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Opened 5 years ago
Last modified 14 months ago
#4199 closed defect
ChimeraX bug report submission — at Initial Version
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Depiction | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
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
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