Error opening zero-length session file in DropBox

[lp212@…]

The following bug report has been submitted:
Platform:        macOS-13.5-arm64-arm-64bit
ChimeraX Version: 1.5.dev202210110346 (2022-10-11 03:46:09 UTC)
Description
Open session
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.5.dev202210110346 (2022-10-11)  
© 2016-2022 Regents of the University of California. All rights reserved.  

> open "/Users/lp212/Dropbox (Cambridge University)/GRANTS/ERG Synergy
> REPLITARG/research/Predictome structures/AND-1/Psf2.cxs"

Log from Wed Oct 11 12:40:04 2023UCSF ChimeraX version: 1.7.dev202306060017
(2023-06-06)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/Users/luca/Dropbox (Cambridge University)/GRANTS/ERG Synergy
> REPLITARG/Predictome structures/AND-1/Psf2.cxs"

Log from Mon Oct 9 16:37:25 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/Users/lp212/Dropbox (Cambridge University)/GRANTS/ERG Synergy
> REPLITARG/Predictome structures/AND-1/Psf2.cxs"

Log from Sun Oct 8 20:39:28 2023You can double click a model's Name or ID in
the model panel to edit those fields  
UCSF ChimeraX version: 1.4.dev202205042108 (2022-05-04)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/lp212/Downloads/DPOLA_HUMAN__WDHD1_HUMAN__2591aa_unrelaxed_af2mv3_model_1.pdb

Chain information for
DPOLA_HUMAN__WDHD1_HUMAN__2591aa_unrelaxed_af2mv3_model_1.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Users/lp212/Downloads/DPOLA_HUMAN__WDHD1_HUMAN__2591aa_unrelaxed_af2mv3_model_4.pdb

Chain information for
DPOLA_HUMAN__WDHD1_HUMAN__2591aa_unrelaxed_af2mv3_model_4.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Users/lp212/Downloads/DPOLA_HUMAN__WDHD1_HUMAN__2591aa_unrelaxed_af2mv3_model_2.pdb

Chain information for
DPOLA_HUMAN__WDHD1_HUMAN__2591aa_unrelaxed_af2mv3_model_2.pdb #3  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> ui tool show Matchmaker

> matchmaker #2-3 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker DPOLA_HUMAN__WDHD1_HUMAN__2591aa_unrelaxed_af2mv3_model_1.pdb,
chain A (#1) with
DPOLA_HUMAN__WDHD1_HUMAN__2591aa_unrelaxed_af2mv3_model_4.pdb, chain A (#2),
sequence alignment score = 7370.4  
RMSD between 976 pruned atom pairs is 0.405 angstroms; (across all 1462 pairs:
23.776)  
  
Matchmaker DPOLA_HUMAN__WDHD1_HUMAN__2591aa_unrelaxed_af2mv3_model_1.pdb,
chain A (#1) with
DPOLA_HUMAN__WDHD1_HUMAN__2591aa_unrelaxed_af2mv3_model_2.pdb, chain A (#3),
sequence alignment score = 7415.4  
RMSD between 869 pruned atom pairs is 0.264 angstroms; (across all 1462 pairs:
38.394)  
  
Drag select of 80 residues  

> select clear

> hide #3 models

> hide #2 models

> select #2/B

8844 atoms, 9023 bonds, 1129 residues, 1 model selected  

> select #1/A

11655 atoms, 11889 bonds, 1462 residues, 1 model selected  

> color sel orange red

> select #1/B

8844 atoms, 9023 bonds, 1129 residues, 1 model selected  

> color sel light sea green

> select clear

> show #2 models

> hide #1 models

> show #1 models

> hide #1 models

> select #2/A

11655 atoms, 11889 bonds, 1462 residues, 1 model selected  

> color sel orange red

> select clear

> select #2/B

8844 atoms, 9023 bonds, 1129 residues, 1 model selected  

> color sel light sea green

> select clear

> show #1 models

> hide #2 models

> show #2 models

> show #3 models

> hide #2 models

> hide #1 models

> select #3/A

11655 atoms, 11889 bonds, 1462 residues, 1 model selected  

> color sel orange red

> select clear

> select #3/B

8844 atoms, 9023 bonds, 1129 residues, 1 model selected  

> color sel light sea green

> select clear

> save "/Users/lp212/Dropbox (Cambridge University)/GRANTS/ERG Synergy
> REPLITARG/Predictome structures/AND-1/POLA1.cxs"

