Opened 2 years ago

Last modified 2 years ago

#9707 accepted defect

EOFError restoring session

Reported by: disha-gajanan.hiregange@… Owned by: Greg Couch
Priority: normal Milestone:
Component: Sessions Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-5.4.115-1.el8.elrepo.x86_64-x86_64-with-glibc2.28
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open /yonath_group/disha/Desktop/RPL22_UL4_curiousity_paper.cxs format
> session

Log from Mon Jan 23 17:12:45 2023UCSF ChimeraX version: 1.2 (2021-04-27)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 1NKW format mmcif fromDatabase pdb

1nkw title:  
Crystal Structure Of The Large Ribosomal Subunit From Deinococcus Radiodurans
[more info...]  
  
Chain information for 1nkw #1  
---  
Chain | Description  
0 | 23S ribosomal RNA  
1 | 50S ribosomal protein L33  
2 | 50S ribosomal protein L34  
3 | 50S ribosomal protein L35  
4 | 50S ribosomal protein L36  
9 | 5S ribosomal RNA  
A | 50S ribosomal protein L2  
B | 50S ribosomal protein L3  
C | 50S ribosomal protein L4  
D | 50S ribosomal protein L5  
E | 50S ribosomal protein L6  
F | 50S ribosomal protein L9  
G | 50S ribosomal protein L11  
H | 50S ribosomal protein L13  
I | 50S ribosomal protein L14  
J | 50S ribosomal protein L15  
K | 50S ribosomal protein L16  
L | 50S ribosomal protein L17  
M | 50S ribosomal protein L18  
N | 50S ribosomal protein L19  
O | 50S ribosomal protein L20  
P | 50S ribosomal protein L21  
Q | 50S ribosomal protein L22  
R | 50S ribosomal protein L23  
S | 50S ribosomal protein L24  
T | general stress protein CTC  
U | 50S ribosomal protein L27  
W | 50S ribosomal protein L29  
X | 50S ribosomal protein L30  
Y | 50S ribosomal protein L31  
Z | 50S ribosomal protein L32  
  

> open 6hma

6hma title:  
Improved model derived from cryo-EM map of Staphylococcus aureus large
ribosomal subunit [more info...]  
  
Chain information for 6hma #2  
---  
Chain | Description  
1 | 50S ribosomal protein L33  
2 | 50S ribosomal protein L34  
3 | 50S ribosomal protein L35  
4 | 50S ribosomal protein L36  
A | 23S ribosomal RNA  
B | 5S ribosomal RNA  
C | 50S ribosomal protein L2  
D | 50S ribosomal protein L3  
E | 50S ribosomal protein L4  
F | 50S ribosomal protein L5  
G | 50S ribosomal protein L6  
H | 50S ribosomal protein L13  
I | 50S ribosomal protein L14  
J | 50S ribosomal protein L15  
K | 50S ribosomal protein L16  
L | 50S ribosomal protein L17  
M | 50S ribosomal protein L18  
N | 50S ribosomal protein L19  
O | 50S ribosomal protein L20  
P | 50S ribosomal protein L21  
Q | 50S ribosomal protein L22  
R | 50S ribosomal protein L23  
S | 50S ribosomal protein L24  
T | 50S ribosomal protein L25  
U | 50S ribosomal protein L27  
V | 50S ribosomal protein L28  
W | 50S ribosomal protein L29  
X | 50S ribosomal protein L30  
Z | 50S ribosomal protein L32  
  
Non-standard residues in 6hma #2  
---  
MG — magnesium ion  
  

> open 4ug0

4ug0 title:  
Structure of the human 80S ribosome [more info...]  
  
