Opened 5 years ago

Closed 13 months ago

#4199 closed defect (not a bug)

Modified nucleotides not depicted as ladder

Reported by: sitins07@… Owned by: Greg Couch
Priority: normal Milestone:
Component: Depiction Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description (last modified by Greg Couch) 

The following bug report has been submitted:
Platform:        Windows-10-10.0.17763
ChimeraX Version: 1.2.dev202011140750 (2020-11-14 07:50:08 UTC)
Description
Ladder depiction of the modified nucleotides like PSU, 3TD, MIA, G7M etc. doesn't work. 

Log:
UCSF ChimeraX version: 1.2.dev202011140750 (2020-11-14)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open D:/Projects/translocation/G3/Figures/tRNA_sites/C-H1-Ch1_tRNA-
> contacts_figure.cxs

Log from Thu Jan 28 14:30:06 2021UCSF ChimeraX version: 1.2.dev202101250432
(2021-01-25)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open D:/Projects/translocation/G3/States/70S_tRNA/models/70S_AP_v2.cif-
> coot-6.pdb

Chain information for 70S_AP_v2.cif-coot-6.pdb #1  
---  
Chain | Description  
0 | No description available  
1 | No description available  
2 | No description available  
3 | No description available  
4 | No description available  
5 | No description available  
6 | No description available  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | 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  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
e | No description available  
f | No description available  
g | No description available  
h | No description available  
i | No description available  
j | No description available  
k | No description available  
l | 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  
y | No description available  
z | No description available  
  

> close

> open D:/Projects/translocation/G3/States/70S_tRNA/models/70S_AP_v2.cif-
> coot-7.pdb

Chain information for 70S_AP_v2.cif-coot-7.pdb #1  
---  
Chain | Description  
0 | No description available  
1 | No description available  
2 | No description available  
3 | No description available  
4 | No description available  
5 | No description available  
6 | No description available  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | 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  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
e | No description available  
f | No description available  
g | No description available  
h | No description available  
i | No description available  
j | No description available  
k | No description available  
l | 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  
y | No description available  
z | No description available  
  

> open D:/Projects/translocation/G3/States/pre1_GDP-Pi/models/Pre1_GDP-
> Pi_RSR-4-coot-52.pdb

Summary of feedback from opening D:/Projects/translocation/G3/States/pre1_GDP-
Pi/models/Pre1_GDP-Pi_RSR-4-coot-52.pdb  
---  
warning | Ignored bad PDB record found on line 153667  
END  
  
Chain information for Pre1_GDP-Pi_RSR-4-coot-52.pdb #2  
---  
Chain | Description  
0 | No description available  
1 | No description available  
2 | No description available  
3 | No description available  
4 | No description available  
5 | No description available  
6 | No description available  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | 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  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
e | No description available  
f | No description available  
g | No description available  
h | No description available  
i | No description available  
j | No description available  
k | No description available  
l | 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  
  

> open
> D:/Projects/translocation/G3/States/Chimeric-1-GDP/models/Chimeric_GDP-1-sw1-v2-RSR-0-coot-22.pdb

Summary of feedback from opening
D:/Projects/translocation/G3/States/Chimeric-1-GDP/models/Chimeric_GDP-1-sw1-v2-RSR-0-coot-22.pdb  
---  
warning | Ignored bad PDB record found on line 157316  
END  
  
Chain information for Chimeric_GDP-1-sw1-v2-RSR-0-coot-22.pdb #3  
---  
Chain | Description  
0 | No description available  
1 | No description available  
2 | No description available  
3 | No description available  
4 | No description available  
5 | No description available  
6 | No description available  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | 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  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
e | No description available  
f | No description available  
g | No description available  
h | No description available  
i | No description available  
j | No description available  
k | No description available  
l | 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  
  

> set bgColor white

> hide atoms

> show cartoons

> cartoon style xsection oval

> cartoon style helix width 1.8 thickness 0.4

> cartoon style strand width 1.5 thickness 0.4

> cartoon style coil width 0.4 thickness 0.4

> cartoon style nucleic width 0.8 thickness 0.8 xsection oval

> cartoon style xsection oval

> cartoon style helix width 2.5 thickness 0.5

> cartoon style strand width 2 thickness 0.8

> cartoon style coil width 0.5 thickness 0.5

> cartoon style nucleic width 1.2 thickness 1.2 xsection oval

> select /a-u

156215 atoms, 168725 bonds, 12023 residues, 3 models selected  

> color sel grey

> select /x

10956 atoms, 11157 bonds, 1414 residues, 3 models selected  

> color sel red

> select /w

4897 atoms, 5463 bonds, 232 residues, 3 models selected  

> select /w,y

4960 atoms, 5526 bonds, 238 residues, 3 models selected  

> color sel midnight blue

> select /v

4938 atoms, 5511 bonds, 234 residues, 3 models selected  

> color sel cyan

> select /A-Z,0-6

276396 atoms, 299934 bonds, 20591 residues, 3 models selected  

> color sel white

> select clear

> select /A-Z,0-6

276396 atoms, 299934 bonds, 20591 residues, 3 models selected  

> hide sel atoms

> hide sel cartoons

> mmaker #2/a:1-929,1068-1107,1381-1600 to #1/a matrix Nucleic

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
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 70S_AP_v2.cif-coot-7.pdb, chain a (#1) with Pre1_GDP-
Pi_RSR-4-coot-52.pdb, chain a (#2), sequence alignment score = 4504.8  
RMSD between 1098 pruned atom pairs is 0.572 angstroms; (across all 1129
pairs: 0.843)  
  