> close session

> open
> /Users/lp212/Downloads/DPOA2_HUMAN__WDHD1_HUMAN__1727aa_unrelaxed_af2mv3_model_1.pdb

Chain information for
DPOA2_HUMAN__WDHD1_HUMAN__1727aa_unrelaxed_af2mv3_model_1.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Users/lp212/Downloads/DPOA2_HUMAN__WDHD1_HUMAN__1727aa_unrelaxed_af2mv3_model_4.pdb

Chain information for
DPOA2_HUMAN__WDHD1_HUMAN__1727aa_unrelaxed_af2mv3_model_4.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Users/lp212/Downloads/DPOA2_HUMAN__WDHD1_HUMAN__1727aa_unrelaxed_af2mv3_model_2.pdb

Chain information for
DPOA2_HUMAN__WDHD1_HUMAN__1727aa_unrelaxed_af2mv3_model_2.pdb #3  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> ui tool show Matchmaker

> matchmaker #2-3 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker DPOA2_HUMAN__WDHD1_HUMAN__1727aa_unrelaxed_af2mv3_model_1.pdb,
chain B (#1) with
DPOA2_HUMAN__WDHD1_HUMAN__1727aa_unrelaxed_af2mv3_model_4.pdb, chain B (#2),
sequence alignment score = 5730.2  
RMSD between 413 pruned atom pairs is 0.467 angstroms; (across all 1129 pairs:
59.540)  
  
Matchmaker DPOA2_HUMAN__WDHD1_HUMAN__1727aa_unrelaxed_af2mv3_model_1.pdb,
chain B (#1) with
DPOA2_HUMAN__WDHD1_HUMAN__1727aa_unrelaxed_af2mv3_model_2.pdb, chain B (#3),
sequence alignment score = 5763.8  
RMSD between 115 pruned atom pairs is 0.318 angstroms; (across all 1129 pairs:
64.594)  
  

> hide #3 models

> hide #2 models

> select #1/A

4635 atoms, 4731 bonds, 598 residues, 1 model selected  

> select #1/A#2/A#3/A

13905 atoms, 14193 bonds, 1794 residues, 3 models selected  

> color (#1 & sel) cornflower blue

> select #1/A#2/A#3/A

13905 atoms, 14193 bonds, 1794 residues, 3 models selected  

> select #1/B#2/B#3/B

26532 atoms, 27069 bonds, 3387 residues, 3 models selected  

> color (#1 & sel) light sea green

> select clear

> show #2 models

> show #3 models

> hide #2 models

> hide #3 models

> show #2 models

> hide #2 models

> show #3 models

> select #1/A#2/A#3/A

13905 atoms, 14193 bonds, 1794 residues, 3 models selected  

> color (#1,3 & sel) cornflower blue

> select #3/B

8844 atoms, 9023 bonds, 1129 residues, 1 model selected  

> color sel light sea green

> select clear

> hide #1 models

> save "/Users/lp212/Dropbox (Cambridge University)/GRANTS/ERG Synergy
> REPLITARG/Predictome structures/AND-1/POLA2.cxs"

> close session

> open
> /Users/lp212/Downloads/PSF2_HUMAN__WDHD1_HUMAN__1314aa_unrelaxed_af2mv3_model_1.pdb

Chain information for
PSF2_HUMAN__WDHD1_HUMAN__1314aa_unrelaxed_af2mv3_model_1.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Users/lp212/Downloads/PSF2_HUMAN__WDHD1_HUMAN__1314aa_unrelaxed_af2mv3_model_4.pdb

Chain information for
PSF2_HUMAN__WDHD1_HUMAN__1314aa_unrelaxed_af2mv3_model_4.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Users/lp212/Downloads/PSF2_HUMAN__WDHD1_HUMAN__1314aa_unrelaxed_af2mv3_model_2.pdb