Chain information for 4ug0 #3  
---  
Chain | Description  
L5 | 28S ribosomal RNA  
L7 | 5S ribosomal RNA  
L8 | 5.8S ribosomal RNA  
LA | 60S ribosomal protein L8  
LB | 60S ribosomal protein L3  
LC | 60S ribosomal protein L4  
LD | 60S ribosomal protein L5  
LE | 60S ribosomal protein L6  
LF | 60S ribosomal protein L7  
LG | 60S ribosomal protein L7A  
LH | 60S ribosomal protein L9  
LI | 60S ribosomal protein L10-like  
LJ | 60S ribosomal protein L11  
LL | 60S ribosomal protein L13  
LM | 60S ribosomal protein L14  
LN | 60S ribosomal protein L15  
LO | 60S ribosomal protein L13A  
LP | 60S ribosomal protein L17  
LQ | 60S ribosomal protein L18  
LR | 60S ribosomal protein L19  
LS | 60S ribosomal protein L18A  
LT | 60S ribosomal protein L21  
LU | 60S ribosomal protein L22  
LV | 60S ribosomal protein L23  
LW | 60S ribosomal protein L24  
LX | 60S ribosomal protein L23A  
LY | 60S ribosomal protein L26  
LZ | 60S ribosomal protein L27  
La | 60S ribosomal protein L27A  
Lb | 60S ribosomal protein L29  
Lc | 60S ribosomal protein L30  
Ld | 60S ribosomal protein L31  
Le | 60S ribosomal protein L32  
Lf | 60S ribosomal protein L35A  
Lg | 60S ribosomal protein L34  
Lh | 60S ribosomal protein L35  
Li | 60S ribosomal protein L36  
Lj | 60S ribosomal protein L37  
Lk | 60S ribosomal protein L38  
Ll | 60S ribosomal protein L39  
Lm | ubiquitin-60S ribosomal protein L40  
Ln | 60S ribosomal protein L41  
Lo | 60S ribosomal protein L36A  
Lp | 60S ribosomal protein L37A  
Lr | 60S ribosomal protein L28  
Lz | 60S ribosomal protein L10A  
S2 | 18S ribosomal RNA  
S6 | human initiator met-TRNA-I  
SA | 40S ribosomal protein sa  
SB | 40S ribosomal protein S3A  
SC | 40S ribosomal protein S2  
SD | 40S ribosomal protein S3  
SE | 40S ribosomal protein S4, X isoform  
SF | 40S ribosomal protein S5  
SG | 40S ribosomal protein S6  
SH | 40S ribosomal protein S7  
SI | 40S ribosomal protein S8  
SJ | 40S ribosomal protein S9  
SK | 40S ribosomal protein S10  
SL | 40S ribosomal protein S11  
SM | 40S ribosomal protein  
SN | 40S ribosomal protein S13  
SO | 40S ribosomal protein S14  
SP | 40S ribosomal protein S15  
SQ | 40S ribosomal protein S16  
SR | 40S ribosomal protein S17-like  
SS | 40S ribosomal protein S18  
ST | 40S ribosomal protein S19  
SU | 40S ribosomal protein S20  
SV | 40S ribosomal protein S21  
SW | 40S ribosomal protein S15A  
SX | 40S ribosomal protein S23  
SY | 40S ribosomal protein S24  
SZ | 40S ribosomal protein S25  
Sa | 40S ribosomal protein S26  
Sb | 40S ribosomal protein S27  
Sc | 40S ribosomal protein S28  
Sd | 40S ribosomal protein S29  
Se | 40S ribosomal protein S30  
Sf | ubiquitin-40S ribosomal protein S27A  
Sg | guanine nucleotide-binding protein subunit β-2-like 1  
  
Non-standard residues in 4ug0 #3  
---  
MG — magnesium ion  
ZN — zinc ion  
  

> open 7k00

7k00 title:  
Structure of the Bacterial Ribosome at 2 Angstrom Resolution [more info...]  
  
