Nucleotides trying to save closed structure

[madhanrt@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.18362
ChimeraX Version: 0.92 (2020-03-03)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
warning | Your computer has Intel graphics driver 7262 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: 0.92 (2020-03-03)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "G:\Halophile-ribosome-project\Ribosome Paper\Structure\LSU_5S.mrc"

Opened LSU_5S.mrc, grid size 150,150,150, pixel 1.81, shown at level 0.752,
step 1, values float32  

> volume #1 level 0.6361

> volume #1 level 0.3766

> ui mousemode rightMode translate

> ui mousemode rightMode translate

> open "G:\Halophile-ribosome-project\Ribosome Paper\Structure\1jj2.pdb"

1jj2.pdb title:  
Fully refined crystal structure of the haloarcula marismortui large ribosomal
subunit At 2.4 angstrom resolution [more info...]  
  
Chain information for 1jj2.pdb #2  
---  
Chain | Description  
0 | 23S RRNA  
1 | ribosomal protein L39E  
2 | ribosomal protein L44E  
9 | 5S RRNA  
A | ribosomal protein L2  
B | ribosomal protein L3  
C | ribosomal protein L4  
D | ribosomal protein L5  
E | ribosomal protein L6  
F | 50S ribosomal protein HS6  
G | ribosomal protein L10  
H | ribosomal protein L10E  
I | ribosomal protein L13  
J | ribosomal protein L14  
K | ribosomal protein L15  
L | ribosomal protein L15E  
M | ribosomal protein L18  
N | ribosomal protein L18E  
O | ribosomal protein L19E  
P | ribosomal protein L21E  
Q | ribosomal protein L22  
R | ribosomal protein L23  
S | ribosomal protein L24  
T | ribosomal protein L24E  
U | ribosomal protein L29  
V | ribosomal protein L30  
W | ribosomal protein L31E  
X | ribosomal protein L32E  
Y | ribosomal protein L37AE  
Z | ribosomal protein L37E  
  
Non-standard residues in 1jj2.pdb #2  
---  
CD — cadmium ion  
CL — chloride ion  
K — potassium ion  
MG — magnesium ion  
NA — sodium ion  
  

> sequence chain #2/9

Alignment identifier is 2.9  

> sequence chain #2/9

Destroying pre-existing alignment with identifier 2.9  
Alignment identifier is 2.9  

> select /9

2738 atoms, 2905 bonds, 7 pseudobonds, 2 models selected  

> lighting full

> ui mousemode rightMode "translate selected models"

> ui mousemode rightMode "translate selected models"

> ui mousemode rightMode "translate selected models"

> ui mousemode rightMode "translate selected models"

> ui mousemode rightMode "translate selected models"

> ui mousemode rightMode "translate selected models"

Drag select of 692 atoms, 1 pseudobonds  

> select /0:2798@N7

1 atom, 1 model selected  

> ui mousemode rightMode rotate

> ui mousemode rightMode "translate selected models"

> ui mousemode rightMode "rotate selected models"

Drag select of 3305 atoms, 58 pseudobonds  

> select clear

> ui mousemode rightMode "rotate selected models"

> ui mousemode rightMode "translate selected models"

> ui mousemode rightMode "rotate selected models"

> ui mousemode rightMode rotate

> ui mousemode rightMode "rotate selected models"

> ui mousemode rightMode "translate selected models"

Drag select of 333 atoms, 4 pseudobonds  

> ui mousemode rightMode "translate selected models"

> ui mousemode rightMode "rotate selected models"

Drag select of 163 atoms  

> select /9

2738 atoms, 2905 bonds, 7 pseudobonds, 2 models selected  

> ui mousemode rightMode "rotate selected models"

> ui mousemode rightMode "rotate selected models"

> ui mousemode rightMode "rotate selected models"

> ui mousemode rightMode "rotate selected models"

> ui mousemode rightMode "translate selected models"

> select #1

2 models selected  

> ui mousemode rightMode "translate selected models"

> ui mousemode rightMode "rotate selected models"

> ui mousemode rightMode "translate selected models"

> ui mousemode rightMode "rotate selected models"

> ui mousemode rightMode rotate

> ui mousemode rightMode "translate selected models"

> ui mousemode rightMode "rotate selected models"