Chain information for
PSF2_HUMAN__WDHD1_HUMAN__1314aa_unrelaxed_af2mv3_model_2.pdb #3  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> ui tool show Matchmaker

> matchmaker #2-3 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker PSF2_HUMAN__WDHD1_HUMAN__1314aa_unrelaxed_af2mv3_model_1.pdb, chain
B (#1) with PSF2_HUMAN__WDHD1_HUMAN__1314aa_unrelaxed_af2mv3_model_4.pdb,
chain B (#2), sequence alignment score = 5751.8  
RMSD between 283 pruned atom pairs is 0.145 angstroms; (across all 1129 pairs:
49.702)  
  
Matchmaker PSF2_HUMAN__WDHD1_HUMAN__1314aa_unrelaxed_af2mv3_model_1.pdb, chain
B (#1) with PSF2_HUMAN__WDHD1_HUMAN__1314aa_unrelaxed_af2mv3_model_2.pdb,
chain B (#3), sequence alignment score = 5748.2  
RMSD between 419 pruned atom pairs is 0.250 angstroms; (across all 1129 pairs:
30.361)  
  

> hide #3 models

> hide #2 models

> show #2 models

> ui tool show Matchmaker

> matchmaker #2-3 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker PSF2_HUMAN__WDHD1_HUMAN__1314aa_unrelaxed_af2mv3_model_1.pdb, chain
B (#1) with PSF2_HUMAN__WDHD1_HUMAN__1314aa_unrelaxed_af2mv3_model_4.pdb,
chain B (#2), sequence alignment score = 5751.8  
RMSD between 283 pruned atom pairs is 0.145 angstroms; (across all 1129 pairs:
49.702)  
  
Matchmaker PSF2_HUMAN__WDHD1_HUMAN__1314aa_unrelaxed_af2mv3_model_1.pdb, chain
B (#1) with PSF2_HUMAN__WDHD1_HUMAN__1314aa_unrelaxed_af2mv3_model_2.pdb,
chain B (#3), sequence alignment score = 5748.2  
RMSD between 419 pruned atom pairs is 0.250 angstroms; (across all 1129 pairs:
30.361)  
  

> hide #2 models

> show #2 models

> ui tool show Matchmaker

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

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker PSF2_HUMAN__WDHD1_HUMAN__1314aa_unrelaxed_af2mv3_model_1.pdb, chain
B (#1) with PSF2_HUMAN__WDHD1_HUMAN__1314aa_unrelaxed_af2mv3_model_4.pdb,
chain B (#2), sequence alignment score = 5751.8  
RMSD between 283 pruned atom pairs is 0.145 angstroms; (across all 1129 pairs:
49.702)  
  

> matchmaker #3/B to #1/B pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker PSF2_HUMAN__WDHD1_HUMAN__1314aa_unrelaxed_af2mv3_model_1.pdb, chain
B (#1) with PSF2_HUMAN__WDHD1_HUMAN__1314aa_unrelaxed_af2mv3_model_2.pdb,
chain B (#3), sequence alignment score = 5748.2  
RMSD between 419 pruned atom pairs is 0.250 angstroms; (across all 1129 pairs:
30.361)  
  

> matchmaker #3/B to #1/B pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker PSF2_HUMAN__WDHD1_HUMAN__1314aa_unrelaxed_af2mv3_model_1.pdb, chain
B (#1) with PSF2_HUMAN__WDHD1_HUMAN__1314aa_unrelaxed_af2mv3_model_2.pdb,
chain B (#3), sequence alignment score = 5748.2  
RMSD between 419 pruned atom pairs is 0.250 angstroms; (across all 1129 pairs:
30.361)  
  

> matchmaker #3/B to #1/B pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker PSF2_HUMAN__WDHD1_HUMAN__1314aa_unrelaxed_af2mv3_model_1.pdb, chain
B (#1) with PSF2_HUMAN__WDHD1_HUMAN__1314aa_unrelaxed_af2mv3_model_2.pdb,
chain B (#3), sequence alignment score = 5748.2  
RMSD between 419 pruned atom pairs is 0.250 angstroms; (across all 1129 pairs:
30.361)  
  

