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Opened 5 years ago
Last modified 5 years ago
#4175 feedback defect
H-bonds not recreated
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Analysis | 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.dev202101250432 (2021-01-25 04:32:42 UTC)
Description
After accidental deletion on the model that corrsponds to the hydrogen bonds it doesnt appear again, which makes newly searched hbonds impossible to visualize.
Log:
UCSF ChimeraX version: 1.2.dev202101250432 (2021-01-25)
© 2016-2020 Regents of the University of California. All rights reserved.
> open D:/Projects/translocation/G3/Figures/D4_interactions/Sites.cxs
Log from Wed Jan 27 09:55:18 2021UCSF 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/D4_interactions/D4_interactions.cxs
Log from Tue Jan 12 15:22:53 2021UCSF ChimeraX version: 1.2.dev202011140750
(2020-11-14)
© 2016-2020 Regents of the University of California. All rights reserved.
> open D:\Projects\g3\Figures\D4_interactions\D4_interactions.cxs format
> session
Opened chimeric_GDP1_job1099_3d512_31A_sharpened.mrc as #2, grid size
512,512,512, pixel 0.652, shown at level 4.2, step 1, values float32
Opened chimeric_GDP1_job1099_3d512_31A_sharpened.mrc zone as #3, grid size
512,512,512, pixel 0.652, shown at level 1.81, step 1, values float32
Log from Fri Jan 8 19:03:36 2021UCSF ChimeraX version: 1.2.dev202011140750
(2020-11-14)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> X:/Work/Projects/EF-G/g3/Final_Modelling/chimeric_GDP1/models/Chimeric_GDP-1-sw1-v2-RSR-0-coot-14.pdb
Chain information for Chimeric_GDP-1-sw1-v2-RSR-0-coot-14.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
x | No description available
y | No description available
z | No description available
> style stick
Changed 153138 atom styles
> set bgColor white
> show cartoons
> select /x:537
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
60 atoms, 61 bonds, 7 residues, 1 model selected
> select up
5473 atoms, 5576 bonds, 704 residues, 1 model selected
> hbonds
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /I PRO 19 N; /I PRO 22 N; /I PRO 25 N; /I PRO 53 N; /I PRO 21
N; /I PRO 55 N; /5 PRO 68 N; /5 PRO 79 N; /I PRO 73 N; /I PRO 74 N; /5 PRO 89
N; /5 PRO 130 N; /I PRO 92 N; /5 PRO 119 N
16031 hydrogen bonds found
> lighting simple
> view sel
> ui tool show "Side View"
> hide sel cartoons
> color sel byhetero
> select /A:1915
21 atoms, 22 bonds, 1 residue, 1 model selected
> select up
62336 atoms, 69815 bonds, 2903 residues, 1 model selected
> hide sel cartoons
> show sel cartoons
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
12 atoms, 12 bonds, 1 residue, 1 model selected
> select up
121 atoms, 122 bonds, 16 residues, 1 model selected
> select up
5473 atoms, 5576 bonds, 704 residues, 1 model selected
> open
> X:/Work/Projects/EF-G/g3/Final_Modelling/chimeric_GDP1/sharpened/chimeric_GDP1_job1099_3d512_31A_sharpened.mrc
Opened chimeric_GDP1_job1099_3d512_31A_sharpened.mrc as #2, grid size
512,512,512, pixel 0.652, shown at level 4.2, step 2, values float32
> volume #2 step 1
> volume zone #2 nearAtoms sel newMap true
Opened chimeric_GDP1_job1099_3d512_31A_sharpened.mrc zone as #3, grid size
512,512,512, pixel 0.652, shown at step 1, values float32
> volume #3 level 2.88
> volume #3 color white
> volume #3 color #ffffff98
> ui mousemode right pivot
> volume #3 level 2.122
> volume #3 level 1.253
> volume #3 level 1.253
> volume #3 level 1.81
> hide #!1 models
> open
> X:/Work/Projects/EF-G/g3/Final_Modelling/chimeric_GDP1/models/Chimeric_GDP-1-sw1-v2-RSR-0-coot-16.pdb
Chain information for Chimeric_GDP-1-sw1-v2-RSR-0-coot-16.pdb #4
---
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
> close #1
> select #4
153138 atoms, 165682 bonds, 11716 residues, 1 model selected
> style sel stick
Changed 153138 atom styles
> select /x
5473 atoms, 5576 bonds, 704 residues, 1 model selected
> hbonds sel
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /I PRO 19 N; /I PRO 22 N; /I PRO 25 N; /I PRO 21 N; /I PRO 53
N; /I PRO 55 N; /I PRO 73 N; /I PRO 74 N; /I PRO 92 N; /5 PRO 68 N; /5 PRO 89
N; /5 PRO 119 N; /5 PRO 130 N; /5 PRO 79 N
433 hydrogen bonds found
Alignment identifier is 4/x
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\toolbar\tool.py", line 202, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 361, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1270, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\shortcuts\\__init__.py", line 52, in run_provider
shortcuts.run_provider(session, name)
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 1221, in run_provider
keyboard_shortcuts(session).try_shortcut(name)
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 376, in try_shortcut
self.run_shortcut(keys)
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 394, in run_shortcut
sc.run(self.session, status = self._enabled)
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 296, in run
f(shortcut_atoms(s))
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 933, in show_sequence
run(session, 'sequence chain %s' % seq_chain_spec, log = False)
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 480, in run
run_command(session, command, **kw)
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2835, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\seqalign\cmd.py", line 140, in seqalign_chain
alignment = session.alignments.new_alignment([chain], ident, seq_viewer="sv",
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\seqalign\manager.py", line 232, in new_alignment
alignment = Alignment(self.session, seqs, identify_as, attrs, markups,
auto_destroy,
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 128, in __init__
self._set_residue_attributes()
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 721, in _set_residue_attributes
self.session.change_tracker.add_modified(assigned, attr_name + " changed")
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\atomic\molobject.py", line 1914, in add_modified
f(self._c_pointer, self._inst_to_int(item), modded._c_pointer,
AttributeError: 'set' object has no attribute '_c_pointer'
AttributeError: 'set' object has no attribute '_c_pointer'
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\atomic\molobject.py", line 1914, in add_modified
f(self._c_pointer, self._inst_to_int(item), modded._c_pointer,
See log for complete Python traceback.
> select /w:39@N3
1 atom, 1 residue, 1 model selected
> select up
20 atoms, 21 bonds, 1 residue, 1 model selected
> select up
1631 atoms, 1821 bonds, 76 residues, 1 model selected
> select up
1634 atoms, 1821 bonds, 79 residues, 1 model selected
> select up
153138 atoms, 165682 bonds, 11716 residues, 1 model selected
> select up
153138 atoms, 165682 bonds, 11716 residues, 5 models selected
> hide #!3 models
> hide #!4 models
> show #!4 models
> select #4
153138 atoms, 165682 bonds, 433 pseudobonds, 11716 residues, 2 models selected
> select clear
> select /x:511@CB
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
38 atoms, 37 bonds, 6 residues, 1 model selected
> select up
5473 atoms, 5576 bonds, 704 residues, 1 model selected
Alignment identifier is 4/x
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\toolbar\tool.py", line 202, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 361, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1270, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\shortcuts\\__init__.py", line 52, in run_provider
shortcuts.run_provider(session, name)
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 1221, in run_provider
keyboard_shortcuts(session).try_shortcut(name)
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 376, in try_shortcut
self.run_shortcut(keys)
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 394, in run_shortcut
sc.run(self.session, status = self._enabled)
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 296, in run
f(shortcut_atoms(s))
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 933, in show_sequence
run(session, 'sequence chain %s' % seq_chain_spec, log = False)
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\shortcuts\shortcuts.py", line 480, in run
run_command(session, command, **kw)
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2835, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\seqalign\cmd.py", line 140, in seqalign_chain
alignment = session.alignments.new_alignment([chain], ident, seq_viewer="sv",
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\seqalign\manager.py", line 232, in new_alignment
alignment = Alignment(self.session, seqs, identify_as, attrs, markups,
auto_destroy,
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 128, in __init__
self._set_residue_attributes()
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\seqalign\alignment.py", line 721, in _set_residue_attributes
self.session.change_tracker.add_modified(assigned, attr_name + " changed")
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\atomic\molobject.py", line 1914, in add_modified
f(self._c_pointer, self._inst_to_int(item), modded._c_pointer,
AttributeError: 'set' object has no attribute '_c_pointer'
AttributeError: 'set' object has no attribute '_c_pointer'
File "C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site-
packages\chimerax\atomic\molobject.py", line 1914, in add_modified
f(self._c_pointer, self._inst_to_int(item), modded._c_pointer,
See log for complete Python traceback.
