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Opened 5 years ago
Closed 5 years ago
#3262 closed defect (duplicate)
Problems both saving and restoring nucleotides
| Reported by: | Owned by: | Greg Couch | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sessions | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Darwin-18.6.0-x86_64-i386-64bit
ChimeraX Version: 0.93 (2020-04-03)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 0.93 (2020-04-03)
© 2016-2020 Regents of the University of California. All rights reserved.
> open /Users/fengwei.zheng/Documents/Draft_PolD/Session/MK/MK3_Fe-
> S_comparison.cxs format session
Log from Wed May 13 21:16:28 2020UCSF ChimeraX version: 0.93 (2020-04-03)
© 2016-2020 Regents of the University of California. All rights reserved.
> open
> /Users/fengwei.zheng/Documents/Draft_PolD/Session/MK/PIPs_comparison.cxs
> format session
Log from Tue May 12 22:58:09 2020UCSF ChimeraX version: 0.93 (2020-04-03)
© 2016-2020 Regents of the University of California. All rights reserved.
> open
> /Users/fengwei.zheng/Documents/Draft_PolD/Session/SI/S2/FigSI_2_409PolD-yst-
> human_comparison3.cxs format session
Log from Fri Apr 24 18:20:38 2020 Startup Messages
---
warnings | No presets found in custom preset folder
/Users/fengwei.zheng/Documents/Draft_PolD/manuscript
No presets found in custom preset folder
/Users/fengwei.zheng/Documents/Draft_PolD/Figure
No presets found in custom preset folder
/Users/fengwei.zheng/Documents/Draft_PolD/Session
UCSF ChimeraX version: 0.93 (2020-04-03)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open2
> /Users/fengwei.zheng/Documents/Structures/PolD/409-ystPolDcplx_rpFG_163_3.pdb
Chain information for 409-ystPolDcplx_rpFG_163_3.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
F | No description available
G | No description available
H | No description available
P | No description available
T | No description available
> hide atoms
> show cartoons
> lighting simple
> lighting simple
> lighting soft
> lighting full
> lighting simple
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> graphics silhouettes false
> graphics silhouettes true
> lighting full
> lighting simple
> graphics silhouettes false
> graphics silhouettes true
> close session
> open
> /Users/fengwei.zheng/Documents/Draft_PolD/Session/SI/S2/FigSI_2_409PolD-yst-
> human_comparison.cxs
opened ChimeraX session
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/nucleotides/_data.py", line 525, in rebuild
_rebuild_molecule('internal', mol)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/nucleotides/_data.py", line 652, in _rebuild_molecule
hide_residues = make_ladder(nd, residues, mol._ladder_params)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/nucleotides/_data.py", line 1237, in make_ladder
va, na, ta = get_cylinder(params.rung_radius, ep0, ep1)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/nucleotides/_data.py", line 733, in get_cylinder
h = distance(p0, p1)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/geometry/vector.py", line 71, in distance
return sqrt(distance_squared(p, q))
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/geometry/vector.py", line 63, in distance_squared
if len(p) == 3:
TypeError: object of type 'NoneType' has no len()
Error processing trigger "new frame":
TypeError: object of type 'NoneType' has no len()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/geometry/vector.py", line 63, in distance_squared
if len(p) == 3:
See log for complete Python traceback.
> close session
> open
> /Users/fengwei.zheng/Documents/Draft_PolD/Session/SI/S2/FigSI_2_409PolD-yst-
> human_comparison.cxs
opened ChimeraX session
> lighting full
> lighting full
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> lighting simple
> lighting simple
> hide #!3 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!3 models
> hide #!3 models
> hide #!1 models
> show #!1 models
> show #!3 models
> hide #!3 models
> show #!3 models
Missing or invalid "text1" argument: Expected a text string
> preset cart
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> undo
> undo
> undo
> undo
> undo
> undo
> undo
> undo
> undo
> cartoon style xsection barbell
> close session
> open
> /Users/fengwei.zheng/Documents/Structures/PolD/409-ystPolDcplx_rpFG_163_3.pdb
> format PDB
Chain information for 409-ystPolDcplx_rpFG_163_3.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
F | No description available
G | No description available
H | No description available
P | No description available
T | No description available
> hide atoms
> show cartoons
> dssp
> undo
> close session
> open
> /Users/fengwei.zheng/Documents/Structures/PolD/409-ystPolDcplx_rpFG_163_3.pdb
> format PDB
Chain information for 409-ystPolDcplx_rpFG_163_3.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
F | No description available
G | No description available
H | No description available
P | No description available
T | No description available
> show cartoons
> hide atoms
> select up
Nothing selected
> dssp
> undo
Expected an atoms specifier or a keyword
> cartoon style xsection barbell
Expected an atoms specifier or a keyword
> preset cart
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> close session
> open
> /Users/fengwei.zheng/Documents/Structures/PolD/409-ystPolDcplx_rpFG_163_3.pdb
> format PDB
Chain information for 409-ystPolDcplx_rpFG_163_3.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
F | No description available
G | No description available
H | No description available
P | No description available
T | No description available
> hide atoms
> show cartoons
> view
> lighting simple
> lighting simple
> lighting full
> lighting shadows false
> lighting shadows true
> graphics silhouettes true
> lighting flat
> lighting flat
> lighting full
> close session
> open
> /Users/fengwei.zheng/Documents/Draft_PolD/Session/SI/S2/FigSI_2_409PolD-yst-
> human_comparison.cxs
opened ChimeraX session
> lighting full
> lighting full
> lighting simple
> graphics silhouettes false
> graphics silhouettes true
> hide #!1 models
> hide #!3 models
> show #!2 models
> hide #!2 models
> hide #!5 models
> show #!2 models
> close #2
> show #!1 models
> open
> /Users/fengwei.zheng/Documents/Structures/PolD/409-ystPolDcplx_rpFG_163_3.pdb
> format PDB
Chain information for 409-ystPolDcplx_rpFG_163_3.pdb #2
---
Chain | Description
A | No description available
B | No description available
C | No description available
F | No description available
G | No description available
H | No description available
P | No description available
T | No description available
> hide #!1-2 atoms
> show #!1-2 cartoons
> hide #!2 models
> hide #!1 models
> show #!4 models
> close #4
> close session
> open
> /Users/fengwei.zheng/Documents/Draft_PolD/Session/SI/S2/FigSI_2_409PolD-yst-
> human_comparison.cxs
opened ChimeraX session
> hide #!5 models
> show #!5 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> close #2
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting full
> graphics silhouettes false
> lighting simple
> lighting simple
> lighting full
> close session
> open
> /Users/fengwei.zheng/Documents/Structures/PolD/409-ystPolDcplx_rpFG_163_3.pdb
> format PDB
Chain information for 409-ystPolDcplx_rpFG_163_3.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
F | No description available
G | No description available
H | No description available
P | No description available
T | No description available
> hide atoms
> show cartoons
> open /Users/fengwei.zheng/Documents/Structures/PolD/409-yst_PolD.pdb
409-yst_PolD.pdb title:
Cryo-em structure of DNA polymerase δ holoenzyme [more info...]
Chain information for 409-yst_PolD.pdb #2
---
Chain | Description
A | DNA polymerase III
B | hydroxyurea-sensitive protein 2
C | DNA polymerase δ subunit 3
P T | DNA (30-mer)
Non-standard residues in 409-yst_PolD.pdb #2
---
CA — calcium ion
DCP — 2'-deoxycytidine-5'-triphosphate
SF4 — iron/sulfur cluster
> hide atoms
> show cartoons
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> open /Users/fengwei.zheng/Documents/Structures/PolD/409-humPolDcplx.pdb
409-humPolDcplx.pdb title:
Processive human polymerase δ holoenzyme [more info...]