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

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker PSF2_HUMAN__WDHD1_HUMAN__1314aa_unrelaxed_af2mv3_model_1.pdb, chain
B (#1) with PSF2_HUMAN__WDHD1_HUMAN__1314aa_unrelaxed_af2mv3_model_4.pdb,
chain B (#2), sequence alignment score = 5751.8  
RMSD between 283 pruned atom pairs is 0.145 angstroms; (across all 1129 pairs:
49.702)  
  

> hide #2 models

> ui tool show Matchmaker

> matchmaker #2/A to #1/A pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker PSF2_HUMAN__WDHD1_HUMAN__1314aa_unrelaxed_af2mv3_model_1.pdb, chain
A (#1) with PSF2_HUMAN__WDHD1_HUMAN__1314aa_unrelaxed_af2mv3_model_4.pdb,
chain A (#2), sequence alignment score = 963.8  
RMSD between 159 pruned atom pairs is 0.585 angstroms; (across all 185 pairs:
6.109)  
  

> matchmaker #3/A to #1/A pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker PSF2_HUMAN__WDHD1_HUMAN__1314aa_unrelaxed_af2mv3_model_1.pdb, chain
A (#1) with PSF2_HUMAN__WDHD1_HUMAN__1314aa_unrelaxed_af2mv3_model_2.pdb,
chain A (#3), sequence alignment score = 966.8  
RMSD between 153 pruned atom pairs is 0.614 angstroms; (across all 185 pairs:
6.820)  
  

> show #2 models

> show #3 models

> save "/Users/lp212/Dropbox (Cambridge University)/GRANTS/ERG Synergy
> REPLITARG/Predictome structures/AND-1/Psf2.cxs"

——— End of log from Sun Oct 8 20:39:28 2023 ———

opened ChimeraX session  

> open 7pfo

7pfo title:  
Core human replisome [more info...]  
  
Chain information for 7pfo #4  
---  
Chain | Description | UniProt  
2 | DNA replication licensing factor MCM2 | MCM2_HUMAN 1-904  
3 | DNA replication licensing factor MCM3 | MCM3_HUMAN 1-808  
4 | DNA replication licensing factor MCM4 | MCM4_HUMAN 1-863  
5 | DNA replication licensing factor MCM5 | MCM5_HUMAN 1-734  
6 | DNA replication licensing factor MCM6 | MCM6_HUMAN 1-821  
7 | DNA replication licensing factor MCM7 | MCM7_HUMAN 1-719  
A | DNA polymerase epsilon subunit 2 | DPOE2_HUMAN 1-527  
B | DNA polymerase epsilon catalytic subunit A | DPOE1_HUMAN 1-2286  
C | Cell division control protein 45 homolog,Cell division control protein 45
homolog | CDC45_HUMAN 1-135 136-566  
D | DNA replication complex GINS protein PSF1 | PSF1_HUMAN 1-196  
E | DNA replication complex GINS protein PSF2 | PSF2_HUMAN 1-185  
F | DNA replication complex GINS protein PSF3 | PSF3_HUMAN 1-216  
G | DNA replication complex GINS protein SLD5 | SLD5_HUMAN 1-223  
H I J | WD repeat and HMG-box DNA-binding protein 1 | WDHD1_HUMAN 1-1129  
K | Protein timeless homolog | TIM_HUMAN 1-1208  
L | TIMELESS-interacting protein | TIPIN_HUMAN 1-301  
M | Leading strand DNA |  
N | Lagging Strand DNA |  
Q | Claspin | CLSPN_HUMAN 1-1339  
  
Non-standard residues in 7pfo #4  
---  
ANP — phosphoaminophosphonic acid-adenylate ester  
MG — magnesium ion  
SO4 — sulfate ion  
ZN — zinc ion  
  