> ui mousemode rightMode select

> select /0:1013@P

1 atom, 1 model selected  

> select /H:162@CB

1 atom, 1 model selected  

> select /H:157@O

1 atom, 1 model selected  

> select /0:5990@O

1 atom, 1 model selected  

> select /0:5990@O

1 atom, 1 model selected  

> ui mousemode rightMode "rotate selected models"

> select /P:16@CA

1 atom, 1 model selected  

> ui mousemode rightMode translate

> ui mousemode rightMode "rotate selected models"

> select /0:714@O4

1 atom, 1 model selected  

> ui mousemode rightMode "translate selected models"

> select #1

2 models selected  
Drag select of 1 LSU_5S.mrc  

> toolshed show "Model Panel"

> show target m

> ui mousemode rightMode "next docked"

> ui mousemode rightMode translate

> help help:user

> help help:user

> view clip false

> show target m

> view clip false

> toolshed show "Fit in Map"

Fit molecule 1jj2.pdb (#2) to map LSU_5S.mrc (#1) using 98543 atoms  
average map value = 0.4599, steps = 172  
shifted from previous position = 7.06  
rotated from previous position = 24.9 degrees  
atoms outside contour = 36118, contour level = 0.37663  
  
Position of 1jj2.pdb (#2) relative to LSU_5S.mrc (#1) coordinates:  
Matrix rotation and translation  
0.93231777 -0.24974766 0.26155208 166.10966937  
-0.22581855 0.16286554 0.96045860 135.16609301  
-0.28247011 -0.95451598 0.09544482 340.87110272  
Axis -0.96186649 0.27325517 0.01201928  
Axis point 0.00000000 286.96340373 75.60304943  
Rotation angle (degrees) 84.53060313  
Shift along axis -118.74346611  
  
Fit molecule 1jj2.pdb (#2) to map LSU_5S.mrc (#1) using 98543 atoms  
average map value = 0.4598, steps = 40  
shifted from previous position = 0.0126  
rotated from previous position = 0.0126 degrees  
atoms outside contour = 36121, contour level = 0.37663  
  
Position of 1jj2.pdb (#2) relative to LSU_5S.mrc (#1) coordinates:  
Matrix rotation and translation  
0.93236376 -0.24966291 0.26146906 166.09440923  
-0.22569676 0.16301765 0.96046143 135.13133828  
-0.28241566 -0.95451218 0.09564367 340.85121433  
Axis -0.96188439 0.27319135 0.01203811  
Axis point 0.00000000 286.96338860 75.60137757  
Rotation angle (degrees) 84.51917934  
Shift along axis -118.74370121  
  
Fit molecule 1jj2.pdb (#2) to map LSU_5S.mrc (#1) using 98543 atoms  
average map value = 0.4598, steps = 44  
shifted from previous position = 0.0369  
rotated from previous position = 0.0156 degrees  
atoms outside contour = 36137, contour level = 0.37663  
  
Position of 1jj2.pdb (#2) relative to LSU_5S.mrc (#1) coordinates:  
Matrix rotation and translation  
0.93236547 -0.24972100 0.26140746 166.12732881  
-0.22570561 0.16275301 0.96050423 135.18959644  
-0.28240292 -0.95454215 0.09538189 340.88290284  
Axis -0.96189664 0.27314711 0.01206254  
Axis point 0.00000000 286.95862722 75.61345597  
Rotation angle (degrees) 84.53427983  
Shift along axis -118.75875857  
  
Average map value = 0.4598 for 98543 atoms, 36137 outside contour  

> toolshed show "Fit in Map"

Average map value = 0.4598 for 98543 atoms, 36137 outside contour  
Fit molecule 1jj2.pdb (#2) to map LSU_5S.mrc (#1) using 98543 atoms  
average map value = 0.4598, steps = 40  
shifted from previous position = 0.00783  
rotated from previous position = 0.00651 degrees  
atoms outside contour = 36147, contour level = 0.37663  
  
Position of 1jj2.pdb (#2) relative to LSU_5S.mrc (#1) coordinates:  
Matrix rotation and translation  
0.93240439 -0.24962565 0.26135973 166.11553693  
-0.22566780 0.16274778 0.96051399 135.18880982  
-0.28230464 -0.95456798 0.09541431 340.88448686  
Axis -0.96191758 0.27307464 0.01203367  
Axis point 0.00000000 286.95108552 75.61405059  
Rotation angle (degrees) 84.53237738  
Shift along axis -118.77072691  
  