Chain information for 7k00 #4  
---  
Chain | Description  
0 | 50S ribosomal protein L33  
1 | 50S ribosomal protein L34  
2 | 50S ribosomal protein L35  
3 | 50S ribosomal protein L36  
4 | 50S ribosomal protein L31  
5 | E-site tRNA  
A | 16S rRNA  
B | 30S ribosomal protein S2  
C | 30S ribosomal protein S3  
D | 30S ribosomal protein S4  
E | 30S ribosomal protein S5  
F | 30S ribosomal protein S6  
G | 30S ribosomal protein S7  
H | 30S ribosomal protein S8  
I | 30S ribosomal protein S9  
J | 30S ribosomal protein S10  
K | 30S ribosomal protein S11  
L | 30S ribosomal protein S12  
M | 30S ribosomal protein S13  
N | 30S ribosomal protein S14  
O | 30S ribosomal protein S15  
P | 30S ribosomal protein S16  
Q | 30S ribosomal protein S17  
R | 30S ribosomal protein S18  
S | 30S ribosomal protein S19  
T | 30S ribosomal protein S20  
U | 30S ribosomal protein S21  
X | mRNA  
Y | A-site tRNA-val  
Z | P-site tRNA-fMet  
a | 23S rRNA  
b | 5S rRNA  
c | 50S ribosomal protein L2  
d | 50S ribosomal protein L3  
e | 50S ribosomal protein L4  
f | 50S ribosomal protein L5  
g | 50S ribosomal protein L6  
h | 50S ribosomal protein L9  
i | 50S ribosomal protein L13  
j | 50S ribosomal protein L14  
k | 50S ribosomal protein L15  
l | 50S ribosomal protein L16  
m | 50S ribosomal protein L17  
n | 50S ribosomal protein L18  
o | 50S ribosomal protein L19  
p | 50S ribosomal protein L20  
q | 50S ribosomal protein L21  
r | 50S ribosomal protein L22  
s | 50S ribosomal protein L23  
t | 50S ribosomal protein L24  
u | 50S ribosomal protein L25  
v | 50S ribosomal protein L27  
w | 50S ribosomal protein L28  
x | 50S ribosomal protein L29  
y | 50S ribosomal protein L30  
z | 50S ribosomal protein L32  
  
Non-standard residues in 7k00 #4  
---  
MG — magnesium ion  
MS6 — (2S)-2-amino-4-(methylsulfanyl)butane-1-thiol  
PAR — paromomycin (paromomycin I; amminosidin; catenulin; crestomycin;
monomycin A; neomycin E)  
SPD — spermidine (N-(2-amino-propyl)-1,4-diaminobutane; Pa(34))  
SPM — spermine  
ZN — zinc ion  
  

> open /yonath_group/disha/Gingivalis/Models_and_maps/delta266/new_map_50S.mrc

Opened new_map_50S.mrc as #5, grid size 440,440,440, pixel 0.852, shown at
level 0.0134, step 2, values float32  

> close #5

> open
> /yonath_group/disha/Gingivalis/Models_and_maps/delta266/50S_new_map_combined_WITH_MOD_09_02.pdb

Summary of feedback from opening
/yonath_group/disha/Gingivalis/Models_and_maps/delta266/50S_new_map_combined_WITH_MOD_09_02.pdb  
---  
warnings | Ignored bad PDB record found on line 75883  
END  
  
Start residue of secondary structure not found: HELIX 17 17 PRO V 13 MET V 22
1 10  
Start residue of secondary structure not found: HELIX 18 18 VAL V 28 PHE V 37
1 10  
Start residue of secondary structure not found: HELIX 19 19 GLU V 41 LYS V 60
5 20  
Start residue of secondary structure not found: SHEET 1 M 3 PHE V 3 LEU V 6 0  
Start residue of secondary structure not found: SHEET 2 M 3 ASN V 102 TYR V
107 -1 N ILE V 106 O ALA V 4  
3 messages similar to the above omitted  
  