Chain information for 409-humPolDcplx.pdb #3
---
Chain | Description
A | DNA polymerase subunit δ P125
B | DNA polymerase δ subunit P50
C | DNA polymerase δ subunit 3
D | DNA polymerase δ subunit P12
E F G | proliferating cell nuclear antigen
P | DNA primer
T | DNA template
Non-standard residues in 409-humPolDcplx.pdb #3
---
DOC — 2',3'-dideoxycytidine-5'-monophosphate
SF4 — iron/sulfur cluster
TTP — thymidine-5'-triphosphate
ZN — zinc ion
> hide #!1,3 atoms
> show #!1,3 cartoons
> show #!2 models
> hide #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> hide #!1 models
> show #!1 models
> show #!3 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> graphics silhouettes true
> hide #!1 models
> graphics silhouettes false
> show #!1 models
> hide #!3 models
> graphics silhouettes true
> show #!3 models
> show #!2 models
> cartoon style #6 xsection barbell
> cartoon style xsection barbell
> nucleotides stubs
> nucleotides ladder
> cartoon style nucleic xsection oval width 1 thickness 1
> dssp
> lighting simple
> lighting simple
> lighting full
> lighting simple
> lighting shadows true
> lighting shadows false
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> color #1 firebrick cartoons
> color #2 cyan
> color #1 firebrick
> show atoms
> hide atoms
> color #3 yellow
> lighting full
> hide #!2 models
> lighting simple
> lighting full
> lighting simple
> color #3 green
> color #3 lime
> color #3 pale green
> color #1 red
> color #1 hot pink
> color #1 deep pink
> color #1 salmon
> dssp
Unknown command: clear select
Unknown command: clear selection
> select clear
> select clear
> ~select
Nothing selected
> graphics silhouettes true
> lighting shadows true
> lighting shadows false
> lighting full
> lighting full
> lighting simple
> lighting soft
> lighting simple
> lighting full
> lighting simple
> select up
Nothing selected
> color #1 firebrick
> color #1 red
> color #1 salmon
> color #1 crimson
> color #1 violet
> show #!2 models
> hide #!3 models
> hide #!2 models
> show #!2 models
> show #!3 models
> color #1 yellow
> color #1 gold
> hide #!3 models
> color #1 magenta
> show #!3 models
> hide #!2 models
> graphics silhouettes false
> lighting shadows true
> lighting shadows false
> lighting flat
> lighting full
> graphics silhouettes false
> graphics silhouettes true
> lighting simple
> color #1 blue
> show #!2 models
> hide #!3 models
> hide #!2 models
> show #!3 models
> color #1 purple
> color #1 magenta
> show #!2 models
> hide #!3 models
> dssp
> measure buriedarea (#1/A&protein) withAtoms2 (#1/H&protein) & ~solvent
Buried area between #1/A & protein and #1/H & protein & ~solvent = 1517.8
area #1/A & protein = 46279, area #1/H & protein & ~solvent = 12708, area both
= 55952
> measure buriedarea (#1/A&protein) withAtoms2 (#1/H&protein)
Buried area between #1/A & protein and #1/H & protein = 1517.8
area #1/A & protein = 46279, area #1/H & protein = 12708, area both = 55952
> measure buriedarea #1/A withAtoms2 #1/H
Buried area between #1/A and #1/H = 1517.8
area #1/A = 46075, area #1/H = 12708, area both = 55747
> measure buriedarea (#1/A& ~:991-998 & protein) withAtoms2 (#1/H&protein) &
> ~solvent
Buried area between #1/A & ~:991-998 & protein and #1/H & protein & ~solvent =
1477.9
area #1/A & ~:991-998 & protein = 46327, area #1/H & protein & ~solvent =
12708, area both = 56080
> hide #!2 models
> show #!3 models
> hide #!1 models
> show #!1 models
> measure buriedarea #3/A withAtoms2 #3/F
Buried area between #3/A and #3/F = 1022.5
area #3/A = 51951, area #3/F = 13257, area both = 63163
> interfaces #1 & protein
6 buried areas: B C 2533, A B 2360, A H 1518, F G 838, H F 728, H G 689
> interfaces #3 & protein
8 buried areas: B C 2606, A B 2015, A F 1022, A D 711, F G 671, E F 614, E G
512, B D 510
> color #1 firebrick
> interfaces #1/A,H & protein
1 buried areas: A H 1518
> interfaces #1/A,H
1 buried areas: A H 1518
> interfaces #1/A ,H & ~#1/A:991-997 & protein
1 buried areas: A H 1490
> interfaces #1/A ,H & ~#1/A:991-998 & protein
1 buried areas: A H 1478
> hide #!1 models
> select #3/A:1001
4 atoms, 3 bonds, 1 model selected
> show #!1 models
> select #1/A:998
4 atoms, 3 bonds, 1 model selected
> interfaces #1/A ,H & ~#1/A:991-997 & protein
1 buried areas: A H 1490
> interfaces #1/A ,H
1 buried areas: A H 1518
> interfaces #1 & protein
6 buried areas: B C 2533, A B 2360, A H 1518, F G 838, H F 728, H G 689
> select clear
> show #!2 models
> hide #!3 models
> cartoon style width 1.5
> undo
> undo
> hide #!3 models
> cartoon style width 1.5
> undo
Unknown command: machmaker #2 to #1
> matchmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 409-ystPolDcplx_rpFG_163_3.pdb, chain A (#1) with 409-yst_PolD.pdb,
chain A (#2), sequence alignment score = 4825.7
RMSD between 958 pruned atom pairs is 0.483 angstroms; (across all 959 pairs:
0.495)
> mmaker #2/A,B,C to #1/A,B,C pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 409-ystPolDcplx_rpFG_163_3.pdb, chain A (#1) with 409-yst_PolD.pdb,
chain A (#2), sequence alignment score = 4825.7
Matchmaker 409-ystPolDcplx_rpFG_163_3.pdb, chain B (#1) with 409-yst_PolD.pdb,
chain B (#2), sequence alignment score = 2238.6
Matchmaker 409-ystPolDcplx_rpFG_163_3.pdb, chain C (#1) with 409-yst_PolD.pdb,
chain C (#2), sequence alignment score = 462.8
RMSD between 1473 pruned atom pairs is 0.647 angstroms; (across all 1524
pairs: 0.876)
> mmaker #2/A to #1/A
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 409-ystPolDcplx_rpFG_163_3.pdb, chain A (#1) with 409-yst_PolD.pdb,
chain A (#2), sequence alignment score = 4825.7
RMSD between 958 pruned atom pairs is 0.483 angstroms; (across all 959 pairs:
0.495)
> mmaker #3/A to #1/A
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 409-ystPolDcplx_rpFG_163_3.pdb, chain A (#1) with
409-humPolDcplx.pdb, chain A (#3), sequence alignment score = 2863.1
RMSD between 724 pruned atom pairs is 1.309 angstroms; (across all 981 pairs:
2.341)
> hide #!2 models
> show #!3 models
> mmaker #3/t,p to #1/t,p pair ss
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 258, in execute
cmd.run(cmd_text)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2865, in run
_used_aliases=used_aliases, log=log)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 3411, in __call__
return self.cmd.run(text, _used_aliases=_used_aliases, log=log)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2848, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/match_maker/match.py", line 670, in cmd_match
gap_open_other=ogap, compute_ss=compute_ss, verbose=verbose)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/match_maker/match.py", line 266, in match
" matrix" % (ref.fullName(), matrix))
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 43, in _getattr_
return base.__getattr__(self, attr_name, look_in_class=base)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 43, in _getattr_
return base.__getattr__(self, attr_name, look_in_class=base)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
AttributeError: 'Sequence' object has no attribute 'fullName'
AttributeError: 'Sequence' object has no attribute 'fullName'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
> mmaker #3/t,p to #1/t,p pair ss
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 258, in execute
cmd.run(cmd_text)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2865, in run
_used_aliases=used_aliases, log=log)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 3411, in __call__
return self.cmd.run(text, _used_aliases=_used_aliases, log=log)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2848, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/match_maker/match.py", line 670, in cmd_match
gap_open_other=ogap, compute_ss=compute_ss, verbose=verbose)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/match_maker/match.py", line 266, in match
" matrix" % (ref.fullName(), matrix))
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 43, in _getattr_