> mmaker #3/a:1-929,1068-1107,1381-1600 to #1/a matrix Nucleic

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
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 70S_AP_v2.cif-coot-7.pdb, chain a (#1) with
Chimeric_GDP-1-sw1-v2-RSR-0-coot-22.pdb, chain a (#3), sequence alignment
score = 4504.8  
RMSD between 1030 pruned atom pairs is 0.739 angstroms; (across all 1129
pairs: 1.296)  
  

> select /a:929-1068,1107-1381 /s,n,c,j,m,g,i

47512 atoms, 50982 bonds, 3886 residues, 3 models selected  

> color sel color sel light grey

Invalid "color" argument: Expected a color or one of 'byatom', 'bychain',
'byelement', 'byhetero', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
or 'random'  

> color sel light grey

> select clear

> save D:/Projects/translocation/G3/Figures/tRNA_sites/C-H1-Ch1_side.cxs
> includeMaps true

> lighting full

> lighting shadows false

> lighting soft

> lighting full

> lighting shadows false

> color /z lime

> select clear

> hide #2 models

> hide #3 models

> select #1/w:39

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select add #1/z:4

40 atoms, 42 bonds, 2 residues, 1 model selected  

> select add #1/v:52

63 atoms, 67 bonds, 3 residues, 1 model selected  

> select up

3503 atoms, 3910 bonds, 164 residues, 1 model selected  

> show #2 models

> show #3 models

> select /a-u,x

167171 atoms, 179882 bonds, 13437 residues, 3 models selected  

> hide sel cartoons

> hide #3 models

> hide #2 models

Drag select of 79 residues  
Drag select of 111 residues  

> select sel @< 5

7680 atoms, 8119 bonds, 591 residues, 3 models selected  

> show sel & #1 cartoons

> select up

10904 atoms, 11987 bonds, 591 residues, 3 models selected  

> show sel & #1 atoms

> style sel & #1 stick

Changed 4241 atom styles  

> nucleotides sel & #1 fill

> style nucleic & sel & #1 stick

Changed 4151 atom styles  

> ui tool show H-Bonds

> hbonds sel restrict both reveal true

1620 hydrogen bonds found  

> hbonds sel restrict both interModel false intraMol false intraRes false
> reveal true

178 hydrogen bonds found  

> select clear

Drag select of 3048 atoms, 223 residues, 3328 bonds, 486 shapes, 455
pseudobonds  

> hbonds sel restrict both reveal true interModel false intraMol false
> intraRes false

76 hydrogen bonds found  

> show #!2 models

> hide #!1 models

Drag select of 2314 atoms, 166 residues, 313 pseudobonds  

> color sel byhetero

> undo

> style sel stick

Changed 4299 atom styles  

> nucleotides sel fill

> style nucleic & sel stick

Changed 4252 atom styles  
Drag select of 2313 atoms, 166 residues, 2528 bonds, 313 pseudobonds, 354
shapes  

> hide sel atoms

Drag select of 166 residues  

> select zone

Missing or invalid "near" argument: empty atom specifier  
Drag select of 166 residues  

> show #!1 models

> hide #!2 models

> ui mousemode right pivot

> save D:/Projects/translocation/G3/Figures/tRNA_sites/C-contacts.cxs

> show #!2 models

> hide #!1 models

> select sel @< 5

10084 atoms, 10612 bonds, 1256 pseudobonds, 794 residues, 7 models selected  

> ~select #1,2,4

2797 atoms, 2790 bonds, 20 pseudobonds, 306 residues, 2 models selected  
Drag select of 166 residues  

> select sel @< 5

10084 atoms, 10612 bonds, 1256 pseudobonds, 794 residues, 7 models selected  

> ~select #1,3,4

4191 atoms, 4544 bonds, 63 pseudobonds, 259 residues, 2 models selected  

> show sel cartoons

> show sel atoms

> style sel stick

Changed 4191 atom styles  

> select up

5211 atoms, 5745 bonds, 63 pseudobonds, 259 residues, 2 models selected  

> show sel atoms

> style sel stick

Changed 5211 atom styles  

> nucleotides sel fill

> style nucleic & sel stick

Changed 5007 atom styles  

> hbonds sel restrict both reveal true interModel false intraMol false
> intraRes false retainCurrent true

96 hydrogen bonds found  

> select clear

> hide #!2 models

> show #!3 models

Drag select of 2168 atoms, 165 residues, 252 pseudobonds  

> hide sel atoms

Drag select of 165 residues  

> select sel @< 5

9197 atoms, 9629 bonds, 822 pseudobonds, 727 residues, 7 models selected  

> ~select #1,2,4

4126 atoms, 4455 bonds, 35 pseudobonds, 273 residues, 2 models selected  

> show sel cartoons

> show sel atoms

> style sel stick

Changed 4126 atom styles  

> select up

5390 atoms, 5942 bonds, 35 pseudobonds, 273 residues, 2 models selected  

> show sel atoms

> style sel stick

Changed 5390 atom styles  

> nucleotides sel fill

> style nucleic & sel stick

Changed 5144 atom styles  

> select clear

Drag select of 3861 atoms, 269 residues, 4200 bonds, 183 pseudobonds, 605
shapes  

> hbonds sel restrict both reveal true interModel false intraMol false
> intraRes false retainCurrent true

