_results/Structure mapping/7ytj.pdb"

7ytj.pdb title:  
Cryo-em structure of VTC complex [more info...]  
  
Chain information for 7ytj.pdb #1  
---  
Chain | Description | UniProt  
A | vacuolar transporter chaperone 1 | VTC1_YEAST  
B C | vacuolar transporter chaperone 1 | VTC1_YEAST  
D | phosphate metabolism protein 3 | VTC4_YEAST  
E | phosphate metabolism protein 2 | VTC3_YEAST  
  
Non-standard residues in 7ytj.pdb #1  
---  
IHP — inositol hexakisphosphate (myo-inositol hexakisphosphate; inositol
1,2,3,4,5,6-hexakisphosphate)  
PC1 — 1,2-diacyl-Sn-glycero-3-phosphocholine (3-Sn-phosphatidylcholine)  
PO4 — phosphate ion  
  

> show cartoons

> hide atoms

> split #1 chains

Split 7ytj.pdb (#1) into 5 models  
Chain information for 7ytj.pdb A #1.1  
---  
Chain | Description  
A | No description available  
  
Chain information for 7ytj.pdb B #1.2  
---  
Chain | Description  
B | No description available  
  
Chain information for 7ytj.pdb C #1.3  
---  
Chain | Description  
C | No description available  
  
Chain information for 7ytj.pdb D #1.4  
---  
Chain | Description  
D | No description available  
  
Chain information for 7ytj.pdb E #1.5  
---  
Chain | Description  
E | No description available  
  

> color #1 #aaaaff models transparency 0

> save "N:/Collaborator/20220429_Osnabruck/Original
> data/20230322new_results/Structure mapping/7ytj_structure_mapping.cxs"

  
Peptide pair mapping of XlinkX evidence file:
N:/Collaborator/20220429_Osnabruck/Original data/20230322new_results/Structure
mapping/SS_unique_lys_crosslink_targetonly_2FDR_for_ChimeraX.csv  
Unique peptide pairs: 16694 out of 16694  
Unique peptide pairs with pseudobonds: 82  
Pseudobonds are stored in N:/Collaborator/20220429_Osnabruck/Original
data/20230322new_results/Structure
mapping/SS_unique_lys_crosslink_targetonly_2FDR_for_ChimeraX_1.1,1.2,1.3,1.4,1.5.pb  
Mapping information is stored in N:/Collaborator/20220429_Osnabruck/Original
data/20230322new_results/Structure
mapping/SS_unique_lys_crosslink_targetonly_2FDR_for_ChimeraX_1.1,1.2,1.3,1.4,1.5.tsv  
Distances updated in N:/Collaborator/20220429_Osnabruck/Original
data/20230322new_results/Structure
mapping/SS_unique_lys_crosslink_targetonly_2FDR_for_ChimeraX_1.1,1.2,1.3,1.4,1.5.tsv  

> hide #2 models

> show #2 models

> hide #2 models

> hide #3 models

> show #3 models

> show #2 models

> hide #2 models

> show #2 models

> hide #3 models

> show #3 models

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> color #3 red models transparency 0

> hide #2 models

> save "N:/Collaborator/20220429_Osnabruck/Original
> data/20230322new_results/Structure mapping/7ytj_structure_mapping.cxs"

> save "N:/Collaborator/20220429_Osnabruck/Original
> data/20230322new_results/Structure mapping/7ytj.gif" width 1434 height 1145
> supersample 3

> close session

> open "N:/Collaborator/20220429_Osnabruck/Original
> data/20230322new_results/Structure mapping/8adl.pdb"

8adl.pdb title:  
Cryo-em structure of the sea complex [more info...]  
  