return base.__getattr__(self, attr_name, look_in_class=base)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 43, in _getattr_
return base.__getattr__(self, attr_name, look_in_class=base)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
AttributeError: 'Sequence' object has no attribute 'fullName'
AttributeError: 'Sequence' object has no attribute 'fullName'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
> mmaker #3/t to #1/t pair ss
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 258, in execute
cmd.run(cmd_text)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2865, in run
_used_aliases=used_aliases, log=log)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 3411, in __call__
return self.cmd.run(text, _used_aliases=_used_aliases, log=log)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2848, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/match_maker/match.py", line 670, in cmd_match
gap_open_other=ogap, compute_ss=compute_ss, verbose=verbose)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/match_maker/match.py", line 266, in match
" matrix" % (ref.fullName(), matrix))
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 43, in _getattr_
return base.__getattr__(self, attr_name, look_in_class=base)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 43, in _getattr_
return base.__getattr__(self, attr_name, look_in_class=base)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
AttributeError: 'Sequence' object has no attribute 'fullName'
AttributeError: 'Sequence' object has no attribute 'fullName'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
> mmaker #3/t to #1/t
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 409-ystPolDcplx_rpFG_163_3.pdb, chain A (#1) with
409-humPolDcplx.pdb, chain A (#3), sequence alignment score = 0
Fewer than 3 residues aligned; cannot match 409-ystPolDcplx_rpFG_163_3.pdb,
chain A with 409-humPolDcplx.pdb, chain A
> mmaker #3/T to #1/T
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 409-ystPolDcplx_rpFG_163_3.pdb, chain A (#1) with
409-humPolDcplx.pdb, chain A (#3), sequence alignment score = 0
Fewer than 3 residues aligned; cannot match 409-ystPolDcplx_rpFG_163_3.pdb,
chain A with 409-humPolDcplx.pdb, chain A
> mmaker #3/P to #1/P
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 409-ystPolDcplx_rpFG_163_3.pdb, chain A (#1) with
409-humPolDcplx.pdb, chain A (#3), sequence alignment score = 0
Fewer than 3 residues aligned; cannot match 409-ystPolDcplx_rpFG_163_3.pdb,
chain A with 409-humPolDcplx.pdb, chain A
> mmaker #3/A to #1/A
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 409-ystPolDcplx_rpFG_163_3.pdb, chain A (#1) with
409-humPolDcplx.pdb, chain A (#3), sequence alignment score = 2863.1
RMSD between 724 pruned atom pairs is 1.309 angstroms; (across all 981 pairs:
2.341)
> mmaker #3/P to #1/P
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 409-ystPolDcplx_rpFG_163_3.pdb, chain A (#1) with
409-humPolDcplx.pdb, chain A (#3), sequence alignment score = 0
Fewer than 3 residues aligned; cannot match 409-ystPolDcplx_rpFG_163_3.pdb,
chain A with 409-humPolDcplx.pdb, chain A
> mmaker #3/A,B,C to #1/A,B,C pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 409-ystPolDcplx_rpFG_163_3.pdb, chain A (#1) with
409-humPolDcplx.pdb, chain A (#3), sequence alignment score = 2863.1
Matchmaker 409-ystPolDcplx_rpFG_163_3.pdb, chain B (#1) with
409-humPolDcplx.pdb, chain B (#3), sequence alignment score = 826.3
Matchmaker 409-ystPolDcplx_rpFG_163_3.pdb, chain C (#1) with
409-humPolDcplx.pdb, chain C (#3), sequence alignment score = 62.2
RMSD between 680 pruned atom pairs is 1.276 angstroms; (across all 1496 pairs:
4.631)
> mmaker #3/A to #1/A pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 409-ystPolDcplx_rpFG_163_3.pdb, chain A (#1) with
409-humPolDcplx.pdb, chain A (#3), sequence alignment score = 2863.1
RMSD between 724 pruned atom pairs is 1.309 angstroms; (across all 981 pairs:
2.341)
> mmaker #3 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 409-ystPolDcplx_rpFG_163_3.pdb, chain A (#1) with
409-humPolDcplx.pdb, chain A (#3), sequence alignment score = 2863.1
RMSD between 724 pruned atom pairs is 1.309 angstroms; (across all 981 pairs:
2.341)
> mmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 409-ystPolDcplx_rpFG_163_3.pdb, chain A (#1) with 409-yst_PolD.pdb,
chain A (#2), sequence alignment score = 4825.7
RMSD between 958 pruned atom pairs is 0.483 angstroms; (across all 959 pairs:
0.495)
> show #!2 models
> hide #!3 models
> hide #!2 models
> show #!3 models
> show #!2 models
> hide #!3 models
> hide #!1 models
> select #2/C:12
9 atoms, 8 bonds, 1 model selected
> show #!1 models
> select clear
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!2 models
> ui mousemode rightMode distance
> ui mousemode rightMode select
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!3 models
> show #!2 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> save2
> /Users/fengwei.zheng/Documents/Draft_PolD/Session/SI/S2/FigSI_2_409PolD-yst-
> human_comparison3.cxs
opened ChimeraX session
> open2
> /Users/fengwei.zheng/Documents/Structures/PolD/templates/PCNA/humFEN1-PCNA_1ul1.pdb
> /Users/fengwei.zheng/Documents/Structures/PolD/templates/PCNA/humPCNA-p21.pdb
> /Users/fengwei.zheng/Documents/Structures/PolD/templates/PCNA/ystRFC-
> PCNA_1sxj.pdb
humFEN1-PCNA_1ul1.pdb title:
Crystal structure of the human FEN1-PCNA complex [more info...]
Chain information for humFEN1-PCNA_1ul1.pdb #4
---
Chain | Description
A B C | proliferating cell nuclear antigen
X Y Z | flap endonuclease-1
Non-standard residues in humFEN1-PCNA_1ul1.pdb #4
---
MG — magnesium ion
humPCNA-p21.pdb title:
Human PCNA [more info...]
Chain information for humPCNA-p21.pdb #5
---
Chain | Description
A C E | proliferating cell nuclear antigen
B D F | P21/WAF1
ystRFC-PCNA_1sxj.pdb title:
Crystal structure of the eukaryotic clamp loader (replication factor C, RFC)
bound to the DNA sliding clamp (proliferating cell nuclear antigen, PCNA)
[more info...]
Chain information for ystRFC-PCNA_1sxj.pdb #6
---
Chain | Description
A | activator 1 95 kda subunit
B | activator 1 37 kda subunit
C | activator 1 40 kda subunit
D | activator 1 41 kda subunit
E | activator 1 40 kda subunit
F G H | PCNA
Non-standard residues in ystRFC-PCNA_1sxj.pdb #6
---
ADP — adenosine-5'-diphosphate
AGS — phosphothiophosphoric acid-adenylate ester (atp-γ-S; adenosine
5'-(3-thiotriphosphate);adenosine 5'-(γ-thiotriphosphate);
adenosine-5'-diphosphate monothiophosphate)
MG — magnesium ion
> hide atoms
> show cartoons
> hide #!2 models
> hide #!3 models
> hide #!5 models
> hide #!6 models
> select #4
13162 atoms, 13361 bonds, 19 pseudobonds, 3 models selected
Drag select of
> select #4
13162 atoms, 13361 bonds, 19 pseudobonds, 3 models selected
> select clear
> ui mousemode rightMode translate
> select #4
13162 atoms, 13361 bonds, 19 pseudobonds, 3 models selected
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> select clear
> ui mousemode rightMode "translate selected models"
> mmaker #4/A to #1/H pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 409-ystPolDcplx_rpFG_163_3.pdb, chain H (#1) with
humFEN1-PCNA_1ul1.pdb, chain A (#4), sequence alignment score = 644
RMSD between 222 pruned atom pairs is 0.904 angstroms; (across all 251 pairs:
1.404)
> mmaker #4/B to #1/H pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 409-ystPolDcplx_rpFG_163_3.pdb, chain H (#1) with
humFEN1-PCNA_1ul1.pdb, chain B (#4), sequence alignment score = 621.8
RMSD between 210 pruned atom pairs is 1.010 angstroms; (across all 254 pairs:
1.944)
> undo
> select clear
> undo
> undo
> mmaker #4/A to #1/H pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 409-ystPolDcplx_rpFG_163_3.pdb, chain H (#1) with
humFEN1-PCNA_1ul1.pdb, chain A (#4), sequence alignment score = 644
RMSD between 222 pruned atom pairs is 0.904 angstroms; (across all 251 pairs:
1.404)
> select clear