Fit molecule 1jj2.pdb (#2) to map LSU_5S.mrc (#1) using 98543 atoms  
average map value = 0.4598, steps = 40  
shifted from previous position = 0.0348  
rotated from previous position = 0.0166 degrees  
atoms outside contour = 36119, contour level = 0.37663  
  
Position of 1jj2.pdb (#2) relative to LSU_5S.mrc (#1) coordinates:  
Matrix rotation and translation  
0.93234914 -0.24970723 0.26147887 166.10606388  
-0.22570447 0.16301027 0.96046087 135.13721125  
-0.28245776 -0.95450185 0.09562248 340.85075020  
Axis -0.96187691 0.27321685 0.01205648  
Axis point 0.00000000 286.96859181 75.59927329  
Rotation angle (degrees) 84.52042265  
Shift along axis -118.74236477  
  
Fit molecule 1jj2.pdb (#2) to map LSU_5S.mrc (#1) using 98543 atoms  
average map value = 0.4598, steps = 40  
shifted from previous position = 0.00299  
rotated from previous position = 0.00636 degrees  
atoms outside contour = 36125, contour level = 0.37663  
  
Position of 1jj2.pdb (#2) relative to LSU_5S.mrc (#1) coordinates:  
Matrix rotation and translation  
0.93232124 -0.24973809 0.26154886 166.10359931  
-0.22578964 0.16295533 0.96045017 135.14791728  
-0.28248176 -0.95450316 0.09553848 340.85906940  
Axis -0.96186447 0.27326187 0.01202910  
Axis point 0.00000000 286.96670722 75.59937337  
Rotation angle (degrees) 84.52522376  
Shift along axis -118.73815127  
  
Fit map 1jj2.pdb map 2.4 in map LSU_5S.mrc using 1455198 points  
correlation = 0.6913, correlation about mean = 0.03668, overlap = 5.949e+05  
steps = 44, shift = 0.0311, angle = 0.0277 degrees  
  
Position of 1jj2.pdb map 2.4 (#3) relative to LSU_5S.mrc (#1) coordinates:  
Matrix rotation and translation  
0.93244511 -0.24968600 0.26115673 166.14645482  
-0.22549059 0.16261886 0.96057745 135.17360251  
-0.28231175 -0.95457417 0.09533135 340.88690914  
Axis -0.96194465 0.27297400 0.01215290  
Axis point 0.00000000 286.92566019 75.65046369  
Rotation angle (degrees) 84.53730349  
Shift along axis -118.78205012  
  
Average map value = 0.4598 for 98543 atoms, 36131 outside contour  
Fit map 1jj2.pdb map 2.4 in map LSU_5S.mrc using 1455198 points  
correlation = 0.6913, correlation about mean = 0.03667, overlap = 5.949e+05  
steps = 44, shift = 0.0282, angle = 0.0153 degrees  
  
Position of 1jj2.pdb map 2.4 (#3) relative to LSU_5S.mrc (#1) coordinates:  
Matrix rotation and translation  
0.93240796 -0.24971819 0.26125855 166.13278422  
-0.22551627 0.16287545 0.96052794 135.12589222  
-0.28241390 -0.95452200 0.09555089 340.85644999  
Axis -0.96191389 0.27308222 0.01215643  
Axis point 0.00000000 286.94226821 75.63435746  
Rotation angle (degrees) 84.52466966  
Shift along axis -118.76135768  
  
Average map value = 0.4598 for 98543 atoms, 36112 outside contour  
Fit map 1jj2.pdb map 2.4 in map LSU_5S.mrc using 1455198 points  
correlation = 0.6913, correlation about mean = 0.03668, overlap = 5.949e+05  
steps = 36, shift = 0.0348, angle = 0.0163 degrees  
  
Position of 1jj2.pdb map 2.4 (#3) relative to LSU_5S.mrc (#1) coordinates:  
Matrix rotation and translation  
0.93244955 -0.24967216 0.26115412 166.14481657  
-0.22549353 0.16260464 0.96057916 135.18054213  
-0.28229474 -0.95458021 0.09532120 340.89244764  
Axis -0.96194762 0.27296388 0.01214446  
Axis point 0.00000000 286.92798005 75.65028118  
Rotation angle (degrees) 84.53787672  
Shift along axis -118.78325193  
  