> select clear
> select /x:511
11 atoms, 10 bonds, 1 residue, 1 model selected
> open
> X:/Work/Projects/EF-G/g3/Final_Modelling/chimeric_GDP1/models/alt_R511_Chimeric_GDP-1-sw1-v2-RSR-0-coot-16.pdb
> select #1/x:511@CZ
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 1 model selected
> hbonds sel
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: Chimeric_GDP-1-sw1-v2-RSR-0-coot-16.pdb #4/I PRO 19 N;
Chimeric_GDP-1-sw1-v2-RSR-0-coot-16.pdb #4/I PRO 22 N;
Chimeric_GDP-1-sw1-v2-RSR-0-coot-16.pdb #4/I PRO 25 N;
Chimeric_GDP-1-sw1-v2-RSR-0-coot-16.pdb #4/I PRO 21 N;
Chimeric_GDP-1-sw1-v2-RSR-0-coot-16.pdb #4/I PRO 53 N;
Chimeric_GDP-1-sw1-v2-RSR-0-coot-16.pdb #4/I PRO 55 N;
Chimeric_GDP-1-sw1-v2-RSR-0-coot-16.pdb #4/5 PRO 68 N;
Chimeric_GDP-1-sw1-v2-RSR-0-coot-16.pdb #4/I PRO 73 N;
Chimeric_GDP-1-sw1-v2-RSR-0-coot-16.pdb #4/I PRO 74 N;
Chimeric_GDP-1-sw1-v2-RSR-0-coot-16.pdb #4/5 PRO 79 N;
Chimeric_GDP-1-sw1-v2-RSR-0-coot-16.pdb #4/5 PRO 89 N;
Chimeric_GDP-1-sw1-v2-RSR-0-coot-16.pdb #4/5 PRO 119 N;
Chimeric_GDP-1-sw1-v2-RSR-0-coot-16.pdb #4/I PRO 92 N;
Chimeric_GDP-1-sw1-v2-RSR-0-coot-16.pdb #4/5 PRO 130 N
0 hydrogen bonds found
> select #4/x:511@CD
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
38 atoms, 37 bonds, 6 residues, 1 model selected
> select up
5473 atoms, 5576 bonds, 704 residues, 1 model selected
> hbonds sel
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: Chimeric_GDP-1-sw1-v2-RSR-0-coot-16.pdb #4/I PRO 19 N;
Chimeric_GDP-1-sw1-v2-RSR-0-coot-16.pdb #4/I PRO 22 N;
Chimeric_GDP-1-sw1-v2-RSR-0-coot-16.pdb #4/I PRO 25 N;
Chimeric_GDP-1-sw1-v2-RSR-0-coot-16.pdb #4/I PRO 21 N;
Chimeric_GDP-1-sw1-v2-RSR-0-coot-16.pdb #4/I PRO 53 N;
Chimeric_GDP-1-sw1-v2-RSR-0-coot-16.pdb #4/I PRO 55 N;
Chimeric_GDP-1-sw1-v2-RSR-0-coot-16.pdb #4/I PRO 73 N;
Chimeric_GDP-1-sw1-v2-RSR-0-coot-16.pdb #4/I PRO 74 N;
Chimeric_GDP-1-sw1-v2-RSR-0-coot-16.pdb #4/I PRO 92 N;
Chimeric_GDP-1-sw1-v2-RSR-0-coot-16.pdb #4/5 PRO 68 N;
Chimeric_GDP-1-sw1-v2-RSR-0-coot-16.pdb #4/5 PRO 89 N;
Chimeric_GDP-1-sw1-v2-RSR-0-coot-16.pdb #4/5 PRO 119 N;
Chimeric_GDP-1-sw1-v2-RSR-0-coot-16.pdb #4/5 PRO 130 N;
Chimeric_GDP-1-sw1-v2-RSR-0-coot-16.pdb #4/5 PRO 79 N
433 hydrogen bonds found
> open
> X:/Work/Projects/EF-G/g3/Final_Modelling/chimeric_GDP1/models/Chimeric_GDP-1-sw1-v2-RSR-0-coot-17.pdb
Chain information for Chimeric_GDP-1-sw1-v2-RSR-0-coot-17.pdb #6
---
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
> select #6
153138 atoms, 165682 bonds, 11716 residues, 1 model selected
> hide #4 models
> style sel stick
Changed 153138 atom styles
> select #6/x:510@N
1 atom, 1 residue, 1 model selected
> select up
4 atoms, 3 bonds, 1 residue, 1 model selected
> select up
38 atoms, 37 bonds, 6 residues, 1 model selected
> select up
5473 atoms, 5576 bonds, 704 residues, 1 model selected
> hbonds sel
28 atoms were skipped as donors/acceptors due to missing heavy-atom bond
partners
1280 hydrogen bonds found
> select #6/z:5@O2
1 atom, 1 residue, 1 model selected
> select add #6/x:510@CA
2 atoms, 2 residues, 1 model selected
> color sel byhetero
> select #6/x:510@N
1 atom, 1 residue, 1 model selected
> color sel byhetero
> select add #6/z:5@O2'
2 atoms, 2 residues, 1 model selected
> ui tool show Distances
> distance #6/x:510@N #6/z:5@O2'
Distance between Chimeric_GDP-1-sw1-v2-RSR-0-coot-17.pdb #6/x GLY 510 N and /z
U 5 O2': 2.875Å
> ~distance #6/x:510@N #6/z:5@O2'
> select #6/x:509@CA
1 atom, 1 residue, 1 model selected
> select up
4 atoms, 3 bonds, 1 residue, 1 model selected
> select up
38 atoms, 37 bonds, 6 residues, 1 model selected
> select up
5473 atoms, 5576 bonds, 704 residues, 1 model selected
> hbonds sel angleSlop 30
28 atoms were skipped as donors/acceptors due to missing heavy-atom bond
partners
1541 hydrogen bonds found
> hbonds sel angleSlop 20
28 atoms were skipped as donors/acceptors due to missing heavy-atom bond
partners
1280 hydrogen bonds found
> hbonds sel angleSlop 25
28 atoms were skipped as donors/acceptors due to missing heavy-atom bond
partners
1418 hydrogen bonds found
> select clear
> show #1,6 cartoons
> 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
> hide #1,6 atoms
> select #6/x:506
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
75 atoms, 75 bonds, 10 residues, 1 model selected
> select up
5473 atoms, 5576 bonds, 704 residues, 1 model selected
> show sel atoms
> show sel atoms
> select clear
> show #1,6 atoms
> hide #1,6 atoms
> select clear
> select /a
66466 atoms, 74328 bonds, 3158 residues, 2 models selected
> select clear
> select #6/x:505
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
75 atoms, 75 bonds, 10 residues, 1 model selected
> select up
5473 atoms, 5576 bonds, 704 residues, 1 model selected
> show sel atoms
> select clear
> select #6/A:1913
22 atoms, 24 bonds, 1 residue, 1 model selected
> select up
62336 atoms, 69815 bonds, 2903 residues, 1 model selected
> show sel atoms
> hide sel atoms
> select #6/A:1913
22 atoms, 24 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select #6/w:36
22 atoms, 24 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select #6/z:4
20 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> select #6/z:5
20 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select #6/z:4@C1'
1 atom, 1 residue, 1 model selected
> select up
20 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #6/z:7
23 atoms, 25 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select #6/x:510
4 atoms, 3 bonds, 1 residue, 1 model selected
> select add #6/x:509
8 atoms, 6 bonds, 2 residues, 1 model selected
> select add #6/x:508
14 atoms, 11 bonds, 3 residues, 1 model selected
> show sel atoms
> show sel atoms
> hide sel cartoons
> select clear
> select #6/w:37
29 atoms, 31 bonds, 1 residue, 1 model selected
> select up
1631 atoms, 1821 bonds, 76 residues, 1 model selected
> color sel nigth blue
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color sel midnight blue
> select clear
> select #6/w:26
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add #6/w:25
42 atoms, 45 bonds, 2 residues, 1 model selected
> select add #6/w:27
65 atoms, 70 bonds, 3 residues, 1 model selected
> select add #6/w:28
88 atoms, 95 bonds, 4 residues, 1 model selected
> select add #6/w:40
108 atoms, 116 bonds, 5 residues, 1 model selected
> select add #6/w:41
128 atoms, 137 bonds, 6 residues, 1 model selected
> hide sel cartoons
> select #6/z:4
20 atoms, 21 bonds, 1 residue, 1 model selected
> select up
208 atoms, 230 bonds, 10 residues, 1 model selected
> color sel lime
> select clear
> select #6/a:1495
20 atoms, 21 bonds, 1 residue, 1 model selected
> select up
33050 atoms, 37004 bonds, 1540 residues, 1 model selected
> color sel grey
> select clear
> select #6/A:1912
22 atoms, 24 bonds, 1 residue, 1 model selected
> select up
62336 atoms, 69815 bonds, 2903 residues, 1 model selected
> color sel white
> select clear
> select #6/A:1911
20 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #6/w:39
20 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #6/x:505
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
75 atoms, 75 bonds, 10 residues, 1 model selected
> select up
5473 atoms, 5576 bonds, 704 residues, 1 model selected
> color sel red
> select clear
> graphics silhouettes true
> select clear
> lighting full
> lighting shadows false
> select #6/x:505
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
75 atoms, 75 bonds, 10 residues, 1 model selected
> select up
5473 atoms, 5576 bonds, 704 residues, 1 model selected
> hbonds sel restrict cross angleSlop 25
28 atoms were skipped as donors/acceptors due to missing heavy-atom bond
partners
959 hydrogen bonds found
> select clear
> select #6/A:1915
21 atoms, 22 bonds, 1 residue, 1 model selected
> select add #6/A:1916
43 atoms, 46 bonds, 2 residues, 1 model selected
> select add #6/A:1910
66 atoms, 71 bonds, 3 residues, 1 model selected
> hide sel cartoons
> select add #6/A:1923
86 atoms, 92 bonds, 4 residues, 1 model selected
> select add #6/A:1922
109 atoms, 117 bonds, 5 residues, 1 model selected
> select add #6/A:1921
132 atoms, 142 bonds, 6 residues, 1 model selected
> select add #6/A:1920
152 atoms, 163 bonds, 7 residues, 1 model selected
> select add #6/A:1919
174 atoms, 187 bonds, 8 residues, 1 model selected
> select add #6/A:1918
196 atoms, 211 bonds, 9 residues, 1 model selected
> hide sel cartoons
> select #6/a:1493
22 atoms, 24 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #6/a:1492
22 atoms, 24 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #6/a:1494
23 atoms, 25 bonds, 1 residue, 1 model selected
> select add #6/a:1495
43 atoms, 46 bonds, 2 residues, 1 model selected
> select add #6/a:1496
63 atoms, 67 bonds, 3 residues, 1 model selected
> select add #6/a:1497
86 atoms, 92 bonds, 4 residues, 1 model selected
> select add #6/a:1498
107 atoms, 114 bonds, 5 residues, 1 model selected
> hide sel cartoons
> undo
> undo
> undo
> undo
> undo
> undo
> undo
> undo
> undo
> undo
> select #6/a:1494
23 atoms, 25 bonds, 1 residue, 1 model selected
> select up
33050 atoms, 37004 bonds, 1540 residues, 1 model selected
> show sel cartoons
> select clear
> select #6/a:1492
22 atoms, 24 bonds, 1 residue, 1 model selected
> hide sel cartoons
> hide #1 models
> show #1 models
> select #1
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel red
> select clear
> select #1/x:511@CZ
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 1 model selected
> color sel pink
> select clear
> select #6/c:159
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
273 atoms, 277 bonds, 35 residues, 1 model selected
> select up
1624 atoms, 1651 bonds, 206 residues, 1 model selected
> hide sel cartoons
> select #6/j:59
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #6/i:119
18 atoms, 16 bonds, 2 residues, 1 model selected
> select add #6/e:28
29 atoms, 26 bonds, 3 residues, 1 model selected
> select up
430 atoms, 433 bonds, 52 residues, 1 model selected
> select up
2949 atoms, 2984 bonds, 382 residues, 1 model selected
> hide sel cartoons
> ui mousemode right select
> select #6/x:541
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #6/a:1210
20 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel cartoons
> select #6/x:541
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel atoms
> show sel atoms
> hide sel cartoons
> hide sel cartoons
> color sel byhetero
Drag select of 1 pseudobonds
> select clear
> select clear
> hide #1 models
> select #6/z:6
20 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> select #6/w:34
23 atoms, 25 bonds, 1 residue, 1 model selected
> show sel atoms
> select #6/w:35
22 atoms, 24 bonds, 1 residue, 1 model selected
> show sel atoms
Drag select of 6 atoms, 2 residues, 7 bonds
> select #6/z:4
20 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> select #6/a:1196
22 atoms, 24 bonds, 1 residue, 1 model selected
> show sel atoms
> select #6/a:1055
22 atoms, 24 bonds, 1 residue, 1 model selected
> show sel atoms
> select #6/a:1054
20 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> select #6/z:7@C2
1 atom, 1 residue, 1 model selected
> select up
23 atoms, 25 bonds, 1 residue, 1 model selected
> hbonds sel restrict cross angleSlop 25
28 atoms were skipped as donors/acceptors due to missing heavy-atom bond
partners
13 hydrogen bonds found
> select add #6/a:1054@C2