> mmaker #4/B to #1/H pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 409-ystPolDcplx_rpFG_163_3.pdb, chain H (#1) with
humFEN1-PCNA_1ul1.pdb, chain B (#4), sequence alignment score = 621.8
RMSD between 210 pruned atom pairs is 1.010 angstroms; (across all 254 pairs:
1.944)
> hide #!4 models
> show #!3 models
> hide #!3 models
> show #!4 models
> mmaker #4/C to #1/H pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 409-ystPolDcplx_rpFG_163_3.pdb, chain H (#1) with
humFEN1-PCNA_1ul1.pdb, chain C (#4), sequence alignment score = 591.2
RMSD between 225 pruned atom pairs is 0.897 angstroms; (across all 254 pairs:
1.445)
> ui mousemode rightMode select
Drag select of
> ui mousemode rightMode translate
> select #1/G:36
8 atoms, 7 bonds, 1 model selected
> select clear
> select #1/F:168
9 atoms, 8 bonds, 1 model selected
> ui mousemode rightMode select
> select #4/B:161
6 atoms, 5 bonds, 1 model selected
> select #1/F:168
9 atoms, 8 bonds, 1 model selected
> select #4/B:160
8 atoms, 7 bonds, 1 model selected
Drag select of 9 residues
Drag select of
> mmaker #4/A to #1/H pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 409-ystPolDcplx_rpFG_163_3.pdb, chain H (#1) with
humFEN1-PCNA_1ul1.pdb, chain A (#4), sequence alignment score = 644
RMSD between 222 pruned atom pairs is 0.904 angstroms; (across all 251 pairs:
1.404)
Drag select of 20 residues
> select clear
Drag select of 12 residues
> select clear
Drag select of 24 residues
> select clear
Drag select of 26 residues
> select clear
Drag select of 28 residues
> select clear
Drag select of
Drag select of 14 residues
> select clear
Drag select of
Drag select of
Drag select of
> hide #1/A-C cartoons
> hide #1/A-C,t,p cartoons
> hide #!4 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!4 models
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show #1/A984-1030 cartoons
> show #1/A:984-1030 cartoons
> name cysA #1/A:984-1030
> show #!3 models
> hide #!3 models
> color cysA blue cartoons
> show #!4 models
> hide cysA cartoons
Drag select of 13 residues
> select clear
> undo
> undo
> undo
> undo
> show #!3 models
> hide #!3 models
> select up
Nothing selected
> select up
Nothing selected
> hide cysA cartoons
> save /Users/fengwei.zheng/Desktop/image1.png supersample 3
> mmaker #4/B to #1/H pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 409-ystPolDcplx_rpFG_163_3.pdb, chain H (#1) with
humFEN1-PCNA_1ul1.pdb, chain B (#4), sequence alignment score = 621.8
RMSD between 210 pruned atom pairs is 1.010 angstroms; (across all 254 pairs:
1.944)
> mmaker #4/C to #1/H pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 409-ystPolDcplx_rpFG_163_3.pdb, chain H (#1) with
humFEN1-PCNA_1ul1.pdb, chain C (#4), sequence alignment score = 591.2
RMSD between 225 pruned atom pairs is 0.897 angstroms; (across all 254 pairs:
1.445)
> show cysA cartoons
> save /Users/fengwei.zheng/Desktop/image1.png supersample 3
> mmaker #4/A to #1/H pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 409-ystPolDcplx_rpFG_163_3.pdb, chain H (#1) with
humFEN1-PCNA_1ul1.pdb, chain A (#4), sequence alignment score = 644
RMSD between 222 pruned atom pairs is 0.904 angstroms; (across all 251 pairs:
1.404)
> mmaker #4/C to #1/H pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 409-ystPolDcplx_rpFG_163_3.pdb, chain H (#1) with
humFEN1-PCNA_1ul1.pdb, chain C (#4), sequence alignment score = 591.2
RMSD between 225 pruned atom pairs is 0.897 angstroms; (across all 254 pairs:
1.445)
> mmaker #4/A to #1/H pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 409-ystPolDcplx_rpFG_163_3.pdb, chain H (#1) with
humFEN1-PCNA_1ul1.pdb, chain A (#4), sequence alignment score = 644
RMSD between 222 pruned atom pairs is 0.904 angstroms; (across all 251 pairs:
1.404)
> mmaker #4/C to #1/H pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 409-ystPolDcplx_rpFG_163_3.pdb, chain H (#1) with
humFEN1-PCNA_1ul1.pdb, chain C (#4), sequence alignment score = 591.2
RMSD between 225 pruned atom pairs is 0.897 angstroms; (across all 254 pairs:
1.445)
> mmaker #4/A to #1/H pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 409-ystPolDcplx_rpFG_163_3.pdb, chain H (#1) with
humFEN1-PCNA_1ul1.pdb, chain A (#4), sequence alignment score = 644
RMSD between 222 pruned atom pairs is 0.904 angstroms; (across all 251 pairs:
1.404)
> hide #!1 models
> show #!1 models
> save /Users/fengwei.zheng/Desktop/image1.png supersample 3
> mmaker #4/C to #1/H pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 409-ystPolDcplx_rpFG_163_3.pdb, chain H (#1) with
humFEN1-PCNA_1ul1.pdb, chain C (#4), sequence alignment score = 591.2
RMSD between 225 pruned atom pairs is 0.897 angstroms; (across all 254 pairs:
1.445)
Drag select of 18 residues
> hide #4/x-z cartoons
> show #4/z:333-360 cartoons
> select clear
> hide #!4 models
> show #!5 models
> select up
Nothing selected
> mmaker #5/C to #1/H pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 409-ystPolDcplx_rpFG_163_3.pdb, chain H (#1) with humPCNA-p21.pdb,
chain C (#5), sequence alignment score = 641.4
RMSD between 226 pruned atom pairs is 0.913 angstroms; (across all 247 pairs:
1.221)
> hide #!1 models
> show #!4 models
> show #!1 models
> hide #!4 models
> show #!4 models
> hide #!1 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> show #!1 models
> hide #!5 models
> mmaker #4/A to #1/H pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 409-ystPolDcplx_rpFG_163_3.pdb, chain H (#1) with
humFEN1-PCNA_1ul1.pdb, chain A (#4), sequence alignment score = 644
RMSD between 222 pruned atom pairs is 0.904 angstroms; (across all 251 pairs:
1.404)
> show #4/x-z cartoons
> hide #!1 models
> show #!1 models
> hide #!4 models
> show #!4 models
> hide #!1 models
> show #!1 models
> hide #4/x-z cartoons
> show #4/x:333-360 cartoons
> hide #!4 models
> show #!4 models
> show #!5 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> mmaker #5/A to #1/H pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 409-ystPolDcplx_rpFG_163_3.pdb, chain H (#1) with humPCNA-p21.pdb,
chain A (#5), sequence alignment score = 651
RMSD between 226 pruned atom pairs is 0.919 angstroms; (across all 248 pairs:
1.240)
> mmaker #5/B to #1/H pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 409-ystPolDcplx_rpFG_163_3.pdb, chain H (#1) with humPCNA-p21.pdb,
chain B (#5), sequence alignment score = 7.1
RMSD between 7 pruned atom pairs is 0.889 angstroms; (across all 7 pairs:
0.889)
> mmaker #5/A to #1/H pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 409-ystPolDcplx_rpFG_163_3.pdb, chain H (#1) with humPCNA-p21.pdb,
chain A (#5), sequence alignment score = 651
RMSD between 226 pruned atom pairs is 0.919 angstroms; (across all 248 pairs:
1.240)
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> mmaker #5/C to #1/H pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 409-ystPolDcplx_rpFG_163_3.pdb, chain H (#1) with humPCNA-p21.pdb,
chain C (#5), sequence alignment score = 641.4
RMSD between 226 pruned atom pairs is 0.913 angstroms; (across all 247 pairs:
1.221)
> mmaker #5/E to #1/H pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 409-ystPolDcplx_rpFG_163_3.pdb, chain H (#1) with humPCNA-p21.pdb,
chain E (#5), sequence alignment score = 649.8
RMSD between 224 pruned atom pairs is 0.913 angstroms; (across all 252 pairs:
1.286)
> hide #!1 models
> show #!1 models
> mmaker #5/E to #4/A pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker humFEN1-PCNA_1ul1.pdb, chain A (#4) with humPCNA-p21.pdb, chain E
(#5), sequence alignment score = 1286
RMSD between 246 pruned atom pairs is 0.575 angstroms; (across all 251 pairs:
0.751)
> show #!4 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> mmaker #5/C to #4/A pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker humFEN1-PCNA_1ul1.pdb, chain A (#4) with humPCNA-p21.pdb, chain C
(#5), sequence alignment score = 1280
RMSD between 245 pruned atom pairs is 0.561 angstroms; (across all 248 pairs:
0.717)