Chain information for 50S_new_map_combined_WITH_MOD_09_02.pdb #5  
---  
Chain | Description  
0 | No description available  
1 | No description available  
2 | No description available  
4 | No description available  
5 | No description available  
6 | No description available  
7 | No description available  
8 | No description available  
A | No description available  
B | No description available  
D | No description available  
E | No description available  
F | No description available  
M | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
V | No description available  
W | No description available  
X | No description available  
Y | No description available  
Z | No description available  
h | No description available  
  

> ui tool show Matchmaker

> matchmaker #!1-4 to #5

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 50S_new_map_combined_WITH_MOD_09_02.pdb, chain D (#5) with 1nkw,
chain A (#1), sequence alignment score = 660.1  
RMSD between 101 pruned atom pairs is 1.185 angstroms; (across all 268 pairs:
5.792)  
  
Matchmaker 50S_new_map_combined_WITH_MOD_09_02.pdb, chain D (#5) with 6hma,
chain C (#2), sequence alignment score = 910  
RMSD between 266 pruned atom pairs is 0.677 angstroms; (across all 272 pairs:
0.872)  
  
Matchmaker 50S_new_map_combined_WITH_MOD_09_02.pdb, chain D (#5) with 4ug0,
chain LA (#3), sequence alignment score = 345.2  
RMSD between 133 pruned atom pairs is 1.126 angstroms; (across all 227 pairs:
8.231)  
  
Matchmaker 50S_new_map_combined_WITH_MOD_09_02.pdb, chain D (#5) with 7k00,
chain c (#4), sequence alignment score = 896  
RMSD between 258 pruned atom pairs is 0.850 angstroms; (across all 271 pairs:
1.152)  
  

> matchmaker #!1-4 to #5

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 50S_new_map_combined_WITH_MOD_09_02.pdb, chain D (#5) with 1nkw,
chain A (#1), sequence alignment score = 660.1  
RMSD between 101 pruned atom pairs is 1.185 angstroms; (across all 268 pairs:
5.792)  
  
Matchmaker 50S_new_map_combined_WITH_MOD_09_02.pdb, chain D (#5) with 6hma,
chain C (#2), sequence alignment score = 910  
RMSD between 266 pruned atom pairs is 0.677 angstroms; (across all 272 pairs:
0.872)  
  
Matchmaker 50S_new_map_combined_WITH_MOD_09_02.pdb, chain D (#5) with 4ug0,
chain LA (#3), sequence alignment score = 345.2  
RMSD between 133 pruned atom pairs is 1.126 angstroms; (across all 227 pairs:
8.231)  
  
Matchmaker 50S_new_map_combined_WITH_MOD_09_02.pdb, chain D (#5) with 7k00,
chain c (#4), sequence alignment score = 896  
RMSD between 258 pruned atom pairs is 0.850 angstroms; (across all 271 pairs:
1.152)  
  

> select 1/Q

Expected an objects specifier or a keyword  

> sel:1/Q

Unknown command: sel:1/Q  

> select #1/Q

130 atoms, 129 pseudobonds, 130 residues, 2 models selected  

> addh sel #1/C

Expected a keyword  

> select #1/Q

130 atoms, 129 pseudobonds, 130 residues, 2 models selected  

> select ~sel

595348 atoms, 633494 bonds, 19395 pseudobonds, 54231 residues, 17 models
selected  

> hide sel atoms

> show sel cartoons

> hide sel atoms

> select #1/Q

130 atoms, 129 pseudobonds, 130 residues, 2 models selected  

> select ~sel

595348 atoms, 633494 bonds, 19395 pseudobonds, 54231 residues, 17 models
selected  