83 hydrogen bonds found  

> show #!2 models

> hide #!2 models

Drag select of 3861 atoms, 269 residues, 4200 bonds, 183 pseudobonds, 605
shapes  

> nucleotides sel ladder

> nucleotides sel fill

> style nucleic & sel stick

Changed 5144 atom styles  

> select clear

> hide #!3 models

> show #!1 models

> save D:/Projects/translocation/G3/Figures/tRNA_sites/C-H1-Ch1_contacts.cxs

> select #1/w:46

24 atoms, 26 bonds, 1 residue, 1 model selected  

> select up

1631 atoms, 1821 bonds, 76 residues, 1 model selected  

> show sel cartoons

> hide sel atoms

> show sel atoms

> nucleotides sel stubs

> select up

147829 atoms, 160245 bonds, 11054 residues, 1 model selected  

> select down

1631 atoms, 1821 bonds, 76 residues, 1 model selected  
Drag select of 2110 atoms, 223 residues, 2297 bonds, 442 pseudobonds, 470
shapes  

> nucleotides sel stubs

> ui tool show "Side View"

Drag select of 77 atoms, 95 residues, 80 bonds, 160 shapes, 145 pseudobonds  

> hide sel cartoons

> hide sel atoms

Drag select of 192 atoms, 128 residues, 194 bonds, 232 pseudobonds, 243 shapes  

> nucleotides sel fill

> style nucleic & sel stick

Changed 2582 atom styles  

> select clear

> select #1/w:31

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select up

1631 atoms, 1821 bonds, 76 residues, 1 model selected  

> select subtract #1/w:34

1608 atoms, 1796 bonds, 75 residues, 1 model selected  

> select subtract #1/w:35

1586 atoms, 1772 bonds, 74 residues, 1 model selected  

> select subtract #1/w:36

1564 atoms, 1748 bonds, 73 residues, 1 model selected  

> select subtract #1/w:37

1535 atoms, 1717 bonds, 72 residues, 1 model selected  

> hide sel atoms

> select clear

Drag select of 1 atoms  
Drag select of 1 atoms  

> hide sel atoms

> select #1/a:529

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select up

33050 atoms, 37004 bonds, 1540 residues, 1 model selected  

> select subtract #1/a:530

33027 atoms, 36979 bonds, 1539 residues, 1 model selected  

> select subtract #1/a:531

33007 atoms, 36958 bonds, 1538 residues, 1 model selected  

> select subtract #1/a:1492

32985 atoms, 36934 bonds, 1537 residues, 1 model selected  

> select subtract #1/a:1493

32963 atoms, 36910 bonds, 1536 residues, 1 model selected  

> select subtract #1/a:1403

32943 atoms, 36889 bonds, 1535 residues, 1 model selected  

> select subtract #1/a:1400

32923 atoms, 36868 bonds, 1534 residues, 1 model selected  

> select subtract #1/a:1401

32900 atoms, 36843 bonds, 1533 residues, 1 model selected  

> select subtract #1/a:1497

32877 atoms, 36818 bonds, 1532 residues, 1 model selected  

> select add #1/a:1497

32900 atoms, 36843 bonds, 1533 residues, 1 model selected  

> select subtract #1/a:1498

32879 atoms, 36821 bonds, 1532 residues, 1 model selected  

> select subtract #1/a:791

32856 atoms, 36796 bonds, 1531 residues, 1 model selected  

> select subtract #1/a:788

32836 atoms, 36775 bonds, 1530 residues, 1 model selected  

> select subtract #1/a:693

32813 atoms, 36750 bonds, 1529 residues, 1 model selected  

> hide sel cartoons

> show sel cartoons

> hide sel atoms

> undo

> undo

> hide sel atoms

> undo

> undo

> hide sel atoms

Drag select of 1 atoms  

> hide sel atoms

> select #1/v:23

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select up

1642 atoms, 1834 bonds, 77 residues, 1 model selected  

> select subtract #1/v:13

1622 atoms, 1813 bonds, 76 residues, 1 model selected  

> select add #1/v:13

1642 atoms, 1834 bonds, 77 residues, 1 model selected  

> select subtract #1/v:12

1619 atoms, 1809 bonds, 76 residues, 1 model selected  

> select subtract #1/v:11

1597 atoms, 1785 bonds, 75 residues, 1 model selected  

> select subtract #1/v:24

1577 atoms, 1764 bonds, 74 residues, 1 model selected  

> select subtract #1/v:25

1557 atoms, 1743 bonds, 73 residues, 1 model selected  

> select subtract #1/v:39

1537 atoms, 1722 bonds, 72 residues, 1 model selected  

> select add #1/v:39

1557 atoms, 1743 bonds, 73 residues, 1 model selected  

> select subtract #1/v:38

1535 atoms, 1719 bonds, 72 residues, 1 model selected  

> select add #1/v:38

1557 atoms, 1743 bonds, 73 residues, 1 model selected  

> select subtract #1/v:38

1535 atoms, 1719 bonds, 72 residues, 1 model selected  

> select subtract #1/v:37

1513 atoms, 1695 bonds, 71 residues, 1 model selected  

> select subtract #1/v:36

1493 atoms, 1674 bonds, 70 residues, 1 model selected  

> select subtract #1/v:35

1471 atoms, 1650 bonds, 69 residues, 1 model selected  