> mmaker #5/A to #4/A pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker humFEN1-PCNA_1ul1.pdb, chain A (#4) with humPCNA-p21.pdb, chain A
(#5), sequence alignment score = 1289.6
RMSD between 246 pruned atom pairs is 0.591 angstroms; (across all 249 pairs:
0.750)
> mmaker #5/C to #4/A pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker humFEN1-PCNA_1ul1.pdb, chain A (#4) with humPCNA-p21.pdb, chain C
(#5), sequence alignment score = 1280
RMSD between 245 pruned atom pairs is 0.561 angstroms; (across all 248 pairs:
0.717)
> show #!1 models
> hide #!4 models
> hide #!5 models
> show #!6 models
> mmaker #6/F to #1/H pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 409-ystPolDcplx_rpFG_163_3.pdb, chain H (#1) with ystRFC-
PCNA_1sxj.pdb, chain F (#6), sequence alignment score = 1162.6
RMSD between 241 pruned atom pairs is 0.861 angstroms; (across all 254 pairs:
1.018)
> hide #!1 models
> show #!1 models
> show #!4 models
Drag select of 212 residues
> select clear
Drag select of
Drag select of
Drag select of
Drag select of
Drag select of
Drag select of
Drag select of
> hide #!1 models
> show #!1 models
> hide #!6 models
> show #!6 models
> hide #!4 models
> show #!4 models
> hide #!1 models
> hide #!4 models
> show #!1 models
> hide #!1 models
> show #!1 models
> mmaker #6/G to #1/H pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 409-ystPolDcplx_rpFG_163_3.pdb, chain H (#1) with ystRFC-
PCNA_1sxj.pdb, chain G (#6), sequence alignment score = 1172.8
RMSD between 243 pruned atom pairs is 0.750 angstroms; (across all 254 pairs:
0.922)
> mmaker #6/F to #1/H pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 409-ystPolDcplx_rpFG_163_3.pdb, chain H (#1) with ystRFC-
PCNA_1sxj.pdb, chain F (#6), sequence alignment score = 1162.6
RMSD between 241 pruned atom pairs is 0.861 angstroms; (across all 254 pairs:
1.018)
> mmaker #6/H to #1/H pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 409-ystPolDcplx_rpFG_163_3.pdb, chain H (#1) with ystRFC-
PCNA_1sxj.pdb, chain H (#6), sequence alignment score = 1190.8
RMSD between 243 pruned atom pairs is 0.829 angstroms; (across all 254 pairs:
1.004)
> mmaker #6/F to #1/H pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 409-ystPolDcplx_rpFG_163_3.pdb, chain H (#1) with ystRFC-
PCNA_1sxj.pdb, chain F (#6), sequence alignment score = 1162.6
RMSD between 241 pruned atom pairs is 0.861 angstroms; (across all 254 pairs:
1.018)
> mmaker #6/H to #1/H pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 409-ystPolDcplx_rpFG_163_3.pdb, chain H (#1) with ystRFC-
PCNA_1sxj.pdb, chain H (#6), sequence alignment score = 1190.8
RMSD between 243 pruned atom pairs is 0.829 angstroms; (across all 254 pairs:
1.004)
> mmaker #6/F to #1/H pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 409-ystPolDcplx_rpFG_163_3.pdb, chain H (#1) with ystRFC-
PCNA_1sxj.pdb, chain F (#6), sequence alignment score = 1162.6
RMSD between 241 pruned atom pairs is 0.861 angstroms; (across all 254 pairs:
1.018)
> mmaker #6/H to #1/H pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 409-ystPolDcplx_rpFG_163_3.pdb, chain H (#1) with ystRFC-
PCNA_1sxj.pdb, chain H (#6), sequence alignment score = 1190.8
RMSD between 243 pruned atom pairs is 0.829 angstroms; (across all 254 pairs:
1.004)
> mmaker #6/F to #1/H pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 409-ystPolDcplx_rpFG_163_3.pdb, chain H (#1) with ystRFC-
PCNA_1sxj.pdb, chain F (#6), sequence alignment score = 1162.6
RMSD between 241 pruned atom pairs is 0.861 angstroms; (across all 254 pairs:
1.018)
> mmaker #6/H to #1/H pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 409-ystPolDcplx_rpFG_163_3.pdb, chain H (#1) with ystRFC-
PCNA_1sxj.pdb, chain H (#6), sequence alignment score = 1190.8
RMSD between 243 pruned atom pairs is 0.829 angstroms; (across all 254 pairs:
1.004)
> mmaker #6/F to #1/H pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 409-ystPolDcplx_rpFG_163_3.pdb, chain H (#1) with ystRFC-
PCNA_1sxj.pdb, chain F (#6), sequence alignment score = 1162.6
RMSD between 241 pruned atom pairs is 0.861 angstroms; (across all 254 pairs:
1.018)
> select #6/A
3377 atoms, 3436 bonds, 9 pseudobonds, 3 models selected
> mmaker #6/G to #1/H pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 409-ystPolDcplx_rpFG_163_3.pdb, chain H (#1) with ystRFC-
PCNA_1sxj.pdb, chain G (#6), sequence alignment score = 1172.8
RMSD between 243 pruned atom pairs is 0.750 angstroms; (across all 254 pairs:
0.922)
> select clear
> select #6/A:398-405
63 atoms, 64 bonds, 1 model selected
> hide #!6 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!6 models
> hide #6/A-E
> undo
> hide #6/A-E cartoons
> show #6/A:398-405 cartoons
> cartoon style xsection barbell
> show #!5 models
> show #!4 models
> hide #!4 models
> hide #!5 models
> color sel green
> select clear
> hide cysA cartoons
> show #1/A:997-1003 cartoons
Expected a keyword
> select #1/A:997-1003
49 atoms, 49 bonds, 1 model selected
> color sel green
> select clear
> hide #!6 models
> show #!4 models
> select sequence QGRLDDFF
204 atoms, 207 bonds, 1 model selected
> select sequence #4/X:QGRLDDFF
Nothing selected
> select sequence #4/QGRLDDFF
Nothing selected
> select sequence QGRLDDFF
204 atoms, 207 bonds, 1 model selected
> color sel green
> hide #4/X cartoons
> show #4/X:337-344 cartoons
> select clear
> hide #!4 models
> show #!5 models
> show #!4 models
> hide #!5 models
> hide #!1 models
> show #!1 models
> hide #!4 models
> show #!5 models
Drag select of 8 residues
> select clear
> select sequence QTSMTDFY
246 atoms, 249 bonds, 1 model selected
> hide #!5 models
> show #!4 models
> hide #!4 models
> show #!5 models
> select up
264 atoms, 267 bonds, 1 model selected
> select sequence QTSMTDFY
246 atoms, 249 bonds, 1 model selected
> show #!4 models
> hide #!4 models
> color sel green
> hide #5/D cartoons
> show #5/D:144-151 cartoons
> hide #5/B,f cartoons
> show #!6 models
> show #!4 models
> mmaker #6/G to #1/H pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 409-ystPolDcplx_rpFG_163_3.pdb, chain H (#1) with ystRFC-
PCNA_1sxj.pdb, chain G (#6), sequence alignment score = 1172.8
RMSD between 243 pruned atom pairs is 0.750 angstroms; (across all 254 pairs:
0.922)
> mmaker #5/C to #1/H pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 409-ystPolDcplx_rpFG_163_3.pdb, chain H (#1) with humPCNA-p21.pdb,
chain C (#5), sequence alignment score = 641.4
RMSD between 226 pruned atom pairs is 0.913 angstroms; (across all 247 pairs:
1.221)
> mmaker #4/A to #1/H pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 409-ystPolDcplx_rpFG_163_3.pdb, chain H (#1) with
humFEN1-PCNA_1ul1.pdb, chain A (#4), sequence alignment score = 644
RMSD between 222 pruned atom pairs is 0.904 angstroms; (across all 251 pairs:
1.404)
Drag select of 96 residues
> select clear
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> select cysA :< 10 & #1 & ~cysA
1295 atoms, 1290 bonds, 4 pseudobonds, 2 models selected
> select #1/A:997-1003 :< 10 & #1 & ~#1/A:997-1003
456 atoms, 456 bonds, 1 model selected
> hide #!1 models
> show #!1 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> name pip1 #1/A:997-1003
> show sel surfaces
> hide surfaces
> select pip1 :< 10 & #1/H & ~pip1
338 atoms, 339 bonds, 1 model selected
> mlp sel
Map values for surface "409-ystPolDcplx_rpFG_163_3.pdb_H SES surface": minimum
-28.28, mean -4.953, maximum 25.16
> select pip1
49 atoms, 49 bonds, 1 model selected
> show sel atoms
> style sel stick
Changed 49 atom styles
> color sel byhetero
> hide #1.3 models
> show #1.3 models
> hide #1.4 models
> show #1.4 models
> hide #1.4 models
> show #1.4 models
> select clear
> hide #1.4 models
> show #1.4 models
> hide #1.3 models
> show #1.3 models
> hide #1.2 models
> show #1.2 models
> hide #1.1 models
> show #1.1 models
> hide #!1 models
> show #!4 models
> name pip4 #4/X:337-344
> select pip4
64 atoms, 65 bonds, 1 model selected
> show sel atoms
> style sel stick
Changed 64 atom styles