> hide sel cartoons

> select #1/Q

130 atoms, 129 pseudobonds, 130 residues, 2 models selected  

> show sel cartoons

> select #1/C

197 atoms, 196 pseudobonds, 197 residues, 2 models selected  

> show sel cartoons

> select #2/Q

854 atoms, 862 bonds, 112 residues, 1 model selected  

> show sel cartoons

> select #2/E

1572 atoms, 1595 bonds, 206 residues, 1 model selected  

> show sel cartoons

> select #3/LU

825 atoms, 839 bonds, 101 residues, 1 model selected  

> show sel cartoons

> select #3/LC

2919 atoms, 2973 bonds, 367 residues, 1 model selected  

> show sel cartoons

> select #3/LP

1243 atoms, 1268 bonds, 1 pseudobond, 154 residues, 2 models selected  

> show sel cartoons

> select #3/LU

825 atoms, 839 bonds, 101 residues, 1 model selected  

> hide sel cartoons

> select #4/r

877 atoms, 864 bonds, 130 residues, 1 model selected  

> show sel cartoons

> select #4/e

1600 atoms, 1571 bonds, 249 residues, 1 model selected  

> show sel cartoons

> select #5/V

1021 atoms, 1034 bonds, 127 residues, 1 model selected  

> show sel cartoons

> select #5/F

1636 atoms, 1659 bonds, 209 residues, 1 model selected  

> show sel cartoons

> select #5

75663 atoms, 81237 bonds, 86 pseudobonds, 6322 residues, 2 models selected  

> show sel surfaces

> ui tool show "Color Actions"

> color sel cornflower blue

> transparency (#!5 & sel) 80

> select clear

> set bgColor white

> select #5/A:2837@C3'

1 atom, 1 residue, 1 model selected  

> select #5/A:1677@OP1

1 atom, 1 residue, 1 model selected  

> select #5/A:1438@O2'

1 atom, 1 residue, 1 model selected  

> select #5/A:1439@C4'

1 atom, 1 residue, 1 model selected  

> select #5

75663 atoms, 81237 bonds, 86 pseudobonds, 6322 residues, 2 models selected  

> transparency (#!5 & sel) 70

> select clear

> color forest green

> undo

> select #1

65300 atoms, 69283 bonds, 5900 pseudobonds, 6306 residues, 3 models selected  

> color (#!1 & sel) forest green

> select #2

86401 atoms, 94020 bonds, 3066 pseudobonds, 6225 residues, 4 models selected  

> ui tool show "Color Actions"

> color sel salmon

> select #3

218776 atoms, 234864 bonds, 4237 pseudobonds, 17789 residues, 4 models
selected  

> ui tool show "Color Actions"

> color sel magenta

> select #4

149338 atoms, 154090 bonds, 6235 pseudobonds, 17719 residues, 4 models
selected  

> ui tool show "Color Actions"

> color sel turquoise

> color sel medium slate blue

> select #5

75663 atoms, 81237 bonds, 86 pseudobonds, 6322 residues, 2 models selected  

> ui tool show "Color Actions"

> color sel maroon

> undo

> select #5/V

1021 atoms, 1034 bonds, 127 residues, 1 model selected  

> color sel fire brick

> select #5/F

1636 atoms, 1659 bonds, 209 residues, 1 model selected  

> color sel fire brick

> select clear

> select #5

75663 atoms, 81237 bonds, 86 pseudobonds, 6322 residues, 2 models selected  

> color sel cornflower blue

> transparency (#!5 & sel) 70

> select #5/A:2758@N3

1 atom, 1 residue, 1 model selected  

> ui tool show "Side View"

> select #3

218776 atoms, 234864 bonds, 4237 pseudobonds, 17789 residues, 4 models
selected  

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.85086,0.45401,0.2644,-64.162,-0.51654,0.63086,0.57897,72.938,0.09606,-0.6292,0.77129,136.65

> select #2

86401 atoms, 94020 bonds, 3066 pseudobonds, 6225 residues, 4 models selected  

> select #5

75663 atoms, 81237 bonds, 86 pseudobonds, 6322 residues, 34 models selected  

> show sel cartoons

> hide sel surfaces

> lighting shadows false

> select #3

218776 atoms, 234864 bonds, 4237 pseudobonds, 17789 residues, 4 models
selected  

> view matrix models
> #3,0.85086,0.45401,0.2644,-65.444,-0.51654,0.63086,0.57897,72.381,0.09606,-0.6292,0.77129,139.04