> select subtract #1/v:34

1451 atoms, 1629 bonds, 68 residues, 1 model selected  

> select subtract #1/v:33

1431 atoms, 1608 bonds, 67 residues, 1 model selected  

> select subtract #1/v:32

1411 atoms, 1587 bonds, 66 residues, 1 model selected  

> hide sel atoms

> select #1/a:1340

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select add #1/a:1339

44 atoms, 48 bonds, 1 pseudobond, 2 residues, 2 models selected  

> select add #1/a:1338

67 atoms, 73 bonds, 1 pseudobond, 3 residues, 2 models selected  

> select add #1/a:1341

87 atoms, 94 bonds, 1 pseudobond, 4 residues, 2 models selected  

> show sel atoms

> select add #1/v:43

109 atoms, 118 bonds, 1 pseudobond, 5 residues, 2 models selected  

> select up

34692 atoms, 38838 bonds, 1 pseudobond, 1617 residues, 2 models selected  

> select down

109 atoms, 118 bonds, 1 pseudobond, 5 residues, 2 models selected  

> select clear

> select #1/v:43

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select up

1642 atoms, 1834 bonds, 77 residues, 1 model selected  

> select add #1/a:1339

1664 atoms, 1858 bonds, 78 residues, 1 model selected  

> select add #1/a:1338

1687 atoms, 1883 bonds, 79 residues, 1 model selected  

> select add #1/a:1341

1707 atoms, 1904 bonds, 80 residues, 1 model selected  

> select add #1/a:1340

1729 atoms, 1928 bonds, 81 residues, 1 model selected  

> hbonds sel restrict both reveal true interModel false intraMol false
> intraRes false retainCurrent true

9 hydrogen bonds found  

> select subtract #1/a:1341

1709 atoms, 1907 bonds, 80 residues, 1 model selected  

> select #1/a:1341

20 atoms, 21 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select add #1/a:1229

42 atoms, 45 bonds, 2 residues, 1 model selected  

> select add #1/a:1230

62 atoms, 66 bonds, 3 residues, 1 model selected  

> select add #1/a:1231

85 atoms, 91 bonds, 4 residues, 1 model selected  

> show sel atoms

> select #1/a:1230

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select add #1/a:1231

43 atoms, 46 bonds, 2 residues, 1 model selected  

> hide sel atoms

> select add #1/a:966

67 atoms, 72 bonds, 3 residues, 1 model selected  

> show sel atoms

> select add #1/a:1196

89 atoms, 96 bonds, 4 residues, 1 model selected  

> show sel atoms

> select add #1/a:1054

109 atoms, 117 bonds, 5 residues, 1 model selected  

> select add #1/a:1053

132 atoms, 142 bonds, 6 residues, 1 model selected  

> show sel atoms

> select #1/a:1053

23 atoms, 25 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select #1/a:955

20 atoms, 21 bonds, 1 residue, 1 model selected  

> show sel atoms

> hide sel atoms

> select clear

> show #!2 models

> hide #!1 models

Drag select of 1127 atoms, 91 residues, 1210 bonds, 179 shapes, 26 pseudobonds  

> hide sel atoms

> hide sel cartoons

Drag select of 190 atoms, 10 residues, 204 bonds, 29 shapes, 11 pseudobonds  
Drag select of 207 atoms, 11 residues, 224 bonds, 31 shapes, 12 pseudobonds  

> select clear

Drag select of 181 atoms, 10 residues, 195 bonds, 27 shapes, 9 pseudobonds  

> hide sel atoms

> hide sel cartoons

Drag select of 2 atoms  

> hide sel atoms

> select #2/w:28

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select up

1631 atoms, 1821 bonds, 76 residues, 1 model selected  

> select subtract #2/w:33

1611 atoms, 1800 bonds, 75 residues, 1 model selected  

> select add #2/w:33

1631 atoms, 1821 bonds, 76 residues, 1 model selected  

> select subtract #2/w:34

1608 atoms, 1796 bonds, 75 residues, 1 model selected  

> select subtract #2/w:35

1586 atoms, 1772 bonds, 74 residues, 1 model selected  

> select subtract #2/w:36

1564 atoms, 1748 bonds, 73 residues, 1 model selected  

> select subtract #2/w:37

1535 atoms, 1717 bonds, 72 residues, 1 model selected  

> hide sel atoms

> select clear

> select add #2/A:1915

21 atoms, 22 bonds, 1 residue, 1 model selected  

> select subtract #2/A:1915

Nothing selected  

> select add #2/A:1914

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select add #2/A:1915

41 atoms, 43 bonds, 2 residues, 1 model selected  

> hide sel atoms

> select clear

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select up

33050 atoms, 37004 bonds, 1540 residues, 1 model selected  

> select clear

> select #2/a:1053

23 atoms, 25 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select #2/a:531

20 atoms, 21 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select #2/a:528

20 atoms, 21 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select add #2/a:1402