Average map value = 0.4598 for 98543 atoms, 36133 outside contour  

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> select #2

98543 atoms, 98255 bonds, 967 pseudobonds, 3 models selected  

> ~select #2

Nothing selected  

> volume #!1 style surface

> volume #!1 style surface

> volume #1 level 0.5535

> volume #1 level 0.8095

> volume #1 level 0.9751

> select /9

2738 atoms, 2905 bonds, 7 pseudobonds, 2 models selected  

> style sel ringFill thin

Changed 260 residue ring styles  

> show sel target ab

> show (sel-residues & sidechain) target ab

> nucleotides sel ladder

> select coil

12299 atoms, 12285 bonds, 10 pseudobonds, 2 models selected  

> select nucleic-acid

61617 atoms, 68981 bonds, 8 pseudobonds, 2 models selected  

> show sel target ab

> preset "molecular surfaces" "chain id coloring (opaque)"

Changed 90418 atom styles  
Preset expands to these ChimeraX commands:

    
    
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    surface
    color bychain targ s trans 0

  

> show #!3 models

> hide #!2 models

> hide #!1 models

> show #!1 models

> show #!2 models

> hide #!3 models

> volume #1 level 0.5084

> volume #1 level 0.3014

> volume #1 level 0.6213

> toolshed show "Fit to Segments"

Density map not found or not selected  
Density map not found or not selected  
Density map not found or not selected  
Density map not found or not selected  
Density map not found or not selected  
Density map not found or not selected  

> select #2

98543 atoms, 98255 bonds, 967 pseudobonds, 3 models selected  

> ~select #2

30 models selected  

> select #2

98543 atoms, 98255 bonds, 967 pseudobonds, 3 models selected  

> ~select #2

30 models selected  

> select #1

2 models selected  

> ~select #1

Nothing selected  

> hide #!2 models

> show #!2 models

> close

Expected a models specifier or a keyword  

Expected a models specifier or a keyword  

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> open "G:\Halophile-ribosome-project\Ribosome Paper\Structure\LSU_5S.mrc"

Opened LSU_5S.mrc, grid size 150,150,150, pixel 1.81, shown at level 0.752,
step 1, values float32  

> close

> open "G:\Halophile-ribosome-project\Ribosome Paper\Structure\LSU_5S.mrc"

Opened LSU_5S.mrc, grid size 150,150,150, pixel 1.81, shown at level 0.752,
step 1, values float32  

> volume #1 level 0.5197

> open "G:\Halophile-ribosome-project\Ribosome Paper\Structure\1jj2.pdb"

1jj2.pdb title:  
Fully refined crystal structure of the haloarcula marismortui large ribosomal
subunit At 2.4 angstrom resolution [more info...]  
  
Chain information for 1jj2.pdb #2  
---  
Chain | Description  
0 | 23S RRNA  
1 | ribosomal protein L39E  
2 | ribosomal protein L44E  
9 | 5S RRNA  
A | ribosomal protein L2  
B | ribosomal protein L3  
C | ribosomal protein L4  
D | ribosomal protein L5  
E | ribosomal protein L6  
F | 50S ribosomal protein HS6  
G | ribosomal protein L10  
H | ribosomal protein L10E  
I | ribosomal protein L13  
J | ribosomal protein L14  
K | ribosomal protein L15  
L | ribosomal protein L15E  
M | ribosomal protein L18  
N | ribosomal protein L18E  
O | ribosomal protein L19E  
P | ribosomal protein L21E  
Q | ribosomal protein L22  
R | ribosomal protein L23  
S | ribosomal protein L24  
T | ribosomal protein L24E  
U | ribosomal protein L29  
V | ribosomal protein L30  
W | ribosomal protein L31E  
X | ribosomal protein L32E  
Y | ribosomal protein L37AE  
Z | ribosomal protein L37E  
  
Non-standard residues in 1jj2.pdb #2  
---  
CD — cadmium ion  
CL — chloride ion  
K — potassium ion  
MG — magnesium ion  
NA — sodium ion  
  

> ui mousemode rightMode "rotate selected models"

> select /0:1113@P

1 atom, 1 model selected  

> select /0:1113@C5'