> select clear

> select #2

86401 atoms, 94020 bonds, 3066 pseudobonds, 6225 residues, 4 models selected  

> view matrix models
> #2,0.58225,0.69513,0.42164,-78.79,-0.073265,0.56137,-0.82432,248.57,-0.8097,0.44907,0.37779,159.49

> select clear

> select #3

218776 atoms, 234864 bonds, 4237 pseudobonds, 17789 residues, 4 models
selected  

> view matrix models
> #3,0.85086,0.45401,0.2644,-65.986,-0.51654,0.63086,0.57897,71.261,0.09606,-0.6292,0.77129,139.65

> select clear

> select #3

218776 atoms, 234864 bonds, 4237 pseudobonds, 17789 residues, 4 models
selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.77007,0.6132,0.17602,-78.176,-0.56296,0.52335,0.63967,89.275,0.30012,-0.59169,0.74822,115.17

> ~select #3

Nothing selected  

> select #3

218776 atoms, 234864 bonds, 4237 pseudobonds, 17789 residues, 4 models
selected  

> view matrix models
> #3,0.80358,0.58892,0.086233,-68.488,-0.49799,0.58588,0.63933,71.73,0.32599,-0.5567,0.76408,104.84

> select clear

> select #3

218776 atoms, 234864 bonds, 4237 pseudobonds, 17789 residues, 4 models
selected  

> view matrix models
> #3,0.82564,0.54313,0.15273,-68.805,-0.50936,0.60114,0.61578,72.362,0.24264,-0.5862,0.77298,117.44

> view matrix models
> #3,0.78472,0.58429,0.20693,-77.385,-0.55928,0.52349,0.64278,88.592,0.26724,-0.62013,0.73758,124.51

> select clear

> cartoon style nucleic xsection round width 1.6 thickness 0.7

> hide #!3 target m

> cartoon style nucleic xsection round width 1.6 thickness 0.4

> select clear

> cartoon style nucleic xsection round width 1.2 thickness 0.4

> select #5

75663 atoms, 81237 bonds, 86 pseudobonds, 6322 residues, 6 models selected  

> show sel surfaces

> hide sel cartoons

> select #5/V

1021 atoms, 1034 bonds, 127 residues, 1 model selected  

> show sel cartoons

> select #5/F

1636 atoms, 1659 bonds, 209 residues, 1 model selected  

> show sel cartoons

> select #5/F

1636 atoms, 1659 bonds, 209 residues, 1 model selected  

> color (#!5 & sel) orange red

> hide sel surfaces

> select #5/V

1021 atoms, 1034 bonds, 127 residues, 1 model selected  

> color (#!5 & sel) orange red

> hide sel surfaces

> select #1

65300 atoms, 69283 bonds, 5900 pseudobonds, 6306 residues, 3 models selected  

> ui tool show "Color Actions"