42 atoms, 44 bonds, 2 residues, 1 model selected  

> select add #2/a:1401

65 atoms, 69 bonds, 3 residues, 1 model selected  

> hide sel atoms

> select add #2/a:1611@MG

66 atoms, 69 bonds, 4 residues, 1 model selected  

> hide sel atoms

> select add #2/a:1400

86 atoms, 90 bonds, 5 residues, 1 model selected  

> hide sel atoms

> select add #2/a:1506

106 atoms, 111 bonds, 6 residues, 1 model selected  

> select add #2/a:1505

129 atoms, 136 bonds, 7 residues, 1 model selected  

> hide sel atoms

> select add #2/a:789

149 atoms, 157 bonds, 8 residues, 1 model selected  

> hide sel atoms

> select add #2/a:966

173 atoms, 183 bonds, 9 residues, 1 model selected  

> hide sel atoms

> select add #2/a:1341

193 atoms, 204 bonds, 10 residues, 1 model selected  

> hide sel atoms

Drag select of 549 atoms, 38 residues, 598 bonds, 9 pseudobonds, 89 shapes  

> hide sel atoms

> hide sel cartoons

> select #2/v:10

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select up

1642 atoms, 1834 bonds, 77 residues, 1 model selected  

> select subtract #2/v:41

1622 atoms, 1813 bonds, 1 pseudobond, 76 residues, 2 models selected  

> select subtract #2/v:40

1602 atoms, 1792 bonds, 1 pseudobond, 75 residues, 2 models selected  

> select subtract #2/v:30

1579 atoms, 1767 bonds, 1 pseudobond, 74 residues, 2 models selected  

> select subtract #2/v:31

1556 atoms, 1742 bonds, 1 pseudobond, 73 residues, 2 models selected  

> select subtract #2/v:35

1534 atoms, 1718 bonds, 1 pseudobond, 72 residues, 2 models selected  

> select subtract #2/v:34

1514 atoms, 1697 bonds, 1 pseudobond, 71 residues, 2 models selected  

> select subtract #2/v:36

1494 atoms, 1676 bonds, 1 pseudobond, 70 residues, 2 models selected  

> select subtract #2/v:37

1472 atoms, 1652 bonds, 1 pseudobond, 69 residues, 2 models selected  

> select subtract #2/v:38

1450 atoms, 1628 bonds, 1 pseudobond, 68 residues, 2 models selected  

> hide sel cartoons

> undo

> hide sel atoms

> show sel cartoons

Drag select of 40 residues  

> hide sel atoms

> hide sel cartoons

> show #!3 models

> hide #!2 models

> show #!1 models

> hide #!3 models

> show #!3 models

> hide #!1 models

> save D:/Projects/translocation/G3/Figures/tRNA_sites/C-H1-Ch1_side.cxs

Drag select of 1710 atoms, 126 residues, 1860 bonds, 48 pseudobonds, 269
shapes  

> hide sel atoms

> hide sel cartoons

Drag select of 76 atoms, 5 residues, 77 bonds, 9 shapes, 4 pseudobonds  

> hide sel atoms

> hide sel cartoons

Drag select of 288 atoms, 18 residues, 316 bonds, 46 shapes  

> hide sel cartoons

> hide sel atoms

> select add #3/a:693@N2

422 atoms, 316 bonds, 22 residues, 1 model selected  

> select add #3/v:38@O2'

423 atoms, 316 bonds, 23 residues, 1 model selected  

> hbonds sel restrict both reveal true interModel false intraMol false
> intraRes false retainCurrent true

0 hydrogen bonds found  

> select add #3/a:694

445 atoms, 340 bonds, 24 residues, 1 model selected  

> select #3/a:694

22 atoms, 24 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select add #3/a:1506

42 atoms, 45 bonds, 2 residues, 1 model selected  

> select add #3/a:1402

64 atoms, 68 bonds, 3 residues, 1 model selected  

> select add #3/a:1400

84 atoms, 89 bonds, 4 residues, 1 model selected  

> select add #3/a:530

107 atoms, 114 bonds, 5 residues, 1 model selected  

> select add #3/a:1053

130 atoms, 139 bonds, 6 residues, 1 model selected  

> select add #3/a:1198

153 atoms, 164 bonds, 7 residues, 1 model selected  

> select add #3/a:965

173 atoms, 185 bonds, 8 residues, 1 model selected  

> select add #3/a:1498

194 atoms, 207 bonds, 9 residues, 1 model selected  

> select add #3/a:790

216 atoms, 231 bonds, 10 residues, 1 model selected  

> select add #3/a:789

236 atoms, 252 bonds, 11 residues, 1 model selected  

> hide sel atoms

> select add #3/v:102@MG

237 atoms, 252 bonds, 12 residues, 1 model selected  

> hide sel atoms

> select add #3/a:944

260 atoms, 277 bonds, 13 residues, 1 model selected  

> select add #3/a:1341

280 atoms, 298 bonds, 14 residues, 1 model selected  

> select add #3/a:1231

303 atoms, 323 bonds, 15 residues, 1 model selected  

> select add #3/a:1230

323 atoms, 344 bonds, 16 residues, 1 model selected  

> select add #3/a:1229

345 atoms, 368 bonds, 17 residues, 1 model selected  

> hide sel atoms

> select add #3/a:956

365 atoms, 389 bonds, 18 residues, 1 model selected  

> select add #3/a:955

385 atoms, 410 bonds, 19 residues, 1 model selected  

> select add #3/a:954

408 atoms, 435 bonds, 20 residues, 1 model selected  

> select add #3/a:953

431 atoms, 460 bonds, 21 residues, 1 model selected  

> hide sel atoms

> select #3/w:40

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select up

1631 atoms, 1821 bonds, 76 residues, 1 model selected  

> select subtract #3/w:37

1602 atoms, 1790 bonds, 75 residues, 1 model selected  

> select subtract #3/w:36

1580 atoms, 1766 bonds, 74 residues, 1 model selected  

> select subtract #3/w:35

1558 atoms, 1742 bonds, 73 residues, 1 model selected  

> select subtract #3/w:34

1535 atoms, 1717 bonds, 72 residues, 1 model selected  

> select subtract #3/w:42

1515 atoms, 1696 bonds, 71 residues, 1 model selected  

> select add #3/w:42

1535 atoms, 1717 bonds, 72 residues, 1 model selected  

> select subtract #3/w:41

1515 atoms, 1696 bonds, 71 residues, 1 model selected  

> hide sel atoms

> select clear

> save D:/Projects/translocation/G3/Figures/tRNA_sites/C-H1-Ch1_side.cxs
> includeMaps true