> color sel byhetero
> select pip4 :< 10 & #4/X & ~pip4
183 atoms, 182 bonds, 1 model selected
> select pip4 :< 10 & #4/A & ~pip4
395 atoms, 394 bonds, 1 model selected
> mlp sel
Map values for surface "humFEN1-PCNA_1ul1.pdb_A SES surface": minimum -30.29,
mean -6.674, maximum 22.76
> hide #!4 models
> show #!5 models
> name pip5 #5/D:144-151
> select pip5 :< 10 & #5/D & ~pip5
90 atoms, 80 bonds, 1 model selected
> select pip5 :< 10 & #5/C & ~pip5
556 atoms, 537 bonds, 1 model selected
> mlp sel
Map values for surface "humPCNA-p21.pdb_C SES surface": minimum -26.79, mean
-6.44, maximum 26.03
> show #!4 models
> hide #!4 models
> hide #!5 models
> show #!4 models
> show #!5 models
> hide #!4 models
> show #!4 models
> hide #!5 models
> show #!5 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!4 models
> hide #!5 models
> hide #!1 models
> show #!5 models
> show #!6 models
> hide #!5 models
> mlp #1/H #4/A #5/C #6/G
Map values for surface "409-ystPolDcplx_rpFG_163_3.pdb_H SES surface": minimum
-28.28, mean -4.953, maximum 25.16
Map values for surface "humFEN1-PCNA_1ul1.pdb_A SES surface": minimum -30.29,
mean -6.674, maximum 22.76
Map values for surface "humPCNA-p21.pdb_C SES surface": minimum -26.79, mean
-6.44, maximum 26.03
Map values for surface "ystRFC-PCNA_1sxj.pdb_G SES surface": minimum -27.4,
mean -5.202, maximum 39.32
> show #!5 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!4 models
> hide #!5 models
> show #!5 models
> hide #!4 models
> hide #!5 models
> show #!1 models
> hide #!1 models
> show #!6 models
> name pip6 #6/A:398-405
> select pip6 :< 10 & #6/G & ~pip6
409 atoms, 409 bonds, 1 model selected
> show #!5 models
> show #!4 models
> show #!1 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> hide #!1 models
> show #!4 models
> hide #!4 models
> show #!5 models
> select pip5
82 atoms, 83 bonds, 1 model selected
> style sel stick
Changed 82 atom styles
> show sel atoms
> color sel byhetero
> show #!1 models
> hide #!5 models
> hide #!1 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!5 models
> select #5/D:146@HG
1 atom, 1 model selected
> select #5/C:43@O
1 atom, 1 model selected
> select #5/D:146@HG
1 atom, 1 model selected
> hide #!5 models
> show #!4 models
> show #!5 models
> hide #!4 models
> hide #!5 models
> show #!6 models
> select pip6
63 atoms, 64 bonds, 1 model selected
> show sel atoms
> style sel stick
Changed 63 atom styles
> color sel byhetero
> hide #!6 models
> show #!5 models
> hide @H & pip5
> hide @H
> select @H & pip5
8 atoms, 1 model selected
> hide sel
> select #5/D:146@HG
1 atom, 1 model selected
> select #5/D:149@OD1
1 atom, 1 model selected
> select #5/D:146@HG
1 atom, 1 model selected
Expected an objects specifier or a keyword
> select pip5 & @H
8 atoms, 1 model selected
> hide sel
> hide #5/D@H
> select #5/D:146@HG
1 atom, 1 model selected
> hide sel atoms
> show #!4 models
> hide #!5 models
> hide #!4 models
> show #!6 models
> show #!5 models
> hide #!6 models
> select @H & pip5
8 atoms, 1 model selected
> hide sel atoms
> select #5/D:148@HG1
1 atom, 1 model selected
> hide sel atoms
> select #5/C:250@CD2
1 atom, 1 model selected
> select #5/C:250@CE2
1 atom, 1 model selected
> select #5/C:250@CE2
1 atom, 1 model selected
> select #5/C:128@CG2
1 atom, 1 model selected
> select #5/C:250@CE2
1 atom, 1 model selected
> select #5/D:151@HH
1 atom, 1 model selected
> hide sel atoms
> select #5/D:145@HG1
1 atom, 1 model selected
> hide sel atoms
> select #5/D:144@HE22
1 atom, 1 model selected
> hide sel atoms
> select #5/D:144@HE21
1 atom, 1 model selected
> hide sel atoms
> select clear
> show #!1 models
> hide #!5 models
> show #!4 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> show #!6 models
> hide #!6 models
> show #!6 models
Drag select of 409-ystPolDcplx_rpFG_163_3.pdb_H SES surface, 20 of 226026
triangles, ystRFC-PCNA_1sxj.pdb_G SES surface, 10 of 243174 triangles, 7
residues
Drag select of 409-ystPolDcplx_rpFG_163_3.pdb_H SES surface, 23 of 226026
triangles, humFEN1-PCNA_1ul1.pdb_A SES surface, 31 of 227924 triangles,
humPCNA-p21.pdb_C SES surface, 77 of 220100 triangles, ystRFC-PCNA_1sxj.pdb_G
SES surface, 94 of 243174 triangles, 8 residues
Drag select of
Drag select of
> hide #!4 models
> hide #!5 models
> hide #!1 models
> show #!1 models
> hide #!6 models
> show #!4 models
> hide #!1 models
> show #!1 models
> hide #!4 models
> show #!4 models
> show #!5 models
> hide #!4 models
> hide #!1 models
> hide #!5 models
> show #!6 models
> show #!1 models
> hide #!6 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!4 models
> show #!1 models
> hide #!4 models
> hide #1/H #4/A #5/C #6/G cartoons
> hide #!1 models
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!6 models
> show #!5 models
> show #!4 models
> show #!1 models
> hide #!1 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> show #!6 models
> show #!5 models
> hide #!6 models
> hide #!5 models
> show #!6 models
> show #!5 models
> hide #!6 models
> hide #!5 models
> show #!6 models
> show #!5 models
> hide #!6 models
> hide #!5 models
> show #!4 models
> hide #!4 models
> show #!1 models
> hide #!1 models
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!6 models
> hide #!6 models
> show #!5 models
> show #!6 models
> hide #!5 models
> show #!5 models
> hide #!6 models
> hide #!5 models
> show #!6 models
> hide #!6 models
> show #!4 models
> hide #!4 models
> show #!5 models
> show #!4 models
> show #!1 models
> hide #!4 models
> hide #!5 models
> hide #!1 models
> show #!3 models
> show #!1 models
> hide #!1 models
> show #!1 models
> select #3/A:1000-1006
41 atoms, 41 bonds, 1 model selected
> color sel green
> mlp #3/F
Map values for surface "409-humPolDcplx.pdb_F SES surface": minimum -29.2,
mean -5.015, maximum 24.14
> hide #!1 models
> hide #3/F cartoons
Expected ',' or a keyword
> hide #3/A & ~:1000-1006 cartoons
> hide #3/b-d cartoons
> hide #3/b-d,t,p cartoons
> show #!1 models
> hide #!3 models
> hide #!1 models
> show #!3 models
> hide #!3 models
> show #!1 models
> hide #1/f-g cartoons
> hide #!1 models
> show #!3 models
> hide #3/e,g cartoons
> hide #!3 models
> show #!4 models
Drag select of humFEN1-PCNA_1ul1.pdb_A SES surface, 75 of 227924 triangles
> select #4/B:159
7 atoms, 6 bonds, 1 model selected
> select #4/B:160
8 atoms, 7 bonds, 1 model selected
> select up
112 atoms, 111 bonds, 1 model selected
> select up
3890 atoms, 3942 bonds, 1 model selected
> hide sel cartoons
> show #!5 models
> hide #!4 models
> select #5/E:159
8 atoms, 7 bonds, 1 model selected
> select up
152 atoms, 151 bonds, 1 model selected
> select up
5171 atoms, 5042 bonds, 1 model selected
> hide sel cartoons
> show #!6 models
> hide #!5 models
> select #6/F:161
8 atoms, 7 bonds, 1 model selected
> select up
134 atoms, 133 bonds, 1 model selected
> select up
4100 atoms, 4163 bonds, 1 model selected
> hide sel cartoons
> show #!5 models
> hide #!6 models
> show #!4 models
> hide #!5 models
> show #!3 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!3 models
> show #!3 models
> show #!1 models
> hide #!4 models
> hide #!3 models
> show #!3 models
> mmaker #3/F to #1/H pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 409-ystPolDcplx_rpFG_163_3.pdb, chain H (#1) with
409-humPolDcplx.pdb, chain F (#3), sequence alignment score = 615.8
RMSD between 222 pruned atom pairs is 1.093 angstroms; (across all 248 pairs:
1.337)
> show #!4 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #!4 models
> show #!4 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!4 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!1 models
> show #!4 models
> show #!5 models
> show #!6 models
> hide #!5 models
> hide #!4 models
> hide #!3 models
> hide #!1 models
> hide #!6 models
> show #!1 models
> show #!6 models
> hide #!1 models
> show #!1 models
> hide #!6 models
> show #!6 models
> hide #!1 models
> hide #!6 models
> show #!1 models
> show #!6 models
> show #!5 models