1 atom, 1 model selected  

> ui mousemode rightMode select

> select /V:132@CG1

1 atom, 1 model selected  
Drag select of 30 atoms  

> select clear

Drag select of 1227 atoms, 3 pseudobonds  

> select clear

> ui mousemode rightMode "rotate selected models"

> ui mousemode rightMode "rotate selected models"

> ui mousemode rightMode "rotate selected models"

> select /0:1742@C2

1 atom, 1 model selected  

> ui mousemode rightMode "rotate selected models"

> ui mousemode rightMode "rotate selected models"

> ui mousemode rightMode "translate selected models"

> volume #1 level 0.8798

> volume #1 level 0.965

> select /9

2738 atoms, 2905 bonds, 7 pseudobonds, 2 models selected  

> select ::name="A"::name="C"::name="G"::name="U"

61617 atoms, 68981 bonds, 8 pseudobonds, 2 models selected  

> select helix

10375 atoms, 10385 bonds, 2 pseudobonds, 2 models selected  

> volume style surface

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> select /9

2738 atoms, 2905 bonds, 7 pseudobonds, 2 models selected  

> select helix

10375 atoms, 10385 bonds, 2 pseudobonds, 2 models selected  

> select helix

10375 atoms, 10385 bonds, 2 pseudobonds, 2 models selected  

> select ~sel

88168 atoms, 87870 bonds, 965 pseudobonds, 5 models selected  

> select /9

2738 atoms, 2905 bonds, 7 pseudobonds, 2 models selected  

> surface sel

> surface hide sel

> color sel bynucleotide

> nucleotides sel ladder

> nucleotides sel stubs

> nucleotides sel stubs

> nucleotides sel ladder

> nucleotides sel tube/slab shape muffler

> nucleotides sel ladder

> nucleotides sel ladder

> nucleotides sel ladder

> volume #1 level 1.19

> ui mousemode rightMode label

> view sel

> rainbow sel

> rainbow sel

> rainbow sel

> color sel bynucleotide

Alignment identifier is 2.9  

> interfaces sel & ~solvent

0 buried areas:  

> show sel atoms

> show sel cartoons

> show sel surfaces

> show sel cartoons

> show sel cartoons

> show sel surfaces

> hide sel surfaces

> show sel cartoons

> show sel atoms

> color sel bychain

> color sel bychain

> color sel bychain

> color sel bychain

> color sel bychain

> color sel byhetero

> color sel bychain

> rainbow sel

> color bfactor sel

2738 atoms, 260 residues, 1 surfaces, atom bfactor range 23.7 to 139  

> rainbow sel

> mlp sel

mlp: no amino acids specified  

> ui mousemode rightMode "mark surface"

> view sel

> select nucleic-acid

61617 atoms, 68981 bonds, 8 pseudobonds, 2 models selected  

> select helix

10375 atoms, 10385 bonds, 2 pseudobonds, 2 models selected  

> help help:user/findseq.html

> select sequence aaacccgguuc

232 atoms, 258 bonds, 1 model selected  

> select sequence aaacccgguuc

232 atoms, 258 bonds, 1 model selected  

> select sequence aaacccgguuc

232 atoms, 258 bonds, 1 model selected  

> select sequence aaacccgguuc

232 atoms, 258 bonds, 1 model selected  

> select sequence aaacccgguuc

232 atoms, 258 bonds, 1 model selected  

> select sequence aaacccgguuc

232 atoms, 258 bonds, 1 model selected  

> select sequence aaacccgguuc

232 atoms, 258 bonds, 1 model selected  

> select sequence aaacccgguuc

232 atoms, 258 bonds, 1 model selected  

> select sequence aaacccgguuc

232 atoms, 258 bonds, 1 model selected  

> select sequence aaacccgguuc

232 atoms, 258 bonds, 1 model selected  
Destroying pre-existing alignment with identifier 2.9  
Alignment identifier is 2.9  

> mlp sel

mlp: no amino acids specified  

> mlp sel

mlp: no amino acids specified  

> color sel bynucleotide

> select nucleic-acid

61617 atoms, 68981 bonds, 8 pseudobonds, 2 models selected  

> toolshed show "Show Volume Menu"

> preset "overall look" interactive

Preset expands to these ChimeraX commands:

    
    
    ~set bg
    graphics silhouettes f

  

> preset "molecular surfaces" "atomic coloring (transparent)"