24 atoms, 25 bonds, 2 residues, 1 model selected
> select up
43 atoms, 46 bonds, 2 residues, 1 model selected
> color sel byhetero
> select clear
> select #6/x:585
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
72 atoms, 74 bonds, 9 residues, 1 model selected
> select up
5473 atoms, 5576 bonds, 704 residues, 1 model selected
> hbonds sel restrict cross angleSlop 25
28 atoms were skipped as donors/acceptors due to missing heavy-atom bond
partners
959 hydrogen bonds found
> select #6/A:1917
20 atoms, 21 bonds, 1 residue, 1 model selected
> select up
62336 atoms, 69815 bonds, 2903 residues, 1 model selected
> show sel cartoons
> select clear
> select add #6/A:1914
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #6/A:1915
41 atoms, 43 bonds, 2 residues, 1 model selected
> show sel atoms
> select clear
> select /x
10957 atoms, 11162 bonds, 919 pseudobonds, 1409 residues, 4 models selected
> color sel dark red
> color sel #8f0100
> color sel #a60000
> select #6/x:584@CG
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel byhetero
> select clear
> color sel #8f0100
> select #6/x:584
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
72 atoms, 74 bonds, 9 residues, 1 model selected
> select up
5473 atoms, 5576 bonds, 704 residues, 1 model selected
> color sel #8f0100
> select clear
> select #6/x:584@CG
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel byhetero
> select clear
> select #6/x:584
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
72 atoms, 74 bonds, 9 residues, 1 model selected
> select up
5473 atoms, 5576 bonds, 704 residues, 1 model selected
> color sel lightblue red
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color sel tomato
> color sel byhetero
> color sel pink
> color sel byhetero
> color sel 100,30,30
> color sel byhetero
> color sel 100,40,40
> color sel byhetero
> color sel 100,60,60
> color sel byhetero
> select /x
10957 atoms, 11162 bonds, 919 pseudobonds, 1409 residues, 4 models selected
> color sel red
> select #6/x:584@OD2
1 atom, 1 residue, 1 model selected
> color sel #8f0100
> select clear
> select #6/x:584@OD2
1 atom, 1 residue, 1 model selected
> color sel maroon
> select clear
> select #6/x:584@OD2
1 atom, 1 residue, 1 model selected
> color sel pink
> select #6/x:512
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /x
10957 atoms, 11162 bonds, 919 pseudobonds, 1409 residues, 4 models selected
> color sel maroon
> select clear
> lighting simple
> lighting simple
> lighting soft
> lighting full
> lighting shadows false
> lighting simple
> lighting shadows true
> lighting shadows false
> lighting full
> lighting shadows false
> lighting simple
> lighting shadows true
> lighting shadows false
> lighting full
> lighting shadows false
> lighting simple
> lighting shadows true
> lighting shadows false
> select #6/x:589
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
161 atoms, 163 bonds, 21 residues, 1 model selected
> select up
5473 atoms, 5576 bonds, 704 residues, 1 model selected
> color sel pink
> select clear
> select #6/x:552
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
121 atoms, 122 bonds, 16 residues, 1 model selected
> select up
5473 atoms, 5576 bonds, 704 residues, 1 model selected
> color sel #ff5959
> select clear
> lighting simple
> lighting shadows true
> lighting shadows false
> lighting full
> lighting shadows false
> color sel #8f0100
> color /ч #8f0100
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color /x #8f0100
> select clear
> select add #6/a:516
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #6/a:517
43 atoms, 46 bonds, 2 residues, 1 model selected
> select add #6/a:518
63 atoms, 67 bonds, 3 residues, 1 model selected
> select add #6/a:519
83 atoms, 88 bonds, 4 residues, 1 model selected
> select subtract #6/a:519
63 atoms, 67 bonds, 3 residues, 1 model selected
> select add #6/a:520
85 atoms, 91 bonds, 4 residues, 1 model selected
> select add #6/a:519
105 atoms, 112 bonds, 5 residues, 1 model selected
> select add #6/a:530
128 atoms, 137 bonds, 6 residues, 1 model selected
> select add #6/a:531
148 atoms, 158 bonds, 7 residues, 1 model selected
> select add #6/a:532
170 atoms, 182 bonds, 8 residues, 1 model selected
> hide sel cartoons
> nucleotides sel fill
> style nucleic & sel stick
Changed 170 atom styles
> select clear
> nucleotides #6 fill
> style nucleic & #6 stick
Changed 101437 atom styles
> select #6/x:511@NH2
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
38 atoms, 37 bonds, 6 residues, 1 model selected
> select up
5473 atoms, 5576 bonds, 704 residues, 1 model selected
> color sel byhetero
> select clear
> select #6/z:9
20 atoms, 21 bonds, 1 residue, 1 model selected
> select subtract #6/z:9
Nothing selected
> select add #6/z:9
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #6/z:8
40 atoms, 42 bonds, 2 residues, 1 model selected
> hide sel cartoons
> select add #6/z:4
60 atoms, 63 bonds, 3 residues, 1 model selected
> select #6/z:3
23 atoms, 25 bonds, 1 residue, 1 model selected
> select add #6/z:2
43 atoms, 46 bonds, 2 residues, 1 model selected
> select add #6/z:1
65 atoms, 70 bonds, 3 residues, 1 model selected
> hide sel cartoons
> select #6/a:1493
22 atoms, 24 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select add #6/z:5
42 atoms, 45 bonds, 2 residues, 1 model selected
> select add #6/z:4
62 atoms, 66 bonds, 3 residues, 1 model selected
> select add #6/z:6
82 atoms, 87 bonds, 4 residues, 1 model selected
> select add #6/z:7
105 atoms, 112 bonds, 5 residues, 1 model selected
> hide sel cartoons
> select clear
> select #6/z:4@C5'
1 atom, 1 residue, 1 model selected
> select up
20 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> undo
> undo
> undo
> undo
> undo
> undo
> undo
> undo
> undo
> select clear
> select #6/x:593
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
161 atoms, 163 bonds, 21 residues, 1 model selected
> select up
5473 atoms, 5576 bonds, 704 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> select #6/x:506
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> select clear
> select #6/x:506
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #6/x:507
18 atoms, 16 bonds, 2 residues, 1 model selected
> select add #6/x:509
22 atoms, 19 bonds, 3 residues, 1 model selected
> select add #6/x:510
26 atoms, 22 bonds, 4 residues, 1 model selected
> select add #6/x:511
37 atoms, 32 bonds, 5 residues, 1 model selected
> show sel atoms
> hide sel atoms
> show sel atoms
> hide sel cartoons
> select #6/x:508
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> show sel atoms
> hide sel cartoons
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> show sel atoms
> hide sel cartoons
> show sel cartoons
> open
> X:/Work/Projects/EF-G/g3/Final_Modelling/chimeric_GDP1/models/Chimeric_GDP-1-sw1-v2-RSR-0-coot-18.pdb
Chain information for Chimeric_GDP-1-sw1-v2-RSR-0-coot-18.pdb #7
---
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
> select #7
153138 atoms, 165682 bonds, 11716 residues, 1 model selected
> hide sel atoms
> style sel stick
Changed 153138 atom styles
> select clear
> select #6/x:505
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
75 atoms, 75 bonds, 10 residues, 1 model selected
> select up
5473 atoms, 5576 bonds, 704 residues, 1 model selected
> show sel cartoons
> select clear
> select #7/a:506,507,509-511,583
129 atoms, 142 bonds, 6 residues, 1 model selected
> show sel atoms
> show sel atoms
> hide #5 models
> show #5 models
> hide #6 models
> hide #7 models
> show #7 models
> show sel atoms
> hide sel atoms
> select #7/x:506,507,509-511,583
47 atoms, 45 bonds, 6 residues, 1 model selected
> show sel atoms
> show #6 models
> select clear
> select #6/x:506@NZ
1 atom, 1 residue, 1 model selected
> color sel byhetero
> color sel byhetero
> select clear
> select #6/x:506@NZ
1 atom, 1 residue, 1 model selected
> color sel byhetero
> color sel byhetero
> color sel byhetero
> color sel byhetero
> color sel byhetero
> color sel byhetero
> color sel byhetero
> color sel byhetero
> color sel byhetero
> select #6/x:506
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #6/x:505
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
75 atoms, 75 bonds, 10 residues, 1 model selected
> select up
5473 atoms, 5576 bonds, 704 residues, 1 model selected
> hide sel atoms
> select clear
> select #7/x:506@NZ
1 atom, 1 residue, 1 model selected
> color sel byhetero
> select clear
> select #7/x:507@NE2
1 atom, 1 residue, 1 model selected
> color sel byhetero
> select #7/x:507@OE1
1 atom, 1 residue, 1 model selected
> color sel byhetero
> select clear
> hide #6 models
Drag select of 47 atoms, 45 bonds
> select clear
> show #6 models
> select #6/x:541
4 atoms, 3 bonds, 1 residue, 1 model selected
> select clear
> select #7/x:506,507,509-511,583,541
51 atoms, 48 bonds, 7 residues, 1 model selected
> show sel atoms
> select clear
> hide #6 models
> hide #5 models
Drag select of 51 atoms, 48 bonds
> hbonds sel restrict cross angleSlop 25
42 atoms were skipped as donors/acceptors due to missing heavy-atom bond
partners
32 hydrogen bonds found
> show #6 models
> show #5 models
> hide #7 models
> show #7 models
> hide #7 models
> select #5
32 pseudobonds, 1 model selected
> ~select #5
Nothing selected
> select #6
153138 atoms, 165682 bonds, 11716 residues, 1 model selected
> ~select #6
Nothing selected
> select #6/x:512
4 atoms, 3 bonds, 1 residue, 1 model selected
> select up
38 atoms, 37 bonds, 6 residues, 1 model selected
> select up
5473 atoms, 5576 bonds, 704 residues, 1 model selected
> show #7 models
> hide #7 models
> show sel atoms
> show #7 models
> hide #6 models
> show #1 models
> show #6 models
> hide #1 models
> show #1 models
> hide #1 models
> select #7/x:511@CZ
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> camera ortho
> select #6/x:583@NE2
1 atom, 1 residue, 1 model selected
> select up
10 atoms, 10 bonds, 1 residue, 1 model selected
> select clear
> select #6/x:512
4 atoms, 3 bonds, 1 residue, 1 model selected
> select up
38 atoms, 37 bonds, 6 residues, 1 model selected
> select up
5473 atoms, 5576 bonds, 704 residues, 1 model selected
> hbonds sel restrict cross angleSlop 25
42 atoms were skipped as donors/acceptors due to missing heavy-atom bond
partners
1895 hydrogen bonds found
> hide #7 models
> select #6/x:506
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
75 atoms, 75 bonds, 10 residues, 1 model selected
> select up
5473 atoms, 5576 bonds, 704 residues, 1 model selected
> hide sel atoms
> select #6/x:506
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #7/x:506,507,509-511,583,541
51 atoms, 48 bonds, 7 residues, 1 model selected
> select #6/x:506,507,509-511,583,541
51 atoms, 48 bonds, 7 residues, 1 model selected
> show sel atoms
> select clear
> select add #6/x:510
4 atoms, 3 bonds, 1 residue, 1 model selected
> select add #6/x:509
8 atoms, 6 bonds, 2 residues, 1 model selected
> hide sel atoms
> show sel atoms
> hide sel cartoons
> select #6/x:508
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> show sel atoms
> hide sel cartoons
> select #6/x:507
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel cartoons
> show sel atoms
> select clear
> select #6/x:590
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
161 atoms, 163 bonds, 21 residues, 1 model selected
> select up