Chain information for 8adl.pdb #1  
---  
Chain | Description  
A I | restriction of telomere capping protein 1  
B J | SEA4 isoform 1  
C Q | MTC5 isoform 1  
D L | SEH1 isoform 1  
E M | SEH1 isoform 1  
F N | SEH1 isoform 1  
G O | SEA4 isoform 1  
H P | SEC13 isoform 1  
S T | NPR2 isoform 1  
U V | required FOR meiotic nuclear division protein 11  
W X | vacuolar membrane-associated protein IML1  
  
Non-standard residues in 8adl.pdb #1  
---  
ZN — zinc ion  
  

> show cartoons

> hide atoms

[Repeated 1 time(s)]

> split #1 chains

Split 8adl.pdb (#1) into 22 models  
Chain information for 8adl.pdb A #1.1  
---  
Chain | Description  
A | No description available  
  
Chain information for 8adl.pdb B #1.2  
---  
Chain | Description  
B | No description available  
  
Chain information for 8adl.pdb C #1.3  
---  
Chain | Description  
C | No description available  
  
Chain information for 8adl.pdb D #1.4  
---  
Chain | Description  
D | No description available  
  
Chain information for 8adl.pdb E #1.5  
---  
Chain | Description  
E | No description available  
  
Chain information for 8adl.pdb F #1.6  
---  
Chain | Description  
F | No description available  
  
Chain information for 8adl.pdb G #1.7  
---  
Chain | Description  
G | No description available  
  
Chain information for 8adl.pdb H #1.8  
---  
Chain | Description  
H | No description available  
  
Chain information for 8adl.pdb I #1.9  
---  
Chain | Description  
I | No description available  
  
Chain information for 8adl.pdb J #1.10  
---  
Chain | Description  
J | No description available  
  
Chain information for 8adl.pdb L #1.11  
---  
Chain | Description  
L | No description available  
  
Chain information for 8adl.pdb M #1.12  
---  
Chain | Description  
M | No description available  
  
Chain information for 8adl.pdb N #1.13  
---  
Chain | Description  
N | No description available  
  
Chain information for 8adl.pdb O #1.14  
---  
Chain | Description  
O | No description available  
  
Chain information for 8adl.pdb P #1.15  
---  
Chain | Description  
P | No description available  
  
Chain information for 8adl.pdb Q #1.16  
---  
Chain | Description  
Q | No description available  
  
Chain information for 8adl.pdb S #1.17  
---  
Chain | Description  
S | No description available  
  
Chain information for 8adl.pdb T #1.18  
---  
Chain | Description  
T | No description available  
  
Chain information for 8adl.pdb U #1.19  
---  
Chain | Description  
U | No description available  
  
Chain information for 8adl.pdb V #1.20  
---  
Chain | Description  
V | No description available  
  
Chain information for 8adl.pdb W #1.21  
---  
Chain | Description  
W | No description available  
  
Chain information for 8adl.pdb X #1.22  
---  
Chain | Description  
X | No description available  
  

> color #1 #aaaaff models transparency 0

  
Peptide pair mapping of XlinkX evidence file:
N:/Collaborator/20220429_Osnabruck/Original data/20230322new_results/Structure
mapping/SS_unique_lys_crosslink_targetonly_2FDR_for_ChimeraX.csv  
Unique peptide pairs: 16694 out of 16694  
Unique peptide pairs with pseudobonds: 17  
Pseudobonds are stored in N:/Collaborator/20220429_Osnabruck/Original
data/20230322new_results/Structure
mapping/SS_unique_lys_crosslink_targetonly_2FDR_for_ChimeraX_1.1,1.2,1.3,1.4,1.5,1.6,1.7,1.8,1.9,1.10,1.11,1.12,1.13,1.14,1.15,1.16,1.17,1.18,1.19,1.20,1.21,1.22.pb  
Mapping information is stored in N:/Collaborator/20220429_Osnabruck/Original
data/20230322new_results/Structure
mapping/SS_unique_lys_crosslink_targetonly_2FDR_for_ChimeraX_1.1,1.2,1.3,1.4,1.5,1.6,1.7,1.8,1.9,1.10,1.11,1.12,1.13,1.14,1.15,1.16,1.17,1.18,1.19,1.20,1.21,1.22.tsv  