> show #!4 models
> show #!3 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> hide #!1 models
> show #!3 models
> select #3/A:1000-1006
41 atoms, 41 bonds, 1 model selected
> show sel atoms
> style sel stick
Changed 41 atom styles
> color sel byhetero
> show #!1 models
> hide #!3 models
> hide #!1 models
> show #!1 models
> show #!3 models
> hide #!1 models
> hide #!3 models
> show #!4 models
> show #!3 models
> hide #!4 models
> select clear
> hide #!3 models
> show #!1 models
> hide #!1 models
> show #!3 models
> show #!1 models
> show #!4 models
> hide #!4 models
> hide #!3 models
> hide #!1 models
> show #!4 models
> show #!3 models
> show #!2 models
> hide #!2 models
> show #!1 models
> show #!5 models
> show #!6 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!6 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> show #!6 models
> hide #!5 models
> hide #!4 models
> show #!5 models
> hide #!6 models
> show #!6 models
> hide #!5 models
> hide #!6 models
> show #!5 models
> hide #!5 models
> show #!4 models
> hide #!4 models
> show #!6 models
> hide #!6 models
> show #!1 models
> show #!6 models
> hide #!1 models
> show #!1 models
> hide #!6 models
> show #!3 models
> hide #!1 models
> hide #!3 models
> show #!1 models
> hide #!1 models
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!6 models
> show #!1 models
> hide #!1 models
> save2
> /Users/fengwei.zheng/Documents/Draft_PolD/Session/MK/PIPs_comparison.cxs
opened ChimeraX session
> show #!1 models
> hide #!6 models
> open
> /Users/fengwei.zheng/Documents/Phenix/PolD/409-ystPolDcplx_rpFG_163_3.pdb
Summary of feedback from opening
/Users/fengwei.zheng/Documents/Phenix/PolD/409-ystPolDcplx_rpFG_163_3.pdb
---
warnings | Start residue of secondary structure not found: HELIX 9 9 ALA H 9
LYS H 20 1 12
Start residue of secondary structure not found: HELIX 10 10 VAL H 54 ALA H 56
5 3
Start residue of secondary structure not found: HELIX 11 11 LEU H 72 CYS H 81
1 10
Start residue of secondary structure not found: HELIX 12 12 SER H 141 LEU H
154 1 14
Start residue of secondary structure not found: HELIX 13 13 ALA H 209 LYS H
217 1 9
15 messages similar to the above omitted
Chain information for 409-ystPolDcplx_rpFG_163_3.pdb #7
---
Chain | Description
A | No description available
B | No description available
C | No description available
E | No description available
F | No description available
G | No description available
P | No description available
T | No description available
> hide #7
> show #7 cartoons
> dssp
> cartoon style xsection barbell
> hide #!7 models
> show #!7 models
> select #1/H:36@CG2
1 atom, 1 model selected
> select #1/H:36@CG2
1 atom, 1 model selected
> select #1/H:36@CG2
1 atom, 1 model selected
> select clear
> select #7/B:324
8 atoms, 7 bonds, 1 model selected
> select #7/B:323
6 atoms, 5 bonds, 1 model selected
> select clear
> select #7/B:323
6 atoms, 5 bonds, 1 model selected
> select clear
> mlp #1/H
Map values for surface "409-ystPolDcplx_rpFG_163_3.pdb_H SES surface": minimum
-28.28, mean -4.953, maximum 25.16
> hide #!1 models
> show #!1 models
> hide #!7 models
> show #!7 models
> preset #1 sticks
No preset name matches '#1 sticks'
> preset #1
No preset name matches '#1'
> select #1/H:179@CB
1 atom, 1 model selected
> select #7/E:114
12 atoms, 12 bonds, 1 model selected
> select #7/E:115
6 atoms, 5 bonds, 1 model selected
> hide #!1 models
> mlp #7/F
Map values for surface "409-ystPolDcplx_rpFG_163_3.pdb_F SES surface": minimum
-28.28, mean -4.953, maximum 25.16
> hide #!7 models
> show #!7 models
> hide #7 cartoons
> show #!1 models
Drag select of 409-ystPolDcplx_rpFG_163_3.pdb_H SES surface, 3701 of 226026
triangles, 409-ystPolDcplx_rpFG_163_3.pdb_F SES surface, 3701 of 226026
triangles
Drag select of 409-ystPolDcplx_rpFG_163_3.pdb_H SES surface, 18108 of 226026
triangles, 409-ystPolDcplx_rpFG_163_3.pdb_F SES surface, 18108 of 226026
triangles
> hide #!1 models
> hide #!7 models
> show #!6 models
> show #!7 models
> hide #!6 models
> show #!6 models
> hide #!7 models
> hide #!6 models
> show #!5 models
> hide #!5 models
> show #!4 models
> hide #!4 models
> show #!1 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!1 models
> show #!1 models
> name pip7 #7/A:997-1003
> hide #!1 models
> select pip7
49 atoms, 49 bonds, 1 model selected
> show sel atoms
> style sel stick
Changed 49 atom styles
> show sel cartoons
> show #!1 models
> hide #!1 models
> color pip7 green
> color sel byhetero
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!1 models
> show #!4 models
> hide #!7 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!6 models
> show #!7 models
> select clear
> hide #!7 models
> hide #!6 models
> show #!7 models
> show #!6 models
> hide #!7 models
> hide #!6 models
> show #!5 models
> show #!4 models
> hide #!5 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!6 models
> hide #!6 models
> show #!7 models
> show #!6 models
> hide #!7 models
> hide #!6 models
> show #!7 models
> show #!6 models
> hide #!7 models
> hide #!6 models
> show #!7 models
> show #!5 models
> hide #!7 models
> hide #!5 models
> show #!4 models
> hide #!4 models
> show #!6 models
> show #!7 models
> hide #!6 models
> show #!6 models
> hide #!7 models
> hide #!6 models
> show #!5 models
> hide #!5 models
> show #!4 models
> hide #!4 models
> show #!7 models
> lighting simple
> lighting full
> lighting flat
> lighting full
> lighting shadows false
> lighting shadows true
> lighting shadows false
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true
> show #!6 models
> hide #!7 models
> lighting shadows false
> lighting shadows true
> lighting shadows false
> hide #!6 models
> show #!7 models
> lighting shadows true
> show #!6 models
> hide #!7 models
> hide #!6 models
> show #!5 models
> hide #!5 models
> show #!4 models
> hide #!4 models
> show #!7 models
> hide #!7 models
> show #!6 models
> hide #!6 models
> show #!5 models
> hide #!5 models
> show #!4 models
> hide #!4 models
> show #!7 models
> hide #!7 models
> show #!6 models
> hide #!6 models
> show #!5 models
> hide #!5 models
> show #!4 models
> lighting shadows false
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!6 models
> hide #!6 models
> show #!7 models
> lighting shadows true
> hide #!7 models
> show #!6 models
> hide #!6 models
> show #!5 models
> hide #!5 models
> show #!4 models
> hide #!4 models
> show #!7 models
> show #!3 models
> hide #!7 models
> hide #!3 models
> show #!7 models
> show #!3 models
> hide #!3 models
> dssp
> hide #!7 models
> show #!6 models
> hide #!6 models
> show #!5 models
> hide #!5 models
> show #!6 models
> hide #!6 models
> show #!7 models
> hide #!7 models
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!6 models
> hide #!6 models
> show #!7 models
> save2
> /Users/fengwei.zheng/Documents/Draft_PolD/Session/MK/PIPs_comparison.cxs
> hide #!7 models
> show #!6 models
> hide #!6 models
> show #!3 models
> show #!4 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!6 models
> show #!7 models
> hide #!6 models
> show #!6 models
> hide #!7 models
> hide #!6 models
> show #!7 models
> show #!6 models
> hide #!7 models
> hide #!6 models
> show #!7 models
> hide #!7 models
> show #!6 models
> hide #!6 models
> show #!5 models
> hide #!5 models
> show #!4 models
> show #!5 models
> hide #!4 models
> show #!4 models
> hide #!5 models
> hide #!4 models
> show #!7 models
> show #!6 models
> hide #!7 models
> hide #!6 models
> show #!7 models
> show #!6 models
> hide #!7 models
> hide #!6 models
> show #!7 models
> hide #!7 models
> show #!6 models
> hide #!6 models
> show #!7 models
> show #!6 models
> hide #!7 models
> hide #!6 models
> show #!5 models
> hide #!5 models
> show #!4 models
> hide #!4 models
> show #!7 models
> hide #!7 models
> show #!3 models
> open /Users/fengwei.zheng/Documents/Structures/PolD/409-humPolDcplx.pdb
409-humPolDcplx.pdb title:
Processive human polymerase δ holoenzyme [more info...]