5473 atoms, 5576 bonds, 704 residues, 1 model selected
> select up
153138 atoms, 165682 bonds, 11716 residues, 1 model selected
> select down
5473 atoms, 5576 bonds, 704 residues, 1 model selected
> color /x #8f0100
> select clear
> select #6/x:506@NZ
1 atom, 1 residue, 1 model selected
> select add #6/x:509@N
2 atoms, 2 residues, 1 model selected
> select add #6/x:510@N
3 atoms, 3 residues, 1 model selected
> select add #6/w:36@O2'
4 atoms, 4 residues, 1 model selected
> select add #6/x:509@O
5 atoms, 4 residues, 1 model selected
> select add #6/x:511@NE
6 atoms, 5 residues, 1 model selected
> select add #6/x:511@NH2
7 atoms, 5 residues, 1 model selected
> select add #6/x:507@NE2
8 atoms, 6 residues, 1 model selected
> select add #6/w:35@O2'
9 atoms, 7 residues, 1 model selected
> select add #6/x:583@NE2
10 atoms, 8 residues, 1 model selected
> color sel byhetero
> select clear
> view name 1
> save X:/Work/Projects/EF-G/g3/Figures/D4_interactions/D4_interactions.cxs
> includeMaps true
> select #6/z:7
23 atoms, 25 bonds, 1 residue, 1 model selected
> select up
208 atoms, 230 bonds, 10 residues, 1 model selected
> show sel cartoons
> ui mousemode right pivot
> ui mousemode right translate
> ui mousemode right select
> select #6/a:1055@C2'
1 atom, 1 residue, 1 model selected
> select #6/a:1056
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #6/a:1055
22 atoms, 24 bonds, 1 residue, 1 model selected
> hide sel atoms
> view 1
> select #6/w:29
23 atoms, 25 bonds, 1 residue, 1 model selected
> select up
1631 atoms, 1821 bonds, 76 residues, 1 model selected
> show sel cartoons
> select #6/x:503
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> view 1
> select clear
> select #6/x:589
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #6/x:550
16 atoms, 15 bonds, 2 residues, 1 model selected
> select up
282 atoms, 285 bonds, 37 residues, 1 model selected
> hide sel cartoons
> select add #6/x:515
286 atoms, 288 bonds, 38 residues, 1 model selected
> select add #6/x:516
296 atoms, 298 bonds, 39 residues, 1 model selected
> select add #6/x:517
303 atoms, 304 bonds, 40 residues, 1 model selected
> hide sel cartoons
> undo
> undo
> undo
> undo
> undo
> undo
> undo
> undo
> select clear
> select clear
Drag select of 4 residues
> cartoon style nucleic width 0.8 thickness 0.8 xsection oval
> cartoon style helix width 1.2 thickness 0.2
> cartoon style helix width 1.8 thickness 0.2
> cartoon style xsection oval
> cartoon style helix width 1.8 thickness 0.2
> cartoon style strand width 2 thickness 0.8
> cartoon style coil width 0.3 thickness 0.3
> cartoon style nucleic width 0.8 thickness 0.8 xsection oval
> cartoon style xsection oval
> cartoon style helix width 1.8 thickness 0.2
> cartoon style strand width 1.5 thickness 0.3
> cartoon style coil width 0.3 thickness 0.3
> cartoon style nucleic width 0.8 thickness 0.8 xsection oval
> cartoon style xsection oval
> cartoon style helix width 1.8 thickness 0.2
> cartoon style strand width 1.5 thickness 0.4
> cartoon style coil width 0.3 thickness 0.3
> cartoon style nucleic width 0.8 thickness 0.8 xsection oval
> cartoon style xsection oval
> cartoon style helix width 1.8 thickness 0.2
> 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 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 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 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
> select clear
> view 1
Drag select of 2 residues
Drag select of 1 residues, 1 bonds
> select clear
> select clear
> select add #6/x:511
11 atoms, 10 bonds, 1 residue, 1 model selected
> style sel stick
Changed 11 atom styles
> hide sel cartoons
> color #7/x:511
> select #7/x:511
11 atoms, 10 bonds, 1 residue, 1 model selected
> show #6 cartoons
> select #7
153138 atoms, 165682 bonds, 11716 residues, 1 model selected
> show #7 models
> hide sel cartoons
> undo
> undo
> undo
> lighting simple
> lighting shadows true
> lighting shadows false
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting simple
> lighting shadows true
> lighting shadows false
> lighting full
> lighting shadows false
> view name 2
> save X:/Work/Projects/EF-G/g3/Figures/D4_interactions/D4_interactions.cxs
> includeMaps true
——— End of log from Fri Jan 8 19:03:36 2021 ———
opened ChimeraX session
> select #6/x:506
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #6/x:507
18 atoms, 16 bonds, 2 residues, 1 model selected
> select add #6/x:508
24 atoms, 21 bonds, 3 residues, 1 model selected
> select add #6/x:509
28 atoms, 24 bonds, 4 residues, 1 model selected
> select add #6/x:510
32 atoms, 27 bonds, 5 residues, 1 model selected
> select add #6/x:511
43 atoms, 37 bonds, 6 residues, 1 model selected
> hide sel cartoons
> select clear
> select add #6/a:1492
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add #6/a:1493
44 atoms, 48 bonds, 2 residues, 1 model selected
> select subtract #6/a:1493
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add #6/a:1494
45 atoms, 49 bonds, 2 residues, 1 model selected
> select add #6/a:1493
67 atoms, 73 bonds, 3 residues, 1 model selected
> select add #6/a:1495
87 atoms, 94 bonds, 4 residues, 1 model selected
> hide sel cartoons
> view 1
> select #6/x:512
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel cartoons
> select clear
> show sel cartoons
> show #7 models
> hide #7 models
> show #7 models
> hide #5 models
> show #5 models
> select #7
153138 atoms, 165682 bonds, 11716 residues, 1 model selected
> hide sel atoms
> select #7/x:512
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel cartoons
> select clear
> select #7/x:511
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel cartoons
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
4 atoms, 3 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #7/w:36
22 atoms, 24 bonds, 1 residue, 1 model selected
> show sel atoms
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> select #7/x
5473 atoms, 5576 bonds, 704 residues, 1 model selected
> show sel cartoons
> select #7/w
1634 atoms, 1821 bonds, 79 residues, 1 model selected
> show sel atoms
> hide sel atoms
> hide sel cartoons
> show sel cartoons
> color sel midnight blue
> select #7/z
208 atoms, 230 bonds, 10 residues, 1 model selected
> show sel cartoons
> color sel lime
> select clear
> select #7/a
33233 atoms, 37164 bonds, 1579 residues, 1 model selected
> show sel cartoons
> color sel grey
> select clear
> select #7/A
62605 atoms, 69815 bonds, 3172 residues, 1 model selected
> show sel cartoons
> show sel cartoons
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> select #7/v
1653 atoms, 1843 bonds, 79 residues, 1 model selected
> show sel cartoons
> select clear
> select #7/v
1653 atoms, 1843 bonds, 79 residues, 1 model selected
> color sel cyan
> select clear
> select #7/x:506-512
47 atoms, 46 bonds, 7 residues, 1 model selected
> show sel atoms
> hide sel atoms
> show sel atoms
> hide sel cartoons
> select #7/x:506-512,583
57 atoms, 56 bonds, 8 residues, 1 model selected
> select #7/x:506-512,583,503
66 atoms, 64 bonds, 9 residues, 1 model selected
> show sel atoms
> show #6 models
> hide #6 models
> select #7/x:506-512,583,503
66 atoms, 64 bonds, 9 residues, 1 model selected
> select #7/x:506-512,583,503
66 atoms, 64 bonds, 9 residues, 1 model selected
> hbonds sel cross
Expected a keyword
> hbonds sel restrict cross angleSlop 25
42 atoms were skipped as donors/acceptors due to missing heavy-atom bond
partners
33 hydrogen bonds found
> show #6 models
> hide #6 models
> close #1,4-6#2-3
> select /x:590
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
161 atoms, 163 bonds, 21 residues, 1 model selected
> select up
5473 atoms, 5576 bonds, 704 residues, 1 model selected
> hbonds sel restrict cross angleSlop 25
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /5 PRO 68 N; /5 PRO 119 N; /5 PRO 130 N; /5 PRO 79 N; /5 PRO 89
N; /I PRO 19 N; /I PRO 21 N; /I PRO 22 N; /I PRO 25 N; /I PRO 53 N; /I PRO 55
N; /I PRO 73 N; /I PRO 74 N; /I PRO 92 N
17 hydrogen bonds found
> hide #7.1 models
> show #7.1 models
> select /w:36
22 atoms, 24 bonds, 1 residue, 1 model selected
> select up
1631 atoms, 1821 bonds, 76 residues, 1 model selected
> show sel atoms
> select /z:7
23 atoms, 25 bonds, 1 residue, 1 model selected
> select up
208 atoms, 230 bonds, 10 residues, 1 model selected
> show sel cartoons
> show sel atoms
> select clear
> hbonds sel restrict cross angleSlop 30
Atom specifier selects no atoms
> select /x:510@CA
1 atom, 1 residue, 1 model selected
> select up
4 atoms, 3 bonds, 1 residue, 1 model selected
> select up
38 atoms, 37 bonds, 6 residues, 1 model selected
> hbonds sel restrict any angleSlop 30
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /5 PRO 68 N; /5 PRO 119 N; /5 PRO 130 N; /5 PRO 79 N; /5 PRO 89
N; /I PRO 19 N; /I PRO 21 N; /I PRO 22 N; /I PRO 25 N; /I PRO 53 N; /I PRO 55
N; /I PRO 73 N; /I PRO 74 N; /I PRO 92 N
3 hydrogen bonds found
> select /x:504
10 atoms, 10 bonds, 1 residue, 1 model selected
> select up
75 atoms, 75 bonds, 10 residues, 1 model selected
> select up
5473 atoms, 5576 bonds, 704 residues, 1 model selected
> hbonds sel restrict any angleSlop 30
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /5 PRO 68 N; /5 PRO 119 N; /5 PRO 130 N; /5 PRO 79 N; /5 PRO 89
N; /I PRO 19 N; /I PRO 21 N; /I PRO 22 N; /I PRO 25 N; /I PRO 53 N; /I PRO 55
N; /I PRO 73 N; /I PRO 74 N; /I PRO 92 N
515 hydrogen bonds found
> open
> D:/Projects/translocation/G3/States/Chimeric-1-GDP/models/Chimeric_GDP-1-sw1-v2-RSR-0-coot-21.pdb
Chain information for Chimeric_GDP-1-sw1-v2-RSR-0-coot-21.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
x | No description available
y | No description available
z | No description available
> select #1
153138 atoms, 165682 bonds, 11716 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 153138 atom styles
> hide sel atoms
> hide #!7 models
> select #7/x
5473 atoms, 5576 bonds, 498 pseudobonds, 704 residues, 2 models selected
> show #1 cartoons
> hide #1 cartoons
> show #1 cartoons
> hide #1 cartoons
> select #1/x
5473 atoms, 5576 bonds, 704 residues, 1 model selected
> show sel 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
> select clear
> color #3/x #8f0100
> color #1/x #8f0100
> select clear
> color #1/ц
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> select #1/w
1634 atoms, 1821 bonds, 79 residues, 1 model selected
> show sel cartoons
> color sel midnight blue
> select #1/v
1653 atoms, 1843 bonds, 79 residues, 1 model selected
> show sel cartoons
> color sel cyan
> select #1/z
208 atoms, 230 bonds, 10 residues, 1 model selected
> show sel cartoons
> color sel lime
> select #1/a
33233 atoms, 37164 bonds, 1579 residues, 1 model selected
> show sel cartoons
> select #1/A
62605 atoms, 69815 bonds, 3172 residues, 1 model selected
> show sel cartoons
> select #1/a:1493
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add #1/a:1492
44 atoms, 48 bonds, 2 residues, 1 model selected
> select add #1/a:1494
67 atoms, 73 bonds, 3 residues, 1 model selected
> select subtract #1/a:1494
44 atoms, 48 bonds, 2 residues, 1 model selected
> select add #1/a:1494
67 atoms, 73 bonds, 3 residues, 1 model selected
> select add #1/a:1495
87 atoms, 94 bonds, 4 residues, 1 model selected
> select add #1/a:1496
107 atoms, 115 bonds, 5 residues, 1 model selected
> hide sel cartoons
> select #1/A