Drag select of 2 atoms, 3 residues, 4 bonds, 1 shapes, 1 pseudobonds  

> select clear

> select add #3/w:103@MG

1 atom, 1 residue, 1 model selected  

> select add #3/w:104@MG

2 atoms, 2 residues, 1 model selected  

> hide sel atoms

> select add #3/A:1910

25 atoms, 25 bonds, 3 residues, 1 model selected  

> select add #3/A:1909

45 atoms, 46 bonds, 4 residues, 1 model selected  

> select add #3/A:1908

65 atoms, 67 bonds, 5 residues, 1 model selected  

> select add #3/A:1922

88 atoms, 92 bonds, 6 residues, 1 model selected  

> hide sel atoms

> select #3/v:39

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select up

1642 atoms, 1834 bonds, 77 residues, 1 model selected  

> select subtract #3/v:41

1622 atoms, 1813 bonds, 76 residues, 1 model selected  

> select subtract #3/v:40

1602 atoms, 1792 bonds, 75 residues, 1 model selected  

> select subtract #3/v:36

1582 atoms, 1771 bonds, 1 pseudobond, 74 residues, 2 models selected  

> select subtract #3/v:37

1560 atoms, 1747 bonds, 1 pseudobond, 73 residues, 2 models selected  

> select subtract #3/v:35

1538 atoms, 1723 bonds, 1 pseudobond, 72 residues, 2 models selected  

> select subtract #3/v:34

1518 atoms, 1702 bonds, 1 pseudobond, 71 residues, 2 models selected  

> hide sel atoms

> select clear

Drag select of 6 residues  

> hide sel cartoons

Drag select of 3 residues  

> hide sel atoms

> hide sel cartoons

> select #3/a:956

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select #3/a:940-980

883 atoms, 988 bonds, 41 residues, 1 model selected  

> show sel cartoons

Drag select of 7 residues  

> hide sel cartoons

> select #3/a:1188-1208

448 atoms, 500 bonds, 1 pseudobond, 21 residues, 2 models selected  

> show sel atoms

> hide sel atoms

> show sel cartoons

> hide sel cartoons

> select #3/a:1193-1203

232 atoms, 258 bonds, 1 pseudobond, 11 residues, 2 models selected  

> show sel atoms

> hide sel atoms

> show sel cartoons

> select #3/a:1049-1059

234 atoms, 260 bonds, 2 pseudobonds, 11 residues, 2 models selected  

> show sel cartoons

> select clear

> select #3/a:1224-1236

274 atoms, 305 bonds, 13 residues, 1 model selected  

> show sel cartoons

> select clear

> select #3/a:1333-1346

300 atoms, 335 bonds, 14 residues, 1 model selected  

> show sel cartoons

> select clear

> select #3/i:129

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

> select up

322 atoms, 324 bonds, 38 residues, 1 model selected  

> show sel cartoons

> select up

1022 atoms, 1034 bonds, 127 residues, 1 model selected  

> show sel cartoons

Drag select of 111 residues  

> hide sel cartoons

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

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

> show sel cartoons

> select up

273 atoms, 277 bonds, 35 residues, 1 model selected  

> show sel cartoons

> select clear

> save D:/Projects/translocation/G3/Figures/tRNA_sites/C-H1-Ch1_tRNA-
> contacts_figure.cxs includeMaps true

> show #!1 models

> hide #!3 models

> show #!2 models

> show #!3 models

> camera

Camera parameters:  
type: mono  
position: 284.05 270.16 231.48  
view direction: -0.67276 -0.72961 -0.12273  
field of view: 30 degrees  

> camera ortho

> hide #!2 models

> hide #!1 models

> graphics silhouettes

Current silhouette settings:  
enabled: False  
width: 1  
color: 0,0,0  
depth jump: 0.03  

> graphics silhouettes width 2

> lighting flat

> lighting soft

> lighting full

> lighting shadows false

> graphics silhouettes false

> graphics silhouettes true

> show #!2 models

> hide #!3 models

> show #!1 models

> hide #!2 models

> select #1/z:-1@N4

1 atom, 1 residue, 1 model selected  

> select clear

> select clear

> show #!2 models

> show #!3 models

> hide #!3 models

> hide #!2 models

> show #!2 models

> hide #!1 models

> show #!1 models

> hide #!2 models

> show #!2 models

> show #!3 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> hide #!3 models