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

Distances updated in N:/Collaborator/20220429_Osnabruck/Original
data/20230322new_results/Structure
mapping/SS_unique_lys_crosslink_targetonly_2FDR_for_ChimeraX_1.1,1.2,1.3,1.4,1.5,1.6,1.7,1.8,1.9,1.10,1.11,1.12,1.13,1.14,1.15,1.16,1.17,1.18,1.19,1.20,1.21,1.22.tsv  

> hide #2 models

> color #3 red models transparency 0

> save "N:/Collaborator/20220429_Osnabruck/Original
> data/20230322new_results/Structure mapping/8adl_structure_mapping.cxs"

[Repeated 1 time(s)]

> save "N:/Collaborator/20220429_Osnabruck/Original
> data/20230322new_results/Structure mapping/8adl.gif" width 1434 height 1145
> supersample 3

> close session

> open "N:/Collaborator/20220429_Osnabruck/Original
> data/20230322new_results/Structure mapping/HOPS_DS_CU.pdb"

Chain information for HOPS_DS_CU.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
  

> show cartoons

> hide atoms

> split #1 chains

Split HOPS_DS_CU.pdb (#1) into 6 models  
Chain information for HOPS_DS_CU.pdb A #1.1  
---  
Chain | Description  
A | No description available  
  
Chain information for HOPS_DS_CU.pdb B #1.2  
---  
Chain | Description  
B | No description available  
  
Chain information for HOPS_DS_CU.pdb C #1.3  
---  
Chain | Description  
C | No description available  
  
Chain information for HOPS_DS_CU.pdb D #1.4  
---  
Chain | Description  
D | No description available  
  
Chain information for HOPS_DS_CU.pdb E #1.5  
---  
Chain | Description  
E | No description available  
  
Chain information for HOPS_DS_CU.pdb F #1.6  
---  
Chain | Description  
F | No description available  
  

> color #1 #aaaaff models transparency 0

  
Peptide pair mapping of XlinkX evidence file:
N:/Collaborator/20220429_Osnabruck/Original data/20230322new_results/Structure
mapping/SS_unique_lys_crosslink_targetonly_2FDR_for_ChimeraX.csv  
Unique peptide pairs: 16694 out of 16694  
Unique peptide pairs with pseudobonds: 20  
Pseudobonds are stored in N:/Collaborator/20220429_Osnabruck/Original
data/20230322new_results/Structure
mapping/SS_unique_lys_crosslink_targetonly_2FDR_for_ChimeraX_1.1,1.2,1.3,1.4,1.5,1.6.pb  
Mapping information is stored in N:/Collaborator/20220429_Osnabruck/Original
data/20230322new_results/Structure
mapping/SS_unique_lys_crosslink_targetonly_2FDR_for_ChimeraX_1.1,1.2,1.3,1.4,1.5,1.6.tsv  

> color #2 red models transparency 0

> save "N:/Collaborator/20220429_Osnabruck/Original
> data/20230322new_results/Structure mapping/7ZU0_structure_mapping.cxs"

——— End of log from Thu Mar 23 12:49:09 2023 ———

opened ChimeraX session  

> color #1.1 #9faaff transparency 0

> color #1.1 #9fa1a3 transparency 0

> hide #!1.1 models

> show #!1.1 models

> hide #!1.1 models

> show #!1.1 models

> hide #!1.2 models

> show #!1.2 models

> color #1.2 #62aaff transparency 0

> color #1.2 #626166 transparency 0

> hide #!1.3 models

> show #!1.3 models

> color #1.3 #0942be transparency 0

> hide #!1.4 models

> show #!1.4 models

> color #1.4 #0d3998 transparency 0

> hide #!1.5 models

> show #!1.5 models

> color #1.5 #04aaff transparency 0

> color #1.5 #0eaaff transparency 0

> color #1.5 #0e89be transparency 0

> color #1.6 #0daaff transparency 0

> color #1.6 #0d3998 transparency 0

> color #1.6 #073998 transparency 0

> color #1.6 #07bdff transparency 0

> color #1.5 #0789be transparency 0

> color #1.5 #07bdbe transparency 0

> color #1.5 #07bdff transparency 0

> color #1.6 #0e89be transparency 0

> lighting full

> ~select #2

Nothing selected  

> save C:/ProgramData/ChimeraX/7ZU0.cxs

> save "N:/Collaborator/20220429_Osnabruck/Paper on crosslinked
> vacuoles/Revision/7ZU0.gif" width 2400 height 3590 supersample 3