> hide #3 models

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> show #3 models

> hide #2 models

> show #2 models

> hide #1 models

> show #1 models

> hide #2 models

> hide #3 models

> ui tool show Matchmaker

> matchmaker #!4 to #1/A pairing bs

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker PSF2_HUMAN__WDHD1_HUMAN__1314aa_unrelaxed_af2mv3_model_1.pdb, chain
A (#1) with 7pfo, chain E (#4), sequence alignment score = 906.8  
RMSD between 138 pruned atom pairs is 0.860 angstroms; (across all 176 pairs:
2.602)  
  

> hide #1#!4 atoms

> show #1#!4 cartoons

> hide #!4 models

> select clear

[Repeated 4 time(s)]

> select #1/A:39

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

> select up

56 atoms, 59 bonds, 8 residues, 1 model selected  

> view sel

> show #!4 models

> hide #1 models

> select #4/E:39

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

> select up

166 atoms, 171 bonds, 22 residues, 1 model selected  

> show sel atoms

> style sel stick

Changed 166 atom styles  

> color sel byhetero

> select #4/C:255

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

> select up

203 atoms, 206 bonds, 24 residues, 1 model selected  

> show sel atoms

> style sel stick

Changed 203 atom styles  

> color sel byhetero

> select clear

> select #4/I:473

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

> select up

64 atoms, 66 bonds, 8 residues, 1 model selected  

> show sel atoms

> style sel stick

Changed 64 atom styles  

> color sel byhetero

> select #4/I:703

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

> select up

107 atoms, 111 bonds, 14 residues, 1 model selected  

> show sel atoms

> style sel stick

Changed 107 atom styles  

> color sel byhetero

> save "/Users/lp212/Dropbox (Cambridge University)/GRANTS/ERG Synergy
> REPLITARG/Predictome structures/AND-1/Psf2.cxs"

> view #4 clip false

> cofr sel

> select #4/I:479

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

> select up

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

> show sel atoms

> style sel stick

Changed 31 atom styles  

> color sel byhetero

> select clear

> ui tool show "Side View"

> select #4/E:59

11 atoms, 10 bonds, 1 residue, 1 model selected  
Drag select of 287 atoms, 183 residues, 251 bonds  

> show sel atoms

> style sel stick

Changed 1496 atom styles  

> color sel byhetero

> style sel stick

Changed 1496 atom styles  

> style sel stick

Changed 1496 atom styles  

> select clear

> select #4/A:227

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

> select up

78 atoms, 81 bonds, 9 residues, 1 model selected  

> select up

4199 atoms, 4310 bonds, 527 residues, 1 model selected  

> view sel

> select clear

> select #4/B

6062 atoms, 6180 bonds, 17 pseudobonds, 760 residues, 3 models selected  

> color (#!4 & sel) hot pink

> select clear

> select #4/A:16

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

> select up

131 atoms, 132 bonds, 16 residues, 1 model selected  

> select down

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

> select #4/A:18

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

> select up

12 atoms, 11 bonds, 2 residues, 1 model selected  

> select add #4/A:17

23 atoms, 21 bonds, 3 residues, 1 model selected  

> select add #4/A:16

31 atoms, 28 bonds, 4 residues, 1 model selected  

> select add #4/A:15

40 atoms, 36 bonds, 5 residues, 1 model selected  

> select add #4/A:20

48 atoms, 43 bonds, 6 residues, 1 model selected  

> select add #4/A:14

59 atoms, 54 bonds, 7 residues, 1 model selected  

> select add #4/A:13

64 atoms, 58 bonds, 8 residues, 1 model selected  

> select add #4/A:12

70 atoms, 63 bonds, 9 residues, 1 model selected  

> select add #4/A:11

78 atoms, 70 bonds, 10 residues, 1 model selected  

> show sel target ab

> style sel stick

Changed 78 atom styles  

> color sel byhetero

> save "/Users/lp212/Dropbox (Cambridge University)/GRANTS/ERG Synergy
> REPLITARG/Predictome structures/AND-1/Psf2.cxs"

——— End of log from Mon Oct 9 16:37:25 2023 ———

opened ChimeraX session  

> select clear

> preset "overall look" "publication 1 (silhouettes)"