> show #!1 models

> hide #!1 models

> show #!1 models

> select add #1/w:14

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select add #1/w:13

42 atoms, 45 bonds, 2 residues, 1 model selected  

> select add #1/w:12

62 atoms, 66 bonds, 3 residues, 1 model selected  

> select add #1/w:11

82 atoms, 87 bonds, 4 residues, 1 model selected  

> select add #1/w:10

105 atoms, 112 bonds, 5 residues, 1 model selected  

> select add #1/w:9

127 atoms, 136 bonds, 6 residues, 1 model selected  

> hide sel cartoons

> select #1/w:46

24 atoms, 26 bonds, 1 residue, 1 model selected  

> hide sel cartoons

> select add #1/w:45

44 atoms, 47 bonds, 1 pseudobond, 2 residues, 2 models selected  

> select add #1/w:44

67 atoms, 72 bonds, 1 pseudobond, 3 residues, 2 models selected  

> hide sel cartoons

> select add #1/A:1915

88 atoms, 94 bonds, 1 pseudobond, 4 residues, 2 models selected  

> select add #1/A:1916

110 atoms, 118 bonds, 1 pseudobond, 5 residues, 2 models selected  

> select add #1/A:1914

130 atoms, 139 bonds, 1 pseudobond, 6 residues, 2 models selected  

> hide sel atoms

> select #1/1909-1914

Nothing selected  

> select #1/A:1909-1914

127 atoms, 141 bonds, 6 residues, 1 model selected  

> show sel cartoons

> select clear

> select add #1/A:1925

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select add #1/A:1924

40 atoms, 42 bonds, 2 residues, 1 model selected  

> hide sel atoms

> select clear

> select #1/A:1909-1925

360 atoms, 401 bonds, 2 pseudobonds, 17 residues, 2 models selected  

> show sel cartoons

> select clear

> select add #1/a:1611@MG

1 atom, 1 residue, 1 model selected  

> hide sel atoms

> select /a:929-1068,1107-1381 /s,n,c,j,m,g,i

47512 atoms, 50982 bonds, 48 pseudobonds, 3886 residues, 7 models selected  

> color sel grey

> color sel silver

> select clear

> select add #1/a:1341

20 atoms, 21 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select add #1/a:1231

43 atoms, 46 bonds, 2 residues, 1 model selected  

> hide sel atoms

Drag select of 3 residues  

> hide sel cartoons

> select #1/a:518

20 atoms, 21 bonds, 1 pseudobond, 1 residue, 2 models selected  

> select #1/a:513-523

233 atoms, 259 bonds, 1 pseudobond, 11 residues, 2 models selected  

> show sel cartoons

Drag select of 2 residues  

> hide sel cartoons

Drag select of 3 residues  

> hide sel cartoons

> select #1/a:531

20 atoms, 21 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select #1/a:527-533

154 atoms, 172 bonds, 7 residues, 1 model selected  

> show sel cartoons

> select clear

> select #1/a:1048-1056

191 atoms, 212 bonds, 9 residues, 1 model selected  

> show sel cartoons

Drag select of 3 residues  

> hide sel cartoons

> select #1/c:161

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

> select up

27 atoms, 26 bonds, 4 residues, 1 model selected  

> show sel cartoons

> select clear

> select #1/a:1193-1200

170 atoms, 189 bonds, 8 residues, 1 model selected  

> show sel cartoons

Drag select of 2 residues  

> hide sel cartoons

Drag select of 1 residues  

> hide sel cartoons

> select #1/a:950-970

447 atoms, 498 bonds, 21 residues, 1 model selected  

> show sel cartoons

> select clear

Drag select of 2 residues  

> hide sel cartoons

> select #1/i:128

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

> select up

249 atoms, 251 bonds, 29 residues, 1 model selected  

> show sel cartoons

Drag select of 22 residues  

> hide sel cartoons

> select #1/a:1227-1232

127 atoms, 141 bonds, 2 pseudobonds, 6 residues, 2 models selected  

> show sel cartoons

> select clear

> select #1/a:1230

20 atoms, 21 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select clear

> select #1/a:1336-1343

173 atoms, 193 bonds, 8 residues, 1 model selected  

> show sel cartoons

> select clear

Drag select of 7 atoms, 3 residues, 6 bonds  

> select up

39 atoms, 38 bonds, 6 residues, 1 model selected  

> hide sel cartoons

> hide sel atoms

> select add #1/z:-1

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

> select add #1/z:-2

81 atoms, 83 bonds, 8 residues, 1 model selected  

> hide sel atoms

Drag select of 3 residues  

> hide sel cartoons

> select add #1/a:693

29 atoms, 25 bonds, 2 residues, 1 model selected  

> select up

43 atoms, 46 bonds, 2 residues, 1 model selected  

> hide sel atoms

> hide sel cartoons

> hide sel cartoons

> select #1/a:1492-1497

130 atoms, 145 bonds, 2 pseudobonds, 6 residues, 2 models selected  

> show sel cartoons

> select #1/a:788-793

127 atoms, 141 bonds, 2 pseudobonds, 6 residues, 2 models selected  

> show sel cartoons

> select clear

> save D:/Projects/translocation/G3/Figures/tRNA_sites/C-H1-Ch1_tRNA-
> contacts_figure.cxs includeMaps true

——— End of log from Thu Jan 28 14:30:06 2021 ———

opened ChimeraX session  

> select #1

147829 atoms, 160245 bonds, 455 pseudobonds, 11054 residues, 3 models selected  

> nucleotides sel ladder

> hide #4 models

> nucleotides sel fill

> style nucleic & sel stick

Changed 101461 atom styles  

> ~select #1

Nothing selected  

> select up

43 atoms, 47 bonds, 2 residues, 1 model selected  

> hide sel atoms

> select #1/a:966

24 atoms, 26 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select clear

> camera

Camera parameters:  
type: orthographic  
position: 305.61 244.37 136.16  
view direction: -0.74457 -0.59425 0.30412  
field width: 114.25  

> save D:/Projects/translocation/G3/Figures/tRNA_sites/Contacts/contacts.cxs
> includeMaps true