> color sel spring green

> select #4

149338 atoms, 154090 bonds, 6235 pseudobonds, 17719 residues, 4 models
selected  

> color sel orchid

> select #2

86401 atoms, 94020 bonds, 3066 pseudobonds, 6225 residues, 4 models selected  

> color sel medium blue

> select clear

> cartoon style nucleic xsection round width 1.2 thickness 0.9

> cartoon style nucleic xsection round width 2.0 thickness 0.9

> cartoon style protein xsection round width 2.0 thickness 0.9

> select #5/A:1297@P

1 atom, 1 residue, 1 model selected  

> select #5

75663 atoms, 81237 bonds, 86 pseudobonds, 6322 residues, 22 models selected  

> color (#!5 & sel) light gray

> transparency (#!5 & sel) 70

> transparency (#!5 & sel) 90

> undo

> undo

> undo

> undo

> undo

> undo

> undo

> undo

> cartoon style protein xsection round width 2.0 thickness 0.9

> select #5

75663 atoms, 81237 bonds, 86 pseudobonds, 6322 residues, 26 models selected  

> show sel surfaces

> color (#!5 & sel) light gray

> transparency (#!5 & sel) 80

> transparency (#!5 & sel) 70

> select #5/V

1021 atoms, 1034 bonds, 127 residues, 1 model selected  

> color (#!5 & sel) orange red

> hide sel surfaces

> select #5/F

1636 atoms, 1659 bonds, 209 residues, 1 model selected  

> color (#!5 & sel) orange red

> hide sel surfaces

> select #5/A:830@C5

1 atom, 1 residue, 1 model selected  

> lighting shadows true

> lighting shadows false

> lighting flat

> lighting flat

> lighting simple

> graphics silhouettes false

> lighting full

> select #5

75663 atoms, 81237 bonds, 86 pseudobonds, 6322 residues, 29 models selected  

> ui tool show "Color Actions"

> color sel light blue

> color sel powder blue

> transparency (#!5 & sel) 80

> select #5/F

1636 atoms, 1659 bonds, 209 residues, 1 model selected  

> color (#!5 & sel) red

> color (#!5 & sel) orange red

> select #5/V

1021 atoms, 1034 bonds, 127 residues, 1 model selected  

> color (#!5 & sel) orange red

> graphics silhouettes true

> graphics silhouettes false

> lighting shadows false

> lighting flat

> lighting flat

> lighting full

> lighting soft

> lighting simple

> graphics silhouettes false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting shadows false

> select #5

75663 atoms, 81237 bonds, 86 pseudobonds, 6322 residues, 29 models selected  

> transparency (#!5 & sel) 60

> color (#!5 & sel) dim gray

> transparency (#!5 & sel) 60

> transparency (#!5 & sel) 80

> ui tool show "Color Actions"

> color sel coral

> transparency (#!5 & sel) 80

> select #5/V

1021 atoms, 1034 bonds, 127 residues, 1 model selected  

> color (#!5 & sel) orange red

> select #5/F

1636 atoms, 1659 bonds, 209 residues, 1 model selected  

> color (#!5 & sel) orange red

> select clear

> select #4

149338 atoms, 154090 bonds, 6235 pseudobonds, 17719 residues, 4 models
selected  

> color sel dark orange

> color sel gold

> color sel sandy brown

> color sel goldenrod

> color sel dark khaki

> select #5/F

1636 atoms, 1659 bonds, 209 residues, 1 model selected  

> color sel dark red

> color sel orange red

> color sel dark red

> select #5/V

1021 atoms, 1034 bonds, 127 residues, 1 model selected  

> color sel dark red

> select #5/A:552@N1

1 atom, 1 residue, 1 model selected  

> select #2

86401 atoms, 94020 bonds, 3066 pseudobonds, 6225 residues, 4 models selected  

> color sel royal blue

> color sel cornflower blue

> color sel medium orchid

> color sel dark slate blue

> color sel slate blue

> color sel medium violet red

> color sel dim gray

> color sel light gray

> color sel gray

> color sel dark gray

> color sel light gray

> color sel gray

> color sel dark gray

> color sel dim gray

> color sel black

> color sel orange

> color sel black

> color sel deep sky blue

> color sel slate gray

> color sel light slate gray

> color sel steel blue

> color sel dodger blue

> select clear

> save /yonath_group/disha/Desktop/RPL22_UL4_curiousity_paper.cxs

——— End of log from Mon Jan 23 17:12:45 2023 ———

opened ChimeraX session  

> select add #5

75663 atoms, 81237 bonds, 86 pseudobonds, 6322 residues, 29 models selected  

> ui tool show "Color Actions"

> color sel royal blue

> transparency (#!5 & sel) 40

> transparency (#!5 & sel) 70

> select clear

> select #5.15.1

1 model selected  

> select #5.10.1

1 model selected  

> ui tool show "Color Actions"