> save "N:/Collaborator/20220429_Osnabruck/Paper on crosslinked
> vacuoles/Revision/ZZU0.cxs"

> save "N:/Collaborator/20220429_Osnabruck/Paper on crosslinked
> vacuoles/Revision/7ZU0.gif" width 2400 height 3590 supersample 3

> save "N:/Collaborator/20220429_Osnabruck/Paper on crosslinked
> vacuoles/Revision/7ZU0.cxs"

——— End of log from Wed Nov 15 16:09:08 2023 ———

opened ChimeraX session  

> lighting full

> lighting soft

> lighting simple

> transparency #0.5

Missing or invalid "percent" argument: Expected a number  

> graphics silhouettes true

> lighting shadows true

> lighting flat

> lighting full

> lighting soft

> lighting simple

[Repeated 1 time(s)]

> open "N:/Collaborator/20220429_Osnabruck/Paper on crosslinked
> vacuoles/Revision/Materials/7ZU0.cxs"

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Users\zhu.ying\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\tool.py", line 158, in model_handler  
self.remove_models(trigger_data)  
File "C:\Users\zhu.ying\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\tool.py", line 231, in remove_models  
root = treewidget.invisibleRootItem()  
AttributeError: 'NoneType' object has no attribute 'invisibleRootItem'  
  
Error processing trigger "remove models":  
AttributeError: 'NoneType' object has no attribute 'invisibleRootItem'  
  
File "C:\Users\zhu.ying\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\tool.py", line 231, in remove_models  
root = treewidget.invisibleRootItem()  
  
See log for complete Python traceback.  
  
Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 691, in restore  
self.reset()  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\session.py", line 535, in reset  
sm.reset_state(container, self)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\atomic\molobject.py", line 588, in reset_state  
for pbg in list(self.group_map.values()):  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\attributes.py", line 57, in _getattr_  
return look_in_class._attr_registration.get_attr(attr_name)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\attributes.py", line 83, in get_attr  
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None  
AttributeError: Execution of 'PseudobondManager' object's 'group_map' property
raised AttributeError  
  
opened ChimeraX session  




OpenGL version: 3.3.0 - Build 27.20.100.8190
OpenGL renderer: Intel(R) UHD Graphics 630
OpenGL vendor: Intel
Manufacturer: Dell Inc.
Model: OptiPlex 5060
OS: Microsoft Windows 10 Pro (Build 19045)
Memory: 16,966,172,672
MaxProcessMemory: 137,438,953,344
CPU: 6 Intel(R) Core(TM) i5-8600 CPU @ 3.10GHz
OSLanguage: en-US
Locale: ('en_US', 'cp1252')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.10.8
    cftime: 1.5.1.1
    charset-normalizer: 2.0.9
    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.31
    ChimeraX-AtomicLibrary: 4.2
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    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: 2.2.2
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    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
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    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: 2.0.4
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    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-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    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-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.6
    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: 1.6.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.7
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    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: 1.0
    ChimeraX-XMAS: 1.1.2
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    comtypes: 1.1.10
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    docutils: 0.17.1
    et-xmlfile: 1.1.0
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.8.0
    numpy: 1.21.2
    openpyxl: 3.0.9
    openvr: 1.16.801
    packaging: 21.3
    pandas: 1.4.2
    ParmEd: 3.2.0
    parso: 0.8.3
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.23
    psutil: 5.8.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.6
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pywin32: 228
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.3
    QtRangeSlider: 0.1.5
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    seaborn: 0.11.2
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    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-jurko: 0.6
    tables: 3.6.1
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0
    WMI: 1.5.1