> show #4 models

> select #1

147829 atoms, 160245 bonds, 455 pseudobonds, 11054 residues, 3 models selected  

> hide sel atoms

> show sel atoms

> undo

> select clear

> undo

> undo

> undo

> select clear

> show #!2 models

> show #!3 models

> view name 1

> hide #!3 models

> hide #!2 models

> view 1

> view 1

> view 1

> view 1

> select #1/i:125

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

> select up

249 atoms, 251 bonds, 29 residues, 1 model selected  

> color sel pink

> select clear

> view 1

> view 1

Drag select of 31 atoms, 4 residues, 35 bonds, 7 shapes  

> select up

33050 atoms, 37004 bonds, 1540 residues, 1 model selected  

> select clear

> select add #1/a:1403

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select add #1/a:1402

42 atoms, 44 bonds, 2 residues, 1 model selected  

> select add #1/a:1401

65 atoms, 69 bonds, 3 residues, 1 model selected  

> select add #1/a:1400

85 atoms, 90 bonds, 4 residues, 1 model selected  

> hide sel atoms

> hide sel cartoons

> select add #1/a:1497

108 atoms, 115 bonds, 5 residues, 1 model selected  

> select add #1/a:1498

129 atoms, 137 bonds, 6 residues, 1 model selected  

> select add #1/a:791

152 atoms, 162 bonds, 7 residues, 1 model selected  

> hide sel atoms

> select clear

> select #1/l:43

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

> select up

66 atoms, 67 bonds, 9 residues, 1 model selected  

> hide sel cartoons

> hide sel atoms

> select #1/c:160

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

> select up

27 atoms, 26 bonds, 4 residues, 1 model selected  

> hide sel cartoons

> view 1

> show #!2 models

> show #!3 models

> hide #!3 models

> hide #!2 models

Drag select of 660 atoms, 160 residues, 156 pseudobonds, 722 bonds, 106 shapes  

> nucleotides sel ladder

> select #1/w:38

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select up

29 atoms, 31 bonds, 1 residue, 1 model selected  

> hide sel atoms

> hide #4 models

> select clear

Drag select of 22 atoms, 160 residues, 8 pseudobonds, 19 bonds, 58 shapes  

> show sel atoms

> nucleotides sel ladder

> style sel stick

Changed 3350 atom styles  

> select clear

Drag select of 226 atoms, 160 residues, 10 pseudobonds, 234 bonds, 287 shapes  

> select up

76 pseudobonds, 1 model selected  

> hide #1.1 models

> select clear

Drag select of 226 atoms, 160 residues, 234 bonds, 287 shapes  

> select clear




OpenGL version: 3.3.0 NVIDIA 431.94
OpenGL renderer: Quadro P4000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: DELL__
Model: Precision 5820 Tower
OS: Microsoft Windows 10 Enterprise (Build 17763)
Memory: 33,716,879,360
MaxProcessMemory: 137,438,953,344
CPU: 12 Intel(R) Xeon(R) W-2135 CPU @ 3.70GHz
OSLanguage: en-US
Locale: ('en_US', 'cp1252')
PyQt version: 5.15.1
Compiled Qt version: 5.15.1
Runtime Qt version: 5.15.1
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.11.8
    cftime: 1.2.1
    chardet: 3.0.4
    ChimeraX-AddH: 2.1.3
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.9.3
    ChimeraX-AtomicLibrary: 1.1
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.0
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.dev202011140750
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.0.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-DataFormats: 1.0.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.0
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.0
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.1
    ChimeraX-Log: 1.1.1
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Map: 1.0.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.1
    ChimeraX-MDcrds: 2.1
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.0
    ChimeraX-mmCIF: 2.2
    ChimeraX-MMTF: 2.0
    ChimeraX-Modeller: 1.0
    ChimeraX-ModelPanel: 1.0
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.0
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0
    ChimeraX-OpenCommand: 1.3.1
    ChimeraX-PDB: 2.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.0.1
    ChimeraX-Read-Pbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.2.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.2.1
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.2.2
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.0
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0
    ChimeraX-ToolshedUtils: 1.0
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.3.1
    ChimeraX-uniprot: 2.0
    ChimeraX-ViewDockX: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.21
    decorator: 4.4.2
    distlib: 0.3.1
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.17
    imagecodecs: 2020.5.30
    imagecodecs-lite: 2020.1.31
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.7
    jupyter-core: 4.6.3
    kiwisolver: 1.3.1
    line-profiler: 2.1.2
    lxml: 4.5.2
    lz4: 3.1.0
    MarkupSafe: 1.1.1
    matplotlib: 3.3.2
    msgpack: 1.0.0
    netCDF4: 1.5.4
    netifaces: 0.10.9
    networkx: 2.5
    numexpr: 2.7.1
    numpy: 1.19.2
    numpydoc: 1.1.0
    openvr: 1.14.1501
    packaging: 20.4
    parso: 0.7.1
    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 20.2.3
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.8
    psutil: 5.7.2
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.7.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.1
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.1
    python-dateutil: 2.8.1
    pytz: 2020.4
    pywin32: 228
    pyzmq: 20.0.0
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    setuptools: 50.3.0
    sfftk-rw: 0.6.7.dev1
    six: 1.15.0
    snowballstemmer: 2.0.0
    sortedcontainers: 2.2.2
    Sphinx: 3.2.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 1.0.3
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.4
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.9.3
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.0.5
    urllib3: 1.25.11
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.35.1
    WMI: 1.5.1

Change History (2)

comment:1 by Eric Pettersen, 5 years ago

Component: Unassigned → Depiction
Owner: set to Greg Couch
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Modified nucleotides not depicted as ladder

Reported by Valentyn Petrychenko

comment:2 by Greg Couch, 13 months ago

Description: modified (diff)
Resolution: → not a bug
Status: assigned → closed

As documented, the ladder code depends on the hbond information. An example, in 1h0q, the modified nucleic acids are missing the hbond information, so the modified nucleic acids are shown as stubs instead of a ladder rung. In the 1h0q case, this is a bug in the data from the PDB and the solution is to run the hbond command before showing the ladders.

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