> color sel sky blue

> select #5.13.1

1 model selected  

> select #5/A:2783@C5'

1 atom, 1 residue, 1 model selected  

> select #5/A:2704@OP2

1 atom, 1 residue, 1 model selected  

> hide #!1 models

> hide #!2 models

> close session

> open "/yonath_group/sarit/pg_W83/files from home/10_02_22/helix10.cxs"

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/session.py", line 708, in restore  
data = fdeserialize(stream)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/serialize.py", line 70, in msgpack_deserialize  
return next(stream)  
File "msgpack/_unpacker.pyx", line 540, in msgpack._cmsgpack.Unpacker.__next__  
File "msgpack/_unpacker.pyx", line 474, in msgpack._cmsgpack.Unpacker._unpack  
File "msgpack/_unpacker.pyx", line 448, in
msgpack._cmsgpack.Unpacker.read_from_file  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/lz4/frame/__init__.py", line 668, in read  
return self._buffer.read(size)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/_compression.py", line 68, in
readinto  
data = self.read(len(byte_view))  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/_compression.py", line 99, in
read  
raise EOFError("Compressed file ended before the "  
EOFError: Compressed file ended before the end-of-stream marker was reached  
  
opened ChimeraX session  




OpenGL version: 3.3.0 NVIDIA 418.113
OpenGL renderer: Quadro RTX 4000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: en_US.UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=plasma
XDG_SESSION_DESKTOP=plasma
XDG_CURRENT_DESKTOP=KDE
DISPLAY=:1
Manufacturer: ASUS
Model: System Product Name
OS: CentOS Stream 8 
Architecture: 64bit ELF
Virtual Machine: none
CPU: 24 AMD Ryzen 9 5900X 12-Core Processor
Cache Size: 512 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:           62Gi        47Gi       4.4Gi       664Mi        11Gi        14Gi
	Swap:          31Gi        10Gi        21Gi

Graphics:
	05:00.0 VGA compatible controller [0300]: NVIDIA Corporation TU104GL [Quadro RTX 4000] [10de:1eb1] (rev a1)	
	Subsystem: NVIDIA Corporation Device [10de:12a0]	
	Kernel driver in use: nvidia

Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2023.5.7
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9.1
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.10
    ChimeraX-AtomicLibrary: 10.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.8
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6.1
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.1
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-LinuxSupport: 1.0.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.0.12
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.3.7
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.1
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.28.4
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    distro: 1.7.0
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.39.3
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.9.26
    imagesize: 1.4.1
    importlib-metadata: 6.6.0
    ipykernel: 6.21.1
    ipython: 8.10.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.6
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.0.2
    jupyter-core: 5.3.0
    jupyterlab-widgets: 3.0.7
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.2
    matplotlib: 3.6.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 2.8.8
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.23.5
    openvr: 1.23.701
    packaging: 23.1
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.3.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.5.0
    prompt-toolkit: 3.0.38
    psutil: 5.9.4
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.4.2
    PyQt6-Qt6: 6.4.3
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.3
    python-dateutil: 2.8.2
    pytz: 2023.3
    pyzmq: 25.0.2
    qtconsole: 5.4.0
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.28.2
    scipy: 1.9.3
    setuptools: 67.4.0
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.4.1
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tcia-utils: 1.2.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.1
    traitlets: 5.9.0
    typing-extensions: 4.5.0
    tzdata: 2023.3
    urllib3: 1.26.15
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7
    zipp: 3.15.0

Change History (2)

comment:1 by Eric Pettersen, 2 years ago

Component: Unassigned → Sessions
Owner: set to Greg Couch
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → EOFError restoring session

Reported by Disha Hiregange

comment:2 by Greg Couch, 2 years ago

Status: assigned → accepted

It appears that your session file has been corrupted. What is the size of "/yonath_group/sarit/pg_W83/files from home/10_02_22/helix10.cxs"?

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