Changed 90418 atom styles  
Preset expands to these ChimeraX commands:

    
    
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    surface
    color fromatoms targ s trans 70

  

> undo

> preset cartoons/nucleotides ribbons/slabs

Changed 90418 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    nucleotides tube/slab shape box

  

> select /9

2738 atoms, 2905 bonds, 7 pseudobonds, 2 models selected  

> preset "initial styles" "space-filling (chain colors)"

Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> preset "initial styles" "space-filling (single color)"

Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> preset "initial styles" "original look"

Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> preset cartoons/nucleotides ribbons/slabs

Changed 90418 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    nucleotides tube/slab shape box

  

> preset cartoons/nucleotides cylinders/stubs

Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    cartoon style nucleic x round width 1.6 thick 1.6
    nucleotides stubs

  

> preset cartoons/nucleotides licorice/ovals

Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    cartoon style protein modeh default arrows f x round width 1 thick 1
    cartoon style nucleic x round width 1.6 thick 1.6
    nucleotides tube/slab shape ellipsoid

  

> preset "molecular surfaces" "atomic coloring (transparent)"

Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    surface
    color fromatoms targ s trans 70

  

> volume #1 level 0.8023

> volume #1 level 0.5662

> volume #1 level 1.093

> ui mousemode rightMode label

> ui mousemode rightMode label

> ui mousemode rightMode label

> ui mousemode rightMode label

> ui mousemode rightMode select

> ui mousemode rightMode rotate

> ui mousemode rightMode label

> ui mousemode rightMode label

> ui mousemode rightMode label

> ui mousemode rightMode label

> color sel bynucleotide

> volume #1 style image showOutlineBox true imageMode "tilted slab"
> tiltedSlabAxis -0.1924,0.6918,0.696 tiltedSlabOffset 231.3 tiltedSlabSpacing
> 1.809 tiltedSlabPlaneCount 30

> volume #1 colorMode opaque8 imageMode "box faces"

> color sel bynucleotide

> color sel bynucleotide

Destroying pre-existing alignment with identifier 2.9  
Alignment identifier is 2.9  

> show sel target ab

> nucleotides sel tube/slab

> lighting full

> lighting full

> lighting full

> toolshed show "Volume Viewer"

> toolshed show "Volume Viewer"

> lighting full

> lighting shadows false

> rainbow sel

Alignment identifier is 2.9  

> color sel bychain

> ui mousemode rightMode "mark surface"

> ui mousemode rightMode "mark plane"

> graphics silhouettes true

> graphics silhouettes false

> lighting shadows true

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting full

> ui mousemode rightMode select

> ui mousemode rightMode select

> select /9:109@C4'

1 atom, 1 model selected  

> select /9:109@C4'

1 atom, 1 model selected  

> select /9:108@O2'

1 atom, 1 model selected  

> select /9:108@O2'

1 atom, 1 model selected  

> select /9:108@O2

1 atom, 1 model selected  

> select /9:108@C4'

1 atom, 1 model selected  

> select /9:109@C5'

1 atom, 1 model selected  

> select /9:109@C5'

1 atom, 1 model selected  

> select /9:108@C4'

1 atom, 1 model selected  

> view sel

> view sel

> ui mousemode rightMode label

> toolshed show "Volume Viewer"

> toolshed show "Volume Viewer"

> toolshed show "Volume Viewer"

> save session "G:/Halophile-ribosome-project/Ribosome Paper/Haloarcula-
> docked-Halococcus-chimeraX.cxs"

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 276, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\structure.py", line 2401, in take_snapshot  
'structure state': Structure.take_snapshot(self, session, flags),  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\structure.py", line 159, in take_snapshot  
data = {'model state': Model.take_snapshot(self, session, flags),  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 325, in take_snapshot  
'positions': self.positions.array(),  
AttributeError: 'NoneType' object has no attribute 'array'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 796, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 556, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 255, in discovery  
self.processed[key] = self.process(obj, parents)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 279, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'nucleotides' ->
<chimerax.atomic.nucleotides._data.NucleotideState object at
0x000001F23AF701C8> -> <chimerax.atomic.structure.AtomicStructure object at
0x000001F217C4F708> '1jj2.pdb'  
  