Using preset: Overall Look / Publication 1 (Silhouettes)  

> set bgColor #ffffff00

Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t
    lighting depthCue f

  

> lighting simple

> lighting soft

> hide #!4 atoms

> select #4/I

3169 atoms, 3244 bonds, 401 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel powder blue target c

> color sel light blue target c

> color sel sky blue target c

> select clear

> select #4/2

5613 atoms, 5717 bonds, 9 pseudobonds, 706 residues, 3 models selected  

> ui tool show "Color Actions"

> color sel light gray target c

> select #4/3

4890 atoms, 4964 bonds, 5 pseudobonds, 622 residues, 3 models selected  

> color sel light gray target c

> select #4/4

4930 atoms, 5013 bonds, 7 pseudobonds, 620 residues, 3 models selected  

> color sel light gray target c

[Repeated 1 time(s)]

> select #4/5

4768 atoms, 4840 bonds, 10 pseudobonds, 608 residues, 3 models selected  

> color sel light gray target c

> select #4/6

5015 atoms, 5095 bonds, 7 pseudobonds, 633 residues, 3 models selected  

> color sel light gray target c

> select #4/7

4723 atoms, 4796 bonds, 8 pseudobonds, 596 residues, 3 models selected  

> color sel light gray target c

> select clear

> ui tool show "Model Panel"

> ui tool show "Side View"

> select #4/B

6062 atoms, 6180 bonds, 17 pseudobonds, 760 residues, 3 models selected  

> hide sel cartoons

> select #4/A

4204 atoms, 4314 bonds, 528 residues, 1 model selected  

> hide sel cartoons

> select #4/K

5215 atoms, 5317 bonds, 2 pseudobonds, 636 residues, 2 models selected  

> hide sel cartoons

> select #4/Q

683 atoms, 693 bonds, 2 pseudobonds, 79 residues, 2 models selected  

> hide sel cartoons

> select #4/L

735 atoms, 750 bonds, 87 residues, 1 model selected  

> hide sel cartoons

> select #4/D

1606 atoms, 1638 bonds, 195 residues, 1 model selected  

> color sel light gray target c

> select #4/E

1431 atoms, 1462 bonds, 176 residues, 1 model selected  

> color sel light gray target c

[Repeated 1 time(s)]

> select #4/F

1546 atoms, 1580 bonds, 1 pseudobond, 194 residues, 2 models selected  

> color sel light gray target c

> select clear

> select #4/F

1546 atoms, 1580 bonds, 1 pseudobond, 194 residues, 2 models selected  

> color sel light gray target c

[Repeated 2 time(s)]

> select #4/G:97

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

> select #4/C:255

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

> cofr sel

> select clear

[Repeated 1 time(s)]

> select #4/E

1431 atoms, 1462 bonds, 176 residues, 1 model selected  

> color sel khaki target c

> select #4/G

1679 atoms, 1711 bonds, 203 residues, 1 model selected  

> color sel light gray target c

> select clear

> select #4/C

4347 atoms, 4439 bonds, 1 pseudobond, 534 residues, 2 models selected  

> color sel light blue target c

> color sel light pink target c

> color sel pink target c

> select clear

> ~pseudobonds

Unknown command: ~pseudobonds  

> ~pseudobond

Unknown command: ~pseudobond  

> hide pseudobonds

> view name view1

> save "/Users/luca/Dropbox (Cambridge University)/GRANTS/ERG Synergy
> REPLITARG/Predictome structures/AND-1/Figs/AND1-CMG.png" width 1848 height
> 993 supersample 3

> save "/Users/luca/Dropbox (Cambridge University)/GRANTS/ERG Synergy
> REPLITARG/Predictome structures/AND-1/Psf2.cxs"

——— End of log from Wed Oct 11 12:40:04 2023 ———

opened ChimeraX session  

> show #1 models

> hide #!4 models

> open "/Users/lp212/Dropbox (Cambridge University)/GRANTS/ERG Synergy
> REPLITARG/research/Predictome structures/AND-1/POLA1.cxs"

Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/dialog.py", line 162, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File
"/Applications/ChimeraX_Daily.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_Daily.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_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File
"/Applications/ChimeraX_Daily.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_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 193, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 458, in collated_open  
return remember_data_format()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 428, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core_formats/__init__.py", line 26, in open  
return cxs_open(session, data, **kw)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 1001, in open  
session.restore(stream, path=path, resize_window=resize_window)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 641, in restore  
use_pickle = stream.peek(1)[0] != ord(b'#')  
IndexError: index out of range  
  
IndexError: index out of range  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 641, in restore  
use_pickle = stream.peek(1)[0] != ord(b'#')  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 83.1
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,3
      Model Number: MKGT3B/A
      Chip: Apple M1 Pro
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 16 GB
      System Firmware Version: 8422.141.2
      OS Loader Version: 8422.141.2

Software:

    System Software Overview:

      System Version: macOS 13.5 (22G74)
      Kernel Version: Darwin 22.6.0
      Time since boot: 1 day, 9 hours, 38 minutes

Graphics/Displays:

    Apple M1 Pro:

      Chipset Model: Apple M1 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 16
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      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


Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.0.8
    Babel: 2.10.3
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.8.0
    certifi: 2021.10.8
    cftime: 1.6.2
    charset-normalizer: 2.1.1
    ChimeraX-AddCharge: 1.4
    ChimeraX-AddH: 2.2
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.6
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.41.4
    ChimeraX-AtomicLibrary: 8.0.2
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3
    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: 2.7.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.1
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.2
    ChimeraX-CommandLine: 1.2.4
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.5.dev202210110346
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.3
    ChimeraX-DockPrep: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 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: 1.1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.1
    ChimeraX-MatchMaker: 2.0.9
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.8
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.6
    ChimeraX-ModelPanel: 1.3.6
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.1
    ChimeraX-MouseModes: 1.1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.9.1
    ChimeraX-PDB: 2.6.8
    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-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    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: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.7.2
    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
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.1.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.24.2
    ChimeraX-uniprot: 2.2.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.1.3
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.1
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.5
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.32
    debugpy: 1.6.3
    decorator: 5.1.1
    docutils: 0.19
    entrypoints: 0.4
    executing: 1.1.1
    filelock: 3.7.1
    fonttools: 4.37.4
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.33
    imagecodecs: 2022.2.22
    imagesize: 1.4.1
    importlib-metadata: 5.0.0
    ipykernel: 6.15.3
    ipython: 8.4.0
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.1.2
    jupyter-client: 7.3.4
    jupyter-core: 4.11.1
    kiwisolver: 1.4.4
    line-profiler: 3.5.1
    lxml: 4.9.1
    lz4: 4.0.2
    MarkupSafe: 2.1.1
    matplotlib: 3.5.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.0
    networkx: 2.8.5
    numexpr: 2.8.3
    numpy: 1.23.1
    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: 9.2.0
    pip: 22.2.2
    pkginfo: 1.8.3
    prompt-toolkit: 3.0.31
    psutil: 5.9.1
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.12.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2022.4
    pyzmq: 24.0.1
    qtconsole: 5.3.1
    QtPy: 2.2.1
    RandomWords: 0.4.0
    requests: 2.28.1
    scipy: 1.9.0
    setuptools: 65.1.1
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 5.1.1
    sphinx-autodoc-typehints: 1.19.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.5.1
    tables: 3.7.0
    tifffile: 2022.7.31
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.3.0
    typing-extensions: 4.4.0
    urllib3: 1.26.12
    wcwidth: 0.2.5
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.4.1
    zipp: 3.9.0

[Tom Goddard]

This error is because your ChimeraX session file POLA1.cxs in DropBox has not actually been downloaded by DropBox and so ChimeraX tries to read it and it contains no data. I don't know why DropBox fails to download the file sometimes. If you copy it from DropBox to your Desktop it should open.

open "/Users/lp212/Dropbox (Cambridge University)/GRANTS/ERG Synergy
REPLITARG/research/Predictome structures/AND-1/POLA1.cxs"

"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 641, in restore
use_pickle = stream.peek(1)[0] != ord(b'#')
IndexError: index out of range