62605 atoms, 69815 bonds, 3172 residues, 1 model selected
> color sel white
> select #1/a
33233 atoms, 37164 bonds, 1579 residues, 1 model selected
> color sel grey
> select clear
> select add #1/a:1408
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add #1/a:1409
42 atoms, 45 bonds, 2 residues, 1 model selected
> hide sel cartoons
> select add #1/A:1915
63 atoms, 67 bonds, 3 residues, 1 model selected
> select add #1/A:1916
85 atoms, 91 bonds, 4 residues, 1 model selected
> select clear
> view 1
> select #1/A:1913
22 atoms, 24 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select #1/x:506
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/x:507
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #1/x:506
18 atoms, 16 bonds, 2 residues, 1 model selected
> select add #1/x:508
24 atoms, 21 bonds, 3 residues, 1 model selected
> select add #1/x:509
28 atoms, 24 bonds, 4 residues, 1 model selected
> select add #1/x:510
32 atoms, 27 bonds, 5 residues, 1 model selected
> select add #1/x:511
43 atoms, 37 bonds, 6 residues, 1 model selected
> select add #1/x:512
47 atoms, 40 bonds, 7 residues, 1 model selected
> show sel atoms
> hide sel cartoons
> select clear
> select #1/x:513
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
92 atoms, 95 bonds, 11 residues, 1 model selected
> select up
5473 atoms, 5576 bonds, 704 residues, 1 model selected
> hbonds sel restrict cross angleSlop 25
28 atoms were skipped as donors/acceptors due to missing heavy-atom bond
partners
1018 hydrogen bonds found
> select #1/z:8
20 atoms, 21 bonds, 1 residue, 1 model selected
> select up
208 atoms, 230 bonds, 10 residues, 1 model selected
> show sel atoms
> select clear
> select #1/w:37
29 atoms, 31 bonds, 1 residue, 1 model selected
> select add #1/w:36
51 atoms, 55 bonds, 2 residues, 1 model selected
> select add #1/w:38
73 atoms, 79 bonds, 3 residues, 1 model selected
> show sel atoms
> select add #1/w:35
95 atoms, 103 bonds, 4 residues, 1 model selected
> show sel atoms
> select add #1/w:34
118 atoms, 128 bonds, 5 residues, 1 model selected
> show sel atoms
> select #1/a:1054
20 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> view 1
> nucleotides #1 fill
> style nucleic & #1 stick
Changed 101437 atom styles
> select clear
> select #1/x:584
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/x:583
10 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> show #7 models
> hide #7 models
> show #7 models
> hide #7 models
> show #7 models
> hide #7 models
> close #7
> select /x:511@NE
1 atom, 1 residue, 1 model selected
> select add /x:511@NH2
2 atoms, 1 residue, 1 model selected
> select add /x:511@NH1
3 atoms, 1 residue, 1 model selected
> color sel byhetero
> select clear
> select /x:583@NE2
1 atom, 1 residue, 1 model selected
> select add /x:583@ND1
2 atoms, 1 residue, 1 model selected
> color sel byhetero
> select clear
> select /x:507@NE2
1 atom, 1 residue, 1 model selected
> select add /x:507@OE1
2 atoms, 1 residue, 1 model selected
> color sel byhetero
> select clear
> select /x:506@NZ
1 atom, 1 residue, 1 model selected
> color sel byhetero
> select add /x:509@N
2 atoms, 2 residues, 1 model selected
> color sel byhetero
> select add /x:510@N
3 atoms, 3 residues, 1 model selected
> color sel byhetero
> select add /w:36@O2'
4 atoms, 4 residues, 1 model selected
> color sel byhetero
> select add /w:35@O2'
5 atoms, 5 residues, 1 model selected
> color sel byhetero
> select add /z:7@O2'
6 atoms, 6 residues, 1 model selected
> color sel byhetero
> select add /z:7@O4'
7 atoms, 6 residues, 1 model selected
> select subtract /z:7@O4'
6 atoms, 6 residues, 1 model selected
> select add /z:7@O4'
7 atoms, 6 residues, 1 model selected
> color sel byhetero
> select add /z:5@O2'
8 atoms, 7 residues, 1 model selected
> select /z:5@O2'
1 atom, 1 residue, 1 model selected
> color sel byhetero
> select clear
> select /x:586
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
72 atoms, 74 bonds, 9 residues, 1 model selected
> select up
5473 atoms, 5576 bonds, 704 residues, 1 model selected
> select add /z:8
5493 atoms, 5597 bonds, 705 residues, 1 model selected
> select subtract /z:8
5473 atoms, 5576 bonds, 704 residues, 1 model selected
> select add /z:7
5496 atoms, 5601 bonds, 705 residues, 1 model selected
> select add /z:6
5516 atoms, 5622 bonds, 706 residues, 1 model selected
> select add /z:5
5536 atoms, 5643 bonds, 707 residues, 1 model selected
> select add /z:4
5556 atoms, 5664 bonds, 708 residues, 1 model selected
> hbonds sel restrict cross angleSlop 25
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /5 PRO 68 N; /5 PRO 79 N; /5 PRO 130 N; /5 PRO 119 N; /5 PRO 89
N; /I PRO 19 N; /I PRO 21 N; /I PRO 22 N; /I PRO 25 N; /I PRO 53 N; /I PRO 73
N; /I PRO 55 N; /I PRO 92 N; /I PRO 74 N
27 hydrogen bonds found
> select clear
> hide atoms
> show atoms
> undo
> undo
> hide sel
> show atoms
> undo
> save
> D:/Projects/translocation/G3/Figures/D4_interactions/D4_interactions.cxs
> includeMaps true
> open
> D:/Projects/translocation/G3/States/Chimeric-1-GDP/models/Chimeric_GDP-1-sw1-v2-RSR-0-coot-21.pdb
Chain information for Chimeric_GDP-1-sw1-v2-RSR-0-coot-21.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
> select #3
153138 atoms, 165682 bonds, 11716 residues, 1 model selected
> hide sel atoms
> select #1/x:512@CA
1 atom, 1 residue, 1 model selected
> select #2/x:512
Nothing selected
> show cartoons
> undo
> select #3/x:512
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel cartoons
> color sel #8f0100
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
4 atoms, 3 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3/x:511
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel cartoons
> color sel #8f0100
> select clear
> select add #1/a:517
23 atoms, 25 bonds, 1 residue, 1 model selected
> select add #1/a:518
43 atoms, 46 bonds, 2 residues, 1 model selected
> select add #1/a:519
63 atoms, 67 bonds, 3 residues, 1 model selected
> select add #1/a:520
85 atoms, 91 bonds, 4 residues, 1 model selected
> hide sel cartoons
> select #3/x:506
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel cartoons
> color sel #8f0100
> select clear
> select #1/x:503
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3/x:506
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #1/x:506@CA
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel cartoons
> select clear
> view 1
> view 1
> view 2
> view list
Named views: 1, 2
> select add #1/w:29
23 atoms, 25 bonds, 1 residue, 1 model selected
> select add #1/w:30
46 atoms, 50 bonds, 2 residues, 1 model selected
> select add #1/w:31
68 atoms, 74 bonds, 3 residues, 1 model selected
> select add #1/w:32
88 atoms, 95 bonds, 4 residues, 1 model selected
> select add #1/w:33
108 atoms, 116 bonds, 5 residues, 1 model selected
> hide sel cartoons
> select add #1/a:954
131 atoms, 141 bonds, 6 residues, 1 model selected
> select add #1/a:953
154 atoms, 166 bonds, 7 residues, 1 model selected
> select add #1/a:955
174 atoms, 187 bonds, 8 residues, 1 model selected
> hide sel cartoons
> select add #1/a:1050
197 atoms, 212 bonds, 9 residues, 1 model selected
> select add #1/a:1051
217 atoms, 233 bonds, 10 residues, 1 model selected
> select add #1/a:1052
237 atoms, 254 bonds, 11 residues, 1 model selected
> select add #1/a:962
257 atoms, 275 bonds, 12 residues, 1 model selected
> select add #1/a:963
280 atoms, 300 bonds, 13 residues, 1 model selected
> select add #1/a:964
302 atoms, 324 bonds, 14 residues, 1 model selected
> hide sel cartoons
> select #1/w:34
23 atoms, 25 bonds, 1 residue, 1 model selected
> select up
1631 atoms, 1821 bonds, 76 residues, 1 model selected
> show sel cartoons
> select clear
> view 1
> select #1/a:1230
20 atoms, 21 bonds, 1 residue, 1 model selected
> select clear
> ui tool show "Side View"
> select #1/a:1053
23 atoms, 25 bonds, 1 residue, 1 model selected
> select add #1/a:1054
43 atoms, 46 bonds, 2 residues, 1 model selected
> select add #1/a:1055
65 atoms, 70 bonds, 3 residues, 1 model selected
> select add #1/a:1056
85 atoms, 91 bonds, 4 residues, 1 model selected
> select add #1/a:1216
107 atoms, 115 bonds, 5 residues, 1 model selected
> select add #1/a:1215
130 atoms, 140 bonds, 6 residues, 1 model selected
> select subtract #1/a:1215
107 atoms, 115 bonds, 5 residues, 1 model selected
> select add #1/a:1215
130 atoms, 140 bonds, 6 residues, 1 model selected
> select add #1/a:1214
150 atoms, 161 bonds, 7 residues, 1 model selected
> select add #1/a:1213
172 atoms, 185 bonds, 8 residues, 1 model selected
> select add #1/a:1212
192 atoms, 206 bonds, 9 residues, 1 model selected
> hide sel cartoons
> select clear
> select #1/a:1049
20 atoms, 21 bonds, 1 residue, 1 model selected
> select up
33050 atoms, 37004 bonds, 1540 residues, 1 model selected
> show sel cartoons
> select clear
> select #1/a:1051
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #1/a:1050
43 atoms, 46 bonds, 2 residues, 1 model selected
> select subtract #1/a:1051
23 atoms, 25 bonds, 1 residue, 1 model selected
> select add #1/a:1049
43 atoms, 46 bonds, 2 residues, 1 model selected
> select add #1/a:1048
66 atoms, 71 bonds, 3 residues, 1 model selected
> select add #1/a:1047
89 atoms, 96 bonds, 4 residues, 1 model selected
> select add #1/a:1046
111 atoms, 120 bonds, 5 residues, 1 model selected
> select add #1/a:1045
131 atoms, 141 bonds, 6 residues, 1 model selected
> select add #1/a:1044
153 atoms, 165 bonds, 7 residues, 1 model selected
> select add #1/a:1043
176 atoms, 190 bonds, 8 residues, 1 model selected
> hide sel cartoons
> select add #1/a:1057
199 atoms, 215 bonds, 9 residues, 1 model selected
> select add #1/a:1056
219 atoms, 236 bonds, 10 residues, 1 model selected
> hide sel cartoons
> select add #1/a:1216
241 atoms, 260 bonds, 11 residues, 1 model selected
> select add #1/a:1215
264 atoms, 285 bonds, 12 residues, 1 model selected
> select add #1/a:1214
284 atoms, 306 bonds, 13 residues, 1 model selected
> select add #1/a:1213
306 atoms, 330 bonds, 14 residues, 1 model selected
> select add #1/a:1212
326 atoms, 351 bonds, 15 residues, 1 model selected
> select add #1/a:991
346 atoms, 372 bonds, 16 residues, 1 model selected
> select add #1/a:992
366 atoms, 393 bonds, 17 residues, 1 model selected
> select add #1/a:993
389 atoms, 418 bonds, 18 residues, 1 model selected
> select add #1/a:994
411 atoms, 442 bonds, 19 residues, 1 model selected
> hide sel cartoons
> select #1/a:990
20 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel cartoons
> camera ortho
> lighting depthCueStart 0.79
> select add #1/a:1498
41 atoms, 43 bonds, 2 residues, 1 model selected
> select add #1/a:1497
64 atoms, 68 bonds, 3 residues, 1 model selected
> select add #1/a:1499
86 atoms, 92 bonds, 4 residues, 1 model selected
> select add #1/a:1496
106 atoms, 113 bonds, 5 residues, 1 model selected
> select add #1/a:1495
126 atoms, 134 bonds, 6 residues, 1 model selected
> select add #1/a:1493
148 atoms, 158 bonds, 7 residues, 1 model selected
> select add #1/a:1492
170 atoms, 182 bonds, 8 residues, 1 model selected
> hide sel cartoons
> select add #1/a:1494
193 atoms, 207 bonds, 9 residues, 1 model selected
> hide sel cartoons
> select add #1/a:1396
215 atoms, 231 bonds, 10 residues, 1 model selected
> select add #1/a:1397
235 atoms, 252 bonds, 11 residues, 1 model selected
> select add #1/a:1398
257 atoms, 276 bonds, 12 residues, 1 model selected
> select add #1/a:1399
277 atoms, 297 bonds, 13 residues, 1 model selected
> select add #1/a:1400
297 atoms, 318 bonds, 14 residues, 1 model selected
> select add #1/a:1401
320 atoms, 343 bonds, 15 residues, 1 model selected
> select add #1/a:1402
342 atoms, 366 bonds, 16 residues, 1 model selected
> select add #1/a:1403
362 atoms, 387 bonds, 17 residues, 1 model selected
> select add #1/a:1404
382 atoms, 408 bonds, 18 residues, 1 model selected
> select add #1/a:1405
405 atoms, 433 bonds, 19 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> select add #1/a:1053
428 atoms, 458 bonds, 20 residues, 1 model selected
> select add #1/a:1052
448 atoms, 479 bonds, 21 residues, 1 model selected
> select add #1/a:1051
468 atoms, 500 bonds, 22 residues, 1 model selected
> hide sel cartoons
> select add #1/a:1211
488 atoms, 521 bonds, 23 residues, 1 model selected
> select add #1/a:1206
511 atoms, 546 bonds, 24 residues, 1 model selected
> select add #1/a:1207
535 atoms, 572 bonds, 25 residues, 1 model selected
> hide sel cartoons
> select add #1/a:987
558 atoms, 597 bonds, 26 residues, 1 model selected
> select add #1/a:985
578 atoms, 618 bonds, 27 residues, 1 model selected
> select add #1/a:986
598 atoms, 639 bonds, 28 residues, 1 model selected
> select add #1/a:1197
620 atoms, 663 bonds, 29 residues, 1 model selected
> select add #1/a:1196
642 atoms, 687 bonds, 30 residues, 1 model selected
> select add #1/a:1195
662 atoms, 708 bonds, 31 residues, 1 model selected
> select add #1/a:959
684 atoms, 732 bonds, 32 residues, 1 model selected
> select add #1/a:958
706 atoms, 756 bonds, 33 residues, 1 model selected
> select add #1/a:957
726 atoms, 777 bonds, 34 residues, 1 model selected
> select add #1/a:956
746 atoms, 798 bonds, 35 residues, 1 model selected
> select add #1/a:955
766 atoms, 819 bonds, 36 residues, 1 model selected
> select add #1/a:954
789 atoms, 844 bonds, 37 residues, 1 model selected
> hide sel cartoons
> select add #1/a:1395
809 atoms, 865 bonds, 38 residues, 1 model selected
> select add #1/a:924
829 atoms, 886 bonds, 39 residues, 1 model selected
> select subtract #1/a:924
809 atoms, 865 bonds, 38 residues, 1 model selected
> select add #1/a:925
832 atoms, 890 bonds, 39 residues, 1 model selected
> select add #1/a:924
852 atoms, 911 bonds, 40 residues, 1 model selected
> select add #1/a:926
875 atoms, 936 bonds, 41 residues, 1 model selected
> select add #1/a:1194
895 atoms, 957 bonds, 42 residues, 1 model selected
> hide sel cartoons
> select #1/w:37
29 atoms, 31 bonds, 1 residue, 1 model selected
> select add #1/w:36
51 atoms, 55 bonds, 2 residues, 1 model selected
> select add #1/w:35
73 atoms, 79 bonds, 3 residues, 1 model selected
> select add #1/w:34
96 atoms, 104 bonds, 4 residues, 1 model selected
> hide sel cartoons
> select clear
> select add #1/w:38
22 atoms, 24 bonds, 1 residue, 1 model selected
> hide sel atoms
> show sel atoms
> hide sel cartoons
> select clear
> select up
22 atoms, 24 bonds, 1 residue, 1 model selected
> hide sel atoms
> show sel cartoons
> select clear
> select add #1/a:984
20 atoms, 21 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select add #1/a:534
40 atoms, 42 bonds, 2 residues, 1 model selected
> select add #1/a:533
62 atoms, 66 bonds, 3 residues, 1 model selected
> select add #1/a:532
84 atoms, 90 bonds, 4 residues, 1 model selected
> select add #1/a:531
104 atoms, 111 bonds, 5 residues, 1 model selected
> select clear
> select add #1/a:792
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add #1/a:791
45 atoms, 49 bonds, 2 residues, 1 model selected
> select add #1/a:790
67 atoms, 73 bonds, 3 residues, 1 model selected
> select add #1/a:789
87 atoms, 94 bonds, 4 residues, 1 model selected
> select add #1/a:788
107 atoms, 115 bonds, 5 residues, 1 model selected
> select add #1/a:787
129 atoms, 139 bonds, 6 residues, 1 model selected
> hide sel cartoons
> view name 3
> select add #1/a:538
152 atoms, 164 bonds, 7 residues, 1 model selected
> select add #1/a:537
175 atoms, 189 bonds, 8 residues, 1 model selected
> select add #1/a:536
195 atoms, 210 bonds, 9 residues, 1 model selected
> select add #1/a:535
217 atoms, 234 bonds, 10 residues, 1 model selected
> select add #1/a:534
237 atoms, 255 bonds, 11 residues, 1 model selected
> select add #1/a:533
259 atoms, 279 bonds, 12 residues, 1 model selected
> select add #1/a:532
281 atoms, 303 bonds, 13 residues, 1 model selected
> select add #1/a:531
301 atoms, 324 bonds, 14 residues, 1 model selected
> select add #1/a:530
324 atoms, 349 bonds, 15 residues, 1 model selected
> select add #1/a:529
347 atoms, 374 bonds, 16 residues, 1 model selected
> select add #1/a:527
371 atoms, 400 bonds, 17 residues, 1 model selected
> select add #1/a:528
391 atoms, 421 bonds, 18 residues, 1 model selected
> select add #1/a:526
411 atoms, 442 bonds, 19 residues, 1 model selected
> select add #1/a:525
431 atoms, 463 bonds, 20 residues, 1 model selected
> select add #1/a:524
454 atoms, 488 bonds, 21 residues, 1 model selected
> select add #1/a:523
476 atoms, 512 bonds, 22 residues, 1 model selected
> select add #1/a:522
496 atoms, 533 bonds, 23 residues, 1 model selected
> select add #1/a:521
519 atoms, 558 bonds, 24 residues, 1 model selected
> select add #1/a:520
541 atoms, 582 bonds, 25 residues, 1 model selected
> select add #1/a:519
561 atoms, 603 bonds, 26 residues, 1 model selected
> select add #1/a:518
581 atoms, 624 bonds, 27 residues, 1 model selected
> select add #1/a:517
604 atoms, 649 bonds, 28 residues, 1 model selected
> select add #1/a:516
624 atoms, 670 bonds, 29 residues, 1 model selected
> select add #1/a:515
647 atoms, 695 bonds, 30 residues, 1 model selected
> select add #1/a:514
667 atoms, 716 bonds, 31 residues, 1 model selected
> select add #1/a:506
690 atoms, 741 bonds, 32 residues, 1 model selected
> select add #1/a:505
713 atoms, 766 bonds, 33 residues, 1 model selected
> hide sel cartoons
> select add #1/a:1200
733 atoms, 787 bonds, 34 residues, 1 model selected
> select add #1/a:1199
753 atoms, 808 bonds, 35 residues, 1 model selected
> select add #1/a:1198
776 atoms, 833 bonds, 36 residues, 1 model selected
> select add #1/a:983
798 atoms, 857 bonds, 37 residues, 1 model selected
> select add #1/a:982
818 atoms, 878 bonds, 38 residues, 1 model selected
> select add #1/a:923
840 atoms, 902 bonds, 39 residues, 1 model selected
> select add #1/a:981
860 atoms, 923 bonds, 40 residues, 1 model selected
> select add #1/a:980
880 atoms, 944 bonds, 41 residues, 1 model selected
> select add #1/a:979
900 atoms, 965 bonds, 42 residues, 1 model selected
> select add #1/a:978
922 atoms, 989 bonds, 43 residues, 1 model selected
> select add #1/a:970
942 atoms, 1010 bonds, 44 residues, 1 model selected
> select add #1/a:969
964 atoms, 1034 bonds, 45 residues, 1 model selected
> select add #1/a:968
986 atoms, 1058 bonds, 46 residues, 1 model selected
> select add #1/a:1385
1009 atoms, 1083 bonds, 47 residues, 1 model selected
> select add #1/a:1386
1032 atoms, 1108 bonds, 48 residues, 1 model selected
> select add #1/a:973
1055 atoms, 1133 bonds, 49 residues, 1 model selected
> select add #1/a:974
1077 atoms, 1157 bonds, 50 residues, 1 model selected
> select add #1/a:1062
1097 atoms, 1178 bonds, 51 residues, 1 model selected
> select add #1/a:1063
1117 atoms, 1199 bonds, 52 residues, 1 model selected
> select add #1/a:967
1138 atoms, 1221 bonds, 53 residues, 1 model selected
> select add #1/a:966
1162 atoms, 1247 bonds, 54 residues, 1 model selected
> select add #1/a:965
1182 atoms, 1268 bonds, 55 residues, 1 model selected
> select add #1/a:964
1204 atoms, 1292 bonds, 56 residues, 1 model selected
> select add #1/a:963
1227 atoms, 1317 bonds, 57 residues, 1 model selected
> select add #1/a:962
1247 atoms, 1338 bonds, 58 residues, 1 model selected
> select add #1/a:961
1267 atoms, 1359 bonds, 59 residues, 1 model selected
> select add #1/a:960
1287 atoms, 1380 bonds, 60 residues, 1 model selected
> select add #1/a:953
1310 atoms, 1405 bonds, 61 residues, 1 model selected
> select add #1/a:952
1330 atoms, 1426 bonds, 62 residues, 1 model selected
> select add #1/a:951
1353 atoms, 1451 bonds, 63 residues, 1 model selected
> select add #1/a:1221
1376 atoms, 1476 bonds, 64 residues, 1 model selected
> select add #1/a:1222
1399 atoms, 1501 bonds, 65 residues, 1 model selected
> select add #1/a:1223
1419 atoms, 1522 bonds, 66 residues, 1 model selected
> select add #1/a:1224
1439 atoms, 1543 bonds, 67 residues, 1 model selected
> select add #1/a:1225
1461 atoms, 1567 bonds, 68 residues, 1 model selected
> select add #1/a:1226
1481 atoms, 1588 bonds, 69 residues, 1 model selected
> hide sel cartoons
> select add #1/a:927
1504 atoms, 1613 bonds, 70 residues, 1 model selected
> select add #1/a:977
1526 atoms, 1637 bonds, 71 residues, 1 model selected
> hide sel cartoons
> select up
23 atoms, 25 bonds, 1 residue, 1 model selected
> select up
1631 atoms, 1821 bonds, 76 residues, 1 model selected
> color sel deep sky blue
> select clear
> select #1/w:33
20 atoms, 21 bonds, 1 residue, 1 model selected
> select up
1631 atoms, 1821 bonds, 76 residues, 1 model selected
> color sel medium blue
> select clear
> undo
> color sel royal blue
> select clear
> select #1/w:35@O2'
1 atom, 1 residue, 1 model selected
> select add #1/w:36@O2'
2 atoms, 2 residues, 1 model selected
> select add #1/w:37@OP1
3 atoms, 3 residues, 1 model selected
> color sel byhetero
> select clear
> lighting depthCueStart 0.6
> view name 4
> save
> D:/Projects/translocation/G3/Figures/D4_interactions/D4_interactions.cxs
> includeMaps true
> view 4
> save
> D:/Projects/translocation/G3/Figures/D4_interactions/D4_interactions.png
> width 4000 height 1972 supersample 3
> select #1/A:1913@O4'
1 atom, 1 residue, 1 model selected
> color sel byhetero
> select clear
> select #1/x:509@O
1 atom, 1 residue, 1 model selected
> color sel byhetero
> select clear
> select #1/a:1210
20 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> show sel atoms
> hide sel atoms
> select #1/x:541
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel cartoons
> show sel cartoons
> select clear
> help help:contact.html
> save
> D:/Projects/translocation/G3/Figures/D4_interactions/D4_interactions.png
> width 4000 height 1972 supersample 3
> view name 5
> select #3/w:33
20 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3/w:33-345
941 atoms, 1044 bonds, 47 residues, 1 model selected
> select #3/w:33-34
43 atoms, 47 bonds, 2 residues, 1 model selected
> show sel atoms
> color sel medium blue
> color sel royal blue
> style sel stick
Changed 43 atom styles
> hide #!1 models
Drag select of 19 atoms, 22 bonds
> hide sel atoms
Drag select of 19 atoms, 20 bonds
> hide sel atoms
> show #!1 models
> undo
> undo
> redo
> redo
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
23 atoms, 25 bonds, 1 residue, 1 model selected
> show sel cartoons
> select #3/w:33@O3'
1 atom, 1 residue, 1 model selected
> select up
20 atoms, 21 bonds, 1 residue, 1 model selected
> select up
1631 atoms, 1821 bonds, 76 residues, 1 model selected
> hide sel atoms
> select #3/w:34
23 atoms, 25 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #3/w:35
22 atoms, 24 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel royal blue
> style sel stick
Changed 22 atom styles
> select #3/w:34-35
45 atoms, 50 bonds, 2 residues, 1 model selected
> show sel atoms
> hide #!1 models
Drag select of 17 atoms, 20 bonds
Drag select of 13 atoms, 14 bonds
> hide sel atoms
Drag select of 1 atoms
> select add #3/w:35@C8
2 atoms, 1 bond, 1 residue, 1 model selected
> select add #3/w:35@N7
3 atoms, 1 bond, 1 residue, 1 model selected
> select add #3/w:35@O4'
4 atoms, 2 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3/w:35@C5'
1 atom, 1 residue, 1 model selected
> hide sel atoms
Drag select of 12 atoms, 13 bonds
> hide sel atoms
Drag select of 7 atoms, 7 bonds
> hide sel atoms
Drag select of 2 atoms, 1 bonds
> hide sel atoms
> show #!1 models
> hide #!1 models
> show #!1 models
> select #3/x:511
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide #!1 models
> show #!1 models
> hide sel cartoons
> select #3/x:512
4 atoms, 3 bonds, 1 residue, 1 model selected
> hide #!1 models
> show #!1 models
> hide sel cartoons
> select #1/x:512
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel cartoons
> select #3/x:512
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 4 atom styles
> select #3/x:511-512
15 atoms, 14 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 15 atom styles
> select #1/x:512
4 atoms, 3 bonds, 1 residue, 1 model selected
> select clear
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
Drag select of 7 atoms, 6 bonds
> hide sel atoms
> show #!1 models
> hide #!1 models
> select #3/x:512@C
1 atom, 1 residue, 1 model selected
> select add #3/x:512@O
2 atoms, 1 residue, 1 model selected
> hide sel atoms
> show #!1 models
> select #3/x:512@N
1 atom, 1 residue, 1 model selected
> hide sel atoms
> show sel atoms
> hide #!1 models
> select #3/x:512@CA
1 atom, 1 residue, 1 model selected
> hide sel atoms
> undo
> show #!1 models
> select clear
> save
> D:/Projects/translocation/G3/Figures/D4_interactions/D4_interactions_512a.png
> width 4000 height 1972 supersample 3
> hide #!1 models
> select #3/x:512@CA
1 atom, 1 residue, 1 model selected
> select add #3/x:512@N
2 atoms, 1 residue, 1 model selected
> hide sel atoms
> show #!1 models
> save
> D:/Projects/translocation/G3/Figures/D4_interactions/D4_interactions_512b.png
> width 4000 height 1972 supersample 3
> view name 5
> save
> D:/Projects/translocation/G3/Figures/D4_interactions/D4_interactions.cxs
> hide #!1 models
> show #!1 models
> select #1/a:1210-1212
60 atoms, 65 bonds, 3 residues, 1 model selected
> show sel cartoons
> select #1/a:1210-1216
147 atoms, 163 bonds, 7 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> show sel atoms
> show sel atoms
> hide sel atoms
> select #1/a:1210
20 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select #1/a:1210@OP1
1 atom, 1 residue, 1 model selected
> color sel byhetero
> select clear
> select #1/x:540
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #1/x:541
13 atoms, 11 bonds, 2 residues, 1 model selected
> hide sel cartoons
> select #3/x:540-541
13 atoms, 12 bonds, 2 residues, 1 model selected
> show sel atoms
> color sel byhetero
> style sel stick
Changed 13 atom styles
> color sel #8f0100
> select #1/x:540
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel cartoons
> hide #!1 models
Drag select of 8 atoms, 8 bonds
> select add #3/x:540@O
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> show #!1 models
> select #3/x:542
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 4 atom styles
> color sel #8f0100
> select clear
> select #1/x:541@O
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #3/x:541@O
1 atom, 1 residue, 1 model selected
> hide sel atoms
> undo
> undo
> undo
> undo
> undo
> undo
> undo
> undo
> undo
> undo
> hide sel atoms
> select #3/x:540-542
17 atoms, 16 bonds, 3 residues, 1 model selected
> hide sel atoms
> select #1/x:540-542
17 atoms, 16 bonds, 3 residues, 1 model selected
> show sel cartoons
> select clear
> save
> D:/Projects/translocation/G3/Figures/D4_interactions/D4_interactions.cxs
> select #1/x:549
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
121 atoms, 122 bonds, 16 residues, 1 model selected
> select up
5473 atoms, 5576 bonds, 704 residues, 1 model selected
> save
> D:/Projects/translocation/G3/Figures/D4_interactions/D4_interactions_v1.png
> width 4000 height 1972 supersample 3
> select #1/x
5473 atoms, 5576 bonds, 704 residues, 1 model selected
> color sel red
> open D:/Projects/translocation/G3/old/pre1_GDP-Pi/models/Pre1_GDP-
> Pi_RSR-4-coot-46.pdb
Chain information for Pre1_GDP-Pi_RSR-4-coot-46.pdb #4
---
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
> hide #4 models
> color sel #c5403f
> color sel ##ba0000
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color sel #c80000
> color sel byhetero
> lighting simple
> lighting shadows true
> lighting shadows false
> lighting full
> lighting shadows false
> lighting soft
> lighting simple
> lighting shadows true
> lighting shadows false
> lighting full
> lighting shadows false
> color sel #c20000
> color sel byhetero
> select clear
> select #1/w:34
23 atoms, 25 bonds, 1 residue, 1 model selected
> select up
1631 atoms, 1821 bonds, 76 residues, 1 model selected
> color sel midnight blue
> select #1/w:35@OP1
1 atom, 1 residue, 1 model selected
> select up
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #1/w:35@OP1
1 atom, 1 residue, 1 model selected
> select up
22 atoms, 24 bonds, 1 residue, 1 model selected
> select up
1631 atoms, 1821 bonds, 76 residues, 1 model selected
> color sel midnight blue
> select #1/w:35@OP1
1 atom, 1 residue, 1 model selected
> select up
22 atoms, 24 bonds, 1 residue, 1 model selected
> select up
1631 atoms, 1821 bonds, 76 residues, 1 model selected
> select add #3/w:34@O3'
1632 atoms, 1821 bonds, 77 residues, 2 models selected
> select up
1654 atoms, 1846 bonds, 77 residues, 2 models selected
> select up
3262 atoms, 3642 bonds, 152 residues, 2 models selected
> color sel midnight blue
> select clear
> select #1/w:34
23 atoms, 25 bonds, 1 residue, 1 model selected
> select add #3/w:34@O3'
24 atoms, 25 bonds, 2 residues, 2 models selected
> select add #1/w:35@OP1
25 atoms, 25 bonds, 3 residues, 2 models selected
> select up
68 atoms, 75 bonds, 3 residues, 2 models selected
> select up
3262 atoms, 3642 bonds, 152 residues, 2 models selected
> save
> D:/Projects/translocation/G3/Figures/D4_interactions/D4_interactions_v2.png
> width 4000 height 1972 supersample 3
> lighting depthCueStart 0.79
> lighting depthCueStart 0.6
> save
> D:/Projects/translocation/G3/Figures/D4_interactions/D4_interactions_v3.png
> width 4000 height 1972 supersample 3
> save
> D:/Projects/translocation/G3/Figures/D4_interactions/D4_interactions.cxs
——— End of log from Tue Jan 12 15:22:53 2021 ———
opened ChimeraX session
> view orient
> view
> camera ortho
> select #1/A:363
23 atoms, 25 bonds, 1 residue, 1 model selected
> select up
62336 atoms, 69815 bonds, 2903 residues, 1 model selected
> hide sel cartoons
> select #1/a:1515
23 atoms, 25 bonds, 1 residue, 1 model selected
> select up
33050 atoms, 37004 bonds, 1540 residues, 1 model selected
> show sel cartoons
> select clear
> hide #3 models
> hide #2 models
> show #2 models
> show #3 models
> select #1/a-u
52011 atoms, 56215 bonds, 3971 residues, 1 model selected
> show sel cartoons
> 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
> show sel atoms
> nucleotides sel fill
> style nucleic & sel stick
Changed 1631 atom styles
> select clear
> select #1/a:954
23 atoms, 25 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> ui mousemode right pivot
> select #1/a:954
23 atoms, 25 bonds, 1 residue, 1 model selected
> select add #1/a:956
43 atoms, 46 bonds, 2 residues, 1 model selected
> select add #1/a:955
63 atoms, 67 bonds, 3 residues, 1 model selected
> select add #1/a:957
83 atoms, 88 bonds, 4 residues, 1 model selected
> select add #1/a:953
106 atoms, 113 bonds, 5 residues, 1 model selected
> show sel atoms
> hide sel cartoons
> select clear
> select #1/a:955@OP1
1 atom, 1 residue, 1 model selected
> select add #1/w:41@O2'
2 atoms, 2 residues, 1 model selected
> ui tool show Distances
> distance #1/a:955@OP1 #1/w:41@O2'
Distance between Chimeric_GDP-1-sw1-v2-RSR-0-coot-21.pdb #1/a U 955 OP1 and /w
C 41 O2': 3.427Å
> select clear
> open 5afi
Summary of feedback from opening 5afi fetched from pdb
---
warning | Unable to infer polymer connectivity due to unspecified label_seq_id
for residue "FME" near line 173617
5afi title:
2.9A Structure of E. coli ribosome-EF-TU complex by cs-corrected cryo-EM [more
info...]
Chain information for 5afi #6
---
Chain | Description
0 | 50S ribosomal protein L32
1 | 50S ribosomal protein L33
2 | 50S ribosomal protein L34
3 | 50S ribosomal protein L35
4 | 50S ribosomal protein L36
5 | 50S ribosomal protein L10
6 | 50S ribosomal protein L31
A | 23S ribosomal RNA
B | 5S ribosomal RNA
C | 50S ribosomal protein L2
D | 50S ribosomal protein L3
E | 50S ribosomal protein L4
F | 50S ribosomal protein L5
G | 50S ribosomal protein L6
H | 50S ribosomal protein L9
I | 50S ribosomal protein L11
J | 50S ribosomal protein L13
K | 50S ribosomal protein L14
L | 50S ribosomal protein L15
M | 50S ribosomal protein L16
N | 50S ribosomal protein L17
O | 50S ribosomal protein L18
P | 50S ribosomal protein L19
Q | 50S ribosomal protein L20
R | 50S ribosomal protein L21
S | 50S ribosomal protein L22
T | 50S ribosomal protein L23
U | 50S ribosomal protein L24
V | 50S ribosomal protein L25
W | 50S ribosomal protein L27
X | 50S ribosomal protein L28
Y | 50S ribosomal protein L29
Z | 50S ribosomal protein L30
a | 16S ribosomal RNA
b | 30S ribosomal protein S2
c | 30S ribosomal protein S3
d | 30S ribosomal protein S4
e | 30S ribosomal protein S5
f | 30S ribosomal protein S6
g | 30S ribosomal protein S7
h | 30S ribosomal protein S8
i | 30S ribosomal protein S9
j | 30S ribosomal protein S10
k | 30S ribosomal protein S11
l | 30S ribosomal protein S12
m | 30S ribosomal protein S13
n | 30S ribosomal protein S14
o | 30S ribosomal protein S15
p | 30S ribosomal protein S16
q | 30S ribosomal protein S17
r | 30S ribosomal protein S18
s | 30S ribosomal protein S19
t | 30S ribosomal protein S20
u | 30S ribosomal protein S21
v w | P-site fMet-tRNAfMet
x | mRNA
y | A/T-site Phe-tRNAPhe
z | Elongation factor Tu 2
Non-standard residues in 5afi #6
---
3TD —
(1S)-1,4-anhydro-1-(3-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-5-O-phosphono-
D-ribitol
CL — chloride ion
KIR — kirromycin (mocimycin; delvomycin; myc-8003)
MG — magnesium ion
NA — sodium ion
ZN — zinc ion
> select #6
152707 atoms, 165374 bonds, 5154 pseudobonds, 11484 residues, 4 models
selected
> hide target m
> show #2-3#!1 target m
> select clear
> select #1/m:114
7 atoms, 7 bonds, 1 residue, 1 model selected
> select up
34 atoms, 35 bonds, 4 residues, 1 model selected
> show sel atoms
> hide sel cartoons
> select clear
> select add #1/a:1197
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add #1/a:1196
44 atoms, 48 bonds, 2 residues, 1 model selected
> select add #1/a:1195
64 atoms, 69 bonds, 3 residues, 1 model selected
> show sel atoms
> select add #1/a:965
84 atoms, 90 bonds, 4 residues, 1 model selected
> select add #1/a:966
108 atoms, 116 bonds, 5 residues, 1 model selected
> show sel atoms
> select add #1/w:32
128 atoms, 137 bonds, 6 residues, 1 model selected
> select add #1/w:31
150 atoms, 161 bonds, 7 residues, 1 model selected
> hide sel cartoons
> select #1/w:34
23 atoms, 25 bonds, 1 residue, 1 model selected
> select up
1631 atoms, 1821 bonds, 76 residues, 1 model selected
> hide sel cartoons
> select clear
> select #1/w:32@OP1
1 atom, 1 residue, 1 model selected
> select add #1/a:965@O4
2 atoms, 2 residues, 1 model selected
> distance #1/w:32@OP1 #1/a:965@O4
Distance between Chimeric_GDP-1-sw1-v2-RSR-0-coot-21.pdb #1/w PSU 32 OP1 and
/a U 965 O4: 3.210Å
> show #!5 models
> show #5.1 models
> select #1/A:1913@P
1 atom, 1 residue, 1 model selected
> select up
22 atoms, 24 bonds, 1 residue, 1 model selected
> select up
62336 atoms, 69815 bonds, 2903 residues, 1 model selected
> show sel cartoons
> select subtract #1/A:1922
62313 atoms, 69790 bonds, 2902 residues, 1 model selected
> select #1/A:1922
23 atoms, 25 bonds, 1 residue, 1 model selected
> select add #1/A:1923
43 atoms, 46 bonds, 2 residues, 1 model selected
> select add #1/A:1924
63 atoms, 67 bonds, 3 residues, 1 model selected
> show sel atoms
> hide sel cartoons
> select add #1/A:1910
86 atoms, 92 bonds, 4 residues, 1 model selected
> select add #1/A:1909
106 atoms, 113 bonds, 5 residues, 1 model selected
> select add #1/A:1908
126 atoms, 134 bonds, 6 residues, 1 model selected
> hide sel cartoons
> show sel atoms
> select #1/A:1908@O2'
1 atom, 1 residue, 1 model selected
> select add #1/w:13@OP1
2 atoms, 2 residues, 1 model selected
> distance #1/A:1908@O2' #1/w:13@OP1
Distance between Chimeric_GDP-1-sw1-v2-RSR-0-coot-21.pdb #1/A C 1908 O2' and
/w C 13 OP1: 3.275Å
> select #1/w:11@O2'
1 atom, 1 residue, 1 model selected
> select add #1/A:1909@O2'
2 atoms, 2 residues, 1 model selected
> distance #1/w:11@O2' #1/A:1909@O2'
Distance between Chimeric_GDP-1-sw1-v2-RSR-0-coot-21.pdb #1/w C 11 O2' and /A
C 1909 O2': 4.146Å
> ~distance #1/w:11@O2' #1/A:1909@O2'
> select #1/a:1492-1493
44 atoms, 49 bonds, 2 residues, 1 model selected
> show sel cartoons
> show sel atoms
> select add #1/a:1495
64 atoms, 70 bonds, 3 residues, 1 model selected
> select add #1/a:1496
84 atoms, 91 bonds, 4 residues, 1 model selected
> select add #1/a:1494
107 atoms, 116 bonds, 5 residues, 1 model selected
> select add #1/a:1497
130 atoms, 141 bonds, 6 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> show sel atoms
> select clear
> select add #1/a:1229
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add #1/a:1230
42 atoms, 45 bonds, 2 residues, 1 model selected
> select add #1/a:1231
65 atoms, 70 bonds, 3 residues, 1 model selected
> show sel atoms
> hide sel cartoons
> select #1/v:29
23 atoms, 25 bonds, 1 residue, 1 model selected
> select up
1642 atoms, 1834 bonds, 77 residues, 1 model selected
> show sel atoms
> hide sel cartoons
> select clear
> select up
17 atoms, 16 bonds, 4 residues, 1 model selected
> select up
85 atoms, 93 bonds, 4 residues, 1 model selected
> select up
92 atoms, 99 bonds, 6 residues, 1 model selected
> select up
131 atoms, 144 bonds, 6 residues, 1 model selected
> select add #1/v:31@OP1
132 atoms, 144 bonds, 7 residues, 1 model selected
> select up
154 atoms, 170 bonds, 7 residues, 1 model selected
> hbonds sel resctict both
Expected a keyword
> hbonds sel restict both
Expected a keyword
> hbonds sel restrict both
2 hydrogen bonds found
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> close #2
> hbonds sel restrict both
2 hydrogen bonds found
> ui tool show H-Bonds
> hbonds sel restrict both select true reveal true
2 hydrogen bonds found
> style sel sphere
Changed 3 atom styles
> style sel stick
Changed 3 atom styles
> select subtract #1/a:1230@O4'
2 atoms, 2 residues, 1 model selected
> distance #1/a:1229@O2' #1/v:30@OP1
Distance between Chimeric_GDP-1-sw1-v2-RSR-0-coot-21.pdb #1/a A 1229 O2' and
/v G 30 OP1: 2.841Å
> select #1/a:954@OP1
1 atom, 1 residue, 1 model selected
> select add #1/w:30@O2'
2 atoms, 2 residues, 1 model selected
> distance #1/a:954@OP1 #1/w:30@O2'
Distance between Chimeric_GDP-1-sw1-v2-RSR-0-coot-21.pdb #1/a G 954 OP1 and /w
G 30 O2': 5.014Å
Must select one or more distances in the table
> distance #1/a:954@OP1 #1/w:30@O2'
Distance already exists; modify distance properties with 'distance style'
> ~distance #1/a:954@OP1 #1/w:30@O2'
> select clear
> select add #1/a:1341
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #1/a:1340
42 atoms, 45 bonds, 2 residues, 1 model selected
> select add #1/a:1339
64 atoms, 69 bonds, 3 residues, 1 model selected
> select add #1/a:1338
87 atoms, 94 bonds, 4 residues, 1 model selected
> show sel atoms
> hide sel cartoons
> select add #1/v:31@O4'
88 atoms, 94 bonds, 5 residues, 1 model selected
> select up
110 atoms, 122 bonds, 5 residues, 1 model selected
> select up
34692 atoms, 38838 bonds, 1617 residues, 1 model selected
> select up
23 atoms, 25 bonds, 1 residue, 1 model selected
> select up
1642 atoms, 1834 bonds, 77 residues, 1 model selected
> select up
1653 atoms, 1843 bonds, 79 residues, 1 model selected
> select up
1740 atoms, 1940 bonds, 83 residues, 1 model selected
> ui tool show H-Bonds
> hbonds sel restrict both select true reveal true
160 hydrogen bonds found
> select add #1/a:790
272 atoms, 24 bonds, 79 residues, 1 model selected
> select add #1/a:789
292 atoms, 45 bonds, 80 residues, 1 model selected
> show sel atoms
> select add #1/a:696
314 atoms, 69 bonds, 81 residues, 1 model selected
> select add #1/a:695
336 atoms, 93 bonds, 82 residues, 1 model selected
> select add #1/a:694
358 atoms, 117 bonds, 83 residues, 1 model selected
> show sel atoms
> select add #1/a:693
381 atoms, 142 bonds, 84 residues, 1 model selected
> show sel atoms
> hide sel cartoons
> select #1/v:38@O2'
1 atom, 1 residue, 1 model selected
> select add #1/a:693@N2
2 atoms, 2 residues, 1 model selected
> hbonds sel restrict both
0 hydrogen bonds found
> select up
45 atoms, 49 bonds, 2 residues, 1 model selected
> hbonds sel restrict both
0 hydrogen bonds found
> select add #1/v:39@P
51 atoms, 49 bonds, 4 residues, 1 model selected
> select up
87 atoms, 96 bonds, 4 residues, 1 model selected
> hbonds sel restrict both
0 hydrogen bonds found
> select #1/v:38@O2'
1 atom, 1 residue, 1 model selected
> select add #1/a:693@N2
2 atoms, 2 residues, 1 model selected
> distance #1/v:38@O2' #1/a:693@N2
Distance between Chimeric_GDP-1-sw1-v2-RSR-0-coot-21.pdb #1/v A 38 O2' and /a
G 693 N2: 2.325Å
> select #1/v:39@OP1
1 atom, 1 residue, 1 model selected
> select add #1/a:694@O2'
2 atoms, 2 residues, 1 model selected
> distance #1/v:39@OP1 #1/a:694@O2'
Distance between Chimeric_GDP-1-sw1-v2-RSR-0-coot-21.pdb #1/v C 39 OP1 and /a
A 694 O2': 3.966Å
> ~distance #1/v:39@OP1 #1/a:694@O2'
> save D:/Projects/translocation/G3/Figures/D4_interactions/Sites.cxs
> includeMaps true
> select #1/A:2125
23 atoms, 25 bonds, 1 residue, 1 model selected
> select up
62336 atoms, 69815 bonds, 2903 residues, 1 model selected
> hide sel cartoons
> select #1/b-u
18778 atoms, 19051 bonds, 2392 residues, 1 model selected
> hide sel cartoons
> select up
18818 atoms, 19093 bonds, 2394 residues, 1 model selected
> select up
22051 atoms, 22706 bonds, 2545 residues, 1 model selected
> show sel cartoons
> hide sel atoms
> select clear
> select #1/a:1198
23 atoms, 25 bonds, 1 residue, 1 model selected
> select up
33050 atoms, 37004 bonds, 1540 residues, 1 model selected
> show sel cartoons
> select subtract #1/a:965
33030 atoms, 36983 bonds, 1539 residues, 1 model selected
> hide sel atoms
> undo
> select clear
> select add #1/w:35
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add #1/w:36
44 atoms, 48 bonds, 2 residues, 1 model selected
> select add #1/w:37
73 atoms, 79 bonds, 3 residues, 1 model selected
> show sel atoms
> select add #1/w:34
96 atoms, 104 bonds, 4 residues, 1 model selected
> show sel atoms
> select clear
> select #1/b-u
18778 atoms, 19051 bonds, 2392 residues, 1 model selected
> hide sel cartoons
> select clear
> save D:/Projects/translocation/G3/Figures/D4_interactions/Sites.cxs
——— End of log from Wed Jan 27 09:55:18 2021 ———
opened ChimeraX session
> select add #1/v:30
23 atoms, 25 bonds, 1 residue, 1 model selected
> select up
25 atoms, 26 bonds, 2 residues, 1 model selected
> select up
45 atoms, 49 bonds, 2 residues, 1 model selected
> hbonds sel restrict both
1 hydrogen bonds found
> toolshed show
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')
PySide2 version: 5.15.2
Qt version: 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.9.0
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2020.12.5
cftime: 1.3.1
chardet: 3.0.4
ChimeraX-AddCharge: 1.0
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: 1.10.5
ChimeraX-AtomicLibrary: 1.2
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: 1.1
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.dev202101250432
ChimeraX-CoreFormats: 1.0
ChimeraX-coulombic: 1.0.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-DataFormats: 1.1
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-Maestro: 1.8.1
ChimeraX-Map: 1.0.2
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: 2.2
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: 1.5
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: 1.4
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SeqView: 2.3
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: 1.3
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.0
ChimeraX-ToolshedUtils: 1.1
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.4.1
ChimeraX-uniprot: 2.1
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
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: 4.7.0
kiwisolver: 1.3.1
line-profiler: 2.1.2
lxml: 4.6.2
lz4: 3.1.0
MarkupSafe: 1.1.1
matplotlib: 3.3.2
msgpack: 1.0.0
netCDF4: 1.5.4
networkx: 2.5
numexpr: 2.7.2
numpy: 1.19.2
numpydoc: 1.1.0
openvr: 1.14.1501
packaging: 20.8
ParmEd: 3.2.0
parso: 0.7.1
pickleshare: 0.7.5
Pillow: 7.2.0
pip: 20.3.1
pkginfo: 1.5.0.1
prompt-toolkit: 3.0.14
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
PySide2: 5.15.2
python-dateutil: 2.8.1
pytz: 2020.5
pywin32: 228
pyzmq: 21.0.1
qtconsole: 4.7.7
QtPy: 1.9.0
RandomWords: 0.3.0
requests: 2.24.0
scipy: 1.5.2
setuptools: 50.3.2
sfftk-rw: 0.6.7.dev1
shiboken2: 5.15.2
six: 1.15.0
snowballstemmer: 2.1.0
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: 0.36.0
wheel-filename: 1.2.0
WMI: 1.5.1
Change History (4)
comment:1 by , 5 years ago
| Component: | Unassigned → Structure Analysis |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → H-bonds not recreated |
comment:2 by , 5 years ago
| Status: | accepted → feedback |
|---|
follow-up: 3 comment:3 by , 5 years ago
Dear Eric, I created the bonds saved and opened the session and only then deleted the model. Respectfully yours, Valentyn Petrychenko ср, 27 січ. 2021 о 18:41 ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> пише:
comment:4 by , 5 years ago
Dear Valentyn,
So I opened 1gcn and 3fx2, ran 'hbonds', saved a session and quit. Started ChimeraX, restored the session, closed the 'hydrogen bonds' group and ran 'hbonds'. The group was recreated and the H-bonds remade.
Presumably you have a session file that it you open it and close the 'hydrogen bonds' group, then the 'hbonds' command doesn't work properly. If so, can you send that session?
--Eric
Note:
See TracTickets
for help on using tickets.
Hi Valentyn,
--Eric