Chain information for 409-humPolDcplx.pdb #8
---
Chain | Description
A | DNA polymerase subunit δ P125
B | DNA polymerase δ subunit P50
C | DNA polymerase δ subunit 3
D | DNA polymerase δ subunit P12
E F G | proliferating cell nuclear antigen
P | DNA primer
T | DNA template
Non-standard residues in 409-humPolDcplx.pdb #8
---
DOC — 2',3'-dideoxycytidine-5'-monophosphate
SF4 — iron/sulfur cluster
TTP — thymidine-5'-triphosphate
ZN — zinc ion
> select #8
19722 atoms, 20206 bonds, 26 pseudobonds, 3 models selected
> hide #8
> show #8 cartoons
> mmaker #8/F to #1/H pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 409-ystPolDcplx_rpFG_163_3.pdb, chain H (#1) with
409-humPolDcplx.pdb, chain F (#8), sequence alignment score = 615.8
RMSD between 222 pruned atom pairs is 1.093 angstroms; (across all 248 pairs:
1.337)
> hide #!8 models
> show #!8 models
> cartoon style xsection barbell
> hide #!8 models
> show #!8 models
> name pip8 #8/A:1000-1006
> color pip8 green
> hide #8 & ~pip8 cartoons
> hide #!3 models
> mlp #8/F
Map values for surface "409-humPolDcplx.pdb_F SES surface": minimum -29.69,
mean -5.022, maximum 24.01
> show #!4 models
> hide #!8 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!8 models
> show #!5 models
> hide #!8 models
> hide #!5 models
> show #!6 models
> hide #!6 models
> show #!7 models
> hide #!7 models
> show #!6 models
> hide #!6 models
> show #!7 models
> hide #!7 models
> show #!8 models
> select clear
> hide #!8 models
> show #!7 models
> hide #!7 models
> show #!6 models
> hide #!6 models
> show #!5 models
> select #5/D:144,147,150,151
47 atoms, 46 bonds, 1 model selected
> color sel red
> color sel byhetero
> select clear
> select #5/D:144,147,150,151
47 atoms, 46 bonds, 1 model selected
> color sel red
> select clear
> select #5/D:144,147,150,151
47 atoms, 46 bonds, 1 model selected
> select clear
> hide #!5 models
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!4 models
> hide #!4 models
> show #!7 models
> hide #!7 models
> show #!6 models
> hide #!6 models
> show #!4 models
> select #4/X:337,340,343,344
39 atoms, 38 bonds, 1 model selected
> color sel red
> select clear
> ui mousemode rightMode select
Drag select of
Drag select of
Drag select of
> select #4/A:97@CG
1 atom, 1 model selected
> select clear
> hide #!4 models
> show #!6 models
> select #6/A:401,404,405
30 atoms, 30 bonds, 1 model selected
> color sel red
> select clear
> hide #!6 models
> show #!7 models
> hide #!7 models
> show #!8 models
> hide #!8 models
> show #!7 models
> hide #!7 models
> show #!8 models
> select pip8
41 atoms, 41 bonds, 1 model selected
> style sel stick
Changed 41 atom styles
> show sel atoms
> color sel byhetero
> select clear
> show #!7 models
> hide #!8 models
> select #7/A:999,1002
19 atoms, 18 bonds, 1 model selected
> color sel red
> select clear
> hide #!7 models
> show #!8 models
> show #!7 models
> hide #!7 models
> select #8/A:1002,1005
19 atoms, 18 bonds, 1 model selected
> color sel red
> select clear
> hide #!8 models
> show #!7 models
> hide #!7 models
> show #!6 models
> hide #!6 models
> show #!7 models
> hide #!7 models
> show #!6 models
> hide #!6 models
> show #!5 models
> hide #!5 models
> show #!4 models
> save2
> /Users/fengwei.zheng/Documents/Draft_PolD/Session/MK/PIPs_comparison.cxs
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!6 models
> hide #!6 models
> show #!7 models
> show #!8 models
> show #!6 models
> show #!5 models
> show #!4 models
> hide #!5 models
> hide #!6 models
> hide #!7 models
> hide #!8 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!4 models
> hide #!4 models
> show #!6 models
> hide #!6 models
> show #!7 models
> hide #!7 models
> show #!8 models
> hide #!8 models
> show #!7 models
> hide #!7 models
> show #!5 models
> hide #!5 models
> show #!4 models
> save2
> /Users/fengwei.zheng/Documents/Draft_PolD/Session/MK/PIPs_comparison.cxs
> save2
> /Users/fengwei.zheng/Documents/Draft_PolD/Figure/MK/humFEN1-PCNA_1ul1.tif
> width 1200 height 900 supersample 3
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!5 models
> save2
> /Users/fengwei.zheng/Documents/Draft_PolD/Figure/MK/humP21-PCNA_1AXC.tif
> width 1200 height 900 supersample 4
> hide #!5 models
> show #!6 models
> save2 /Users/fengwei.zheng/Documents/Draft_PolD/Figure/MK/ystRFC-
> PCNA_1SXJ.tif width 1200 height 900 supersample 3
> hide #!6 models
> show #!7 models
> save2 /Users/fengwei.zheng/Documents/Draft_PolD/Figure/MK/ystPolD-
> PCNA_409.tif width 1200 height 900 supersample 3
> hide #!7 models
> show #!8 models
> save2 /Users/fengwei.zheng/Documents/Draft_PolD/Figure/MK/humPolD-PCNA.tif
> width 1200 height 900 supersample 3
> show #!3 models
> select #3
19722 atoms, 20206 bonds, 26 pseudobonds, 3 models selected
> show sel cartoons
> hide #!3 models
> show #!1 models
> select #1
19534 atoms, 19981 bonds, 62 pseudobonds, 3 models selected
> show sel cartoons
> hide #!8 models
> show #!8 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> hide #!3 models
> select cysA
338 atoms, 340 bonds, 1 model selected
> show sel cartoons
> show sel atoms
> show #!1 models
> hide sel atoms
> hide #!8 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #1 & ~cysA
> hide #1 & ~cysA cartoons
> hide pip7
> color cysA blue
> color cysA blue cartoons
> hide #!7 models
> show #!7 models
> hide pip7 cartoons
> select ions
37 atoms, 36 pseudobonds, 9 models selected
> show sel atoms
> select #1/A:1101@S2
1 atom, 1 model selected
> select up
8 atoms, 1 model selected
> hide sel atoms
> select #7/A:1101@S2
1 atom, 1 model selected
> select up
8 atoms, 1 model selected
> hide sel atoms
> select #1/A:1105@ZN
1 atom, 1 model selected
> color sel red
> color sel red atoms
> select #1/A:1105@ZN
1 atom, 1 model selected
> color sel red
> select clear
> select #1/A:1105@ZN
1 atom, 1 model selected
> color sel red
> color sel red target a
> hide sel atoms
> select #7/A:1105@ZN
1 atom, 1 model selected
> hide sel atoms
> show #1/1105
> select #1/1105
Nothing selected
> select #1/A:1105
1 atom, 1 model selected
> show sel atoms
> hide #!7 models
> hide #!1 models
> show #!5 models
> show #5/D cartoons
> color #5/D blue
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide #5/D
> show #!7 models
> show #!1 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!7 models
> hide #!5 models
> show #!7 models
> show #!5 models
> hide #!5 models
> select clear
> select #1/A:1103@MG
1 atom, 1 model selected
> hide sel atoms
> select #7/A:1103@MG
1 atom, 1 model selected
> hide sel atoms
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!5 models
> hide #!1 models
> show #!1 models
> show #!7 models
> hide #!5 models
> hide #!7 models
> show #!6 models
> hide #!1 models
> hide #!6 models
> show #!5 models
> hide #!5 models
> show #!6 models
> hide #!6 models
> show #!5 models
> hide #!5 models
> show #!8 models
> hide #!8 models
> show #!7 models
> show #!1 models
> save2 /Users/fengwei.zheng/Documents/Draft_PolD/Session/MK/MK2_CysA-
> PCNA_comparison.cxs
> show #!5 models
> hide #!1 models
> hide #!7 models
> show #!7 models
> hide #!5 models
> show #!1 models
> save2
> /Users/fengwei.zheng/Documents/Draft_PolD/Figure/MK/S2/MK2_humP21-PCNA_comparison.tif
> width 1200 height 900 supersample 3
> hide #!7 models
> hide #!1 models
> show #!5 models
> save2
> /Users/fengwei.zheng/Documents/Draft_PolD/Figure/MK/S2/MK2_humP21-PCNA_comparison1.tif
> width 1200 height 900 supersample 3
> hide #!5 models
> show #!1 models
> hide #!1 models
> show #!7 models
> select #7
19534 atoms, 19981 bonds, 62 pseudobonds, 3 models selected
> show sel cartoons
Drag select of
> close session
> open2 /Users/fengwei.zheng/Downloads/3l9q.pdb
> /Users/fengwei.zheng/Downloads/3lgb.pdb
> /Users/fengwei.zheng/Downloads/6dhw.pdb
> /Users/fengwei.zheng/Downloads/6di6.pdb
3l9q.pdb title:
Crystal structure of human polymerase α-primase P58 iron-sulfur cluster domain
[more info...]
Chain information for 3l9q.pdb #1
---
Chain | Description
A B | DNA primase large subunit
Non-standard residues in 3l9q.pdb #1
---
SF4 — iron/sulfur cluster
SO4 — sulfate ion
3lgb.pdb title:
Crystal structure of the Fe-S domain of the yeast DNA primase [more info...]
Chain information for 3lgb.pdb #2
---
Chain | Description
A B | DNA primase large subunit
Non-standard residues in 3lgb.pdb #2
---
EPE — 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid (HEPES)
GOL — glycerol (glycerin; propane-1,2,3-triol)
SF4 — iron/sulfur cluster
ZN — zinc ion
6dhw.pdb title:
Crystal structure of primase iron-sulfur domain (266-457) [more info...]
Chain information for 6dhw.pdb #3
---
Chain | Description
A B | DNA primase large subunit
Non-standard residues in 6dhw.pdb #3
---
SF4 — iron/