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:
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"
> close session
> open "N:/Collaborator/20220429_Osnabruck/Original
> data/20230322new_results/Structure mapping/7fda.pdb"
7fda.pdb title:
Cryoem structure of reconstituted V-atpase, STATE1 [more info...]
Chain information for 7fda.pdb #1
---
Chain | Description | UniProt
A C E | yeast vacuolar atpase A subunit |
B | V-atpase subunit B | VATB_YEAST
D | V-atpase subunit B | VATB_YEAST
F | V-atpase subunit B | VATB_YEAST
G I K | V-atpase subunit E | VATE_YEAST
H J L | V-type proton atpase subunit G |
M | V-atpase subunit D | VATD_YEAST
N | V-atpase subunit F | VATF_YEAST
O | V-atpase subunit C | VATC_YEAST
P | V-atpase subunit H | VATH_HUMAN
Q | yeast vacuolar atpase A subunit | VPH1_YEAST
S | V-atpase subunit D | VA0D_YEAST
T | V-atpase subunit C'' | VATO_YEAST
U | V-atpase subunit C' | VATL2_YEAST
V W X Z a c | V-atpase subunit C | VATL1_YEAST
Y b | V-atpase subunit C | VATL1_YEAST
d | V-atpase subunit E | VA0E_YEAST
e | V0 assembly protein 1 | VOA1_YEAST
f | yeast vacuolar atpase F subunit | YP17B_YEAST
> show cartoons
> hide atoms
> split #1 chains
Split 7fda.pdb (#1) into 31 models
Chain information for 7fda.pdb A #1.1
---
Chain | Description
A | No description available
Chain information for 7fda.pdb B #1.2
---
Chain | Description
B | No description available
Chain information for 7fda.pdb C #1.3
---
Chain | Description
C | No description available
Chain information for 7fda.pdb D #1.4
---
Chain | Description
D | No description available
Chain information for 7fda.pdb E #1.5
---
Chain | Description
E | No description available
Chain information for 7fda.pdb F #1.6
---
Chain | Description
F | No description available
Chain information for 7fda.pdb G #1.7
---
Chain | Description
G | No description available
Chain information for 7fda.pdb H #1.8
---
Chain | Description
H | No description available
Chain information for 7fda.pdb I #1.9
---
Chain | Description
I | No description available
Chain information for 7fda.pdb J #1.10
---
Chain | Description
J | No description available
Chain information for 7fda.pdb K #1.11
---
Chain | Description
K | No description available
Chain information for 7fda.pdb L #1.12
---
Chain | Description
L | No description available
Chain information for 7fda.pdb M #1.13
---
Chain | Description
M | No description available
Chain information for 7fda.pdb N #1.14
---
Chain | Description
N | No description available
Chain information for 7fda.pdb O #1.15
---
Chain | Description
O | No description available
Chain information for 7fda.pdb P #1.16
---
Chain | Description
P | No description available
Chain information for 7fda.pdb Q #1.17
---
Chain | Description
Q | No description available
Chain information for 7fda.pdb S #1.18
---
Chain | Description
S | No description available
Chain information for 7fda.pdb T #1.19
---
Chain | Description
T | No description available
Chain information for 7fda.pdb U #1.20
---
Chain | Description
U | No description available
Chain information for 7fda.pdb V #1.21
---
Chain | Description
V | No description available
Chain information for 7fda.pdb W #1.22
---
Chain | Description
W | No description available
Chain information for 7fda.pdb X #1.23
---
Chain | Description
X | No description available
Chain information for 7fda.pdb Y #1.24
---
Chain | Description
Y | No description available
Chain information for 7fda.pdb Z #1.25
---
Chain | Description
Z | No description available
Chain information for 7fda.pdb a #1.26
---
Chain | Description
a | No description available
Chain information for 7fda.pdb b #1.27
---
Chain | Description
b | No description available
Chain information for 7fda.pdb c #1.28
---
Chain | Description
c | No description available
Chain information for 7fda.pdb d #1.29
---
Chain | Description
d | No description available
Chain information for 7fda.pdb e #1.30
---
Chain | Description
e | No description available
Chain information for 7fda.pdb f #1.31
---
Chain | Description
f | No description available
> color #1 #aaaaff models transparency 0
> color #1.21 #cccccc transparency 0
> color #1.22 #cccccc transparency 0
> color #1.23 #cccccc transparency 0
> color #1.24 #cccccc transparency 0
> color #1.25 #cccccc transparency 0
> color #1.19 #cccccc transparency 0
> save "N:/Collaborator/20220429_Osnabruck/Original
> data/20230322new_results/Structure mapping/7fda_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: 238
Traceback (most recent call last):
File "C:\Users\zhu.ying\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\tool.py", line 286, in <lambda>
function = lambda _, s=selector, t=key: self.map_button_clicked(s,
File "C:\Users\zhu.ying\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\tool.py", line 444, in map_button_clicked
self.map_crosslinks(self.checked_models, checked_files)
File "C:\Users\zhu.ying\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\tool.py", line 527, in map_crosslinks
self.align_peptides(peptide_pairs, checked_models)
File "C:\Users\zhu.ying\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\tool.py", line 681, in align_peptides
self.create_pseudobonds(peptide_pairs)
File "C:\Users\zhu.ying\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\tool.py", line 745, in create_pseudobonds
self.create_files(pbonds, info_file_path)
File "C:\Users\zhu.ying\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\tool.py", line 758, in create_files
created_model = self.create_pseudobonds_model(pbonds,
File "C:\Users\zhu.ying\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\tool.py", line 838, in create_pseudobonds_model
self.write_file(file_path, group, file_type=".pb")
File "C:\Users\zhu.ying\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\tool.py", line 948, in write_file
created_file = open(file_path, "w")
FileNotFoundError: [Errno 2] No such file or directory:
'N:/Collaborator/20220429_Osnabruck/Original
data/20230322new_results/Structure
mapping/SS_unique_lys_crosslink_targetonly_2FDR_for_ChimeraX_1.1,1.2,1.3,1.4,1.5,1.6,1.7,1.8,1.9,1.10,1.11,1.12,1.13,1.14,1.15,1.16,1.17,1.18,1.19,1.20,1.21,1.22,1.23,1.24,1.25,1.26,1.27,1.28,1.29,1.30,1.31.pb'
FileNotFoundError: [Errno 2] No such file or directory:
'N:/Collaborator/20220429_Osnabruck/Original
data/20230322new_results/Structure
mapping/SS_unique_lys_crosslink_targetonly_2FDR_for_ChimeraX_1.1,1.2,1.3,1.4,1.5,1.6,1.7,1.8,1.9,1.10,1.11,1.12,1.13,1.14,1.15,1.16,1.17,1.18,1.19,1.20,1.21,1.22,1.23,1.24,1.25,1.26,1.27,1.28,1.29,1.30,1.31.pb'
File "C:\Users\zhu.ying\AppData\Local\UCSF\ChimeraX\1.3\site-
packages\chimerax\xmas\tool.py", line 948, in write_file
created_file = open(file_path, "w")
See log for complete Python traceback.
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
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Fixed with newest release of XMAS (1.1.3)