RuntimeError: Error while saving session data for 'nucleotides' -> ->
'1jj2.pdb'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 279, in process  
raise RuntimeError(msg) from e  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 276, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\structure.py", line 2401, in take_snapshot  
'structure state': Structure.take_snapshot(self, session, flags),  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\structure.py", line 159, in take_snapshot  
data = {'model state': Model.take_snapshot(self, session, flags),  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 325, in take_snapshot  
'positions': self.positions.array(),  
AttributeError: 'NoneType' object has no attribute 'array'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 929, in <lambda>  
save_action.triggered.connect(lambda arg, s=self, sess=session:
s.file_save_cb(sess))  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 647, in file_save_cb  
self.save_dialog.display(self, session)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\save_dialog.py", line 139, in display  
fmt.save(session, filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 1100, in save  
run(session, cmd)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
results = command.run(text, log=log)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2845, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 992, in save_session  
save(session, filename, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\save.py", line 61, in save  
fmt.export(session, filename, fmt.nicknames[0], **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\io.py",
line 229, in export  
result = self.export_func(session, path, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 796, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 556, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 255, in discovery  
self.processed[key] = self.process(obj, parents)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 279, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'nucleotides' ->
<chimerax.atomic.nucleotides._data.NucleotideState object at
0x000001F23AF701C8> -> <chimerax.atomic.structure.AtomicStructure object at
0x000001F217C4F708> '1jj2.pdb'  
  
RuntimeError: Error while saving session data for 'nucleotides' -> ->
'1jj2.pdb'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 279, in process  
raise RuntimeError(msg) from e  
  
See log for complete Python traceback.  
  

> save session "G:/Halophile-ribosome-project/Ribosome Paper/Haloarcula-
> docked-Halococcus-chimeraX.cxs"

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 276, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\structure.py", line 2401, in take_snapshot  
'structure state': Structure.take_snapshot(self, session, flags),  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\structure.py", line 159, in take_snapshot  
data = {'model state': Model.take_snapshot(self, session, flags),  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 325, in take_snapshot  
'positions': self.positions.array(),  
AttributeError: 'NoneType' object has no attribute 'array'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 796, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 556, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 255, in discovery  
self.processed[key] = self.process(obj, parents)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 279, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'nucleotides' ->
<chimerax.atomic.nucleotides._data.NucleotideState object at
0x000001F23AF701C8> -> <chimerax.atomic.structure.AtomicStructure object at
0x000001F217C4F708> '1jj2.pdb'  
  
RuntimeError: Error while saving session data for 'nucleotides' -> ->
'1jj2.pdb'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 279, in process  
raise RuntimeError(msg) from e  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 276, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\structure.py", line 2401, in take_snapshot  
'structure state': Structure.take_snapshot(self, session, flags),  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\structure.py", line 159, in take_snapshot  
data = {'model state': Model.take_snapshot(self, session, flags),  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 325, in take_snapshot  
'positions': self.positions.array(),  
AttributeError: 'NoneType' object has no attribute 'array'  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 929, in <lambda>  
save_action.triggered.connect(lambda arg, s=self, sess=session:
s.file_save_cb(sess))  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 647, in file_save_cb  
self.save_dialog.display(self, session)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\save_dialog.py", line 139, in display  
fmt.save(session, filename)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 1100, in save  
run(session, cmd)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
results = command.run(text, log=log)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2845, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 992, in save_session  
save(session, filename, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\save.py", line 61, in save  
fmt.export(session, filename, fmt.nicknames[0], **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\io.py",
line 229, in export  
result = self.export_func(session, path, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 796, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 556, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 255, in discovery  
self.processed[key] = self.process(obj, parents)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 279, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'nucleotides' ->
<chimerax.atomic.nucleotides._data.NucleotideState object at
0x000001F23AF701C8> -> <chimerax.atomic.structure.AtomicStructure object at
0x000001F217C4F708> '1jj2.pdb'  
  
RuntimeError: Error while saving session data for 'nucleotides' -> ->
'1jj2.pdb'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 279, in process  
raise RuntimeError(msg) from e  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 26.20.100.7262
OpenGL renderer: Intel(R) UHD Graphics 630
OpenGL vendor: Intel

[Greg Couch]

Able to reproduce by opening NMR ensemble with nucleotides, eg., 176d. Then hiding one of the submodels, then closing the submodel, and then trying to save a session.

[Greg Couch]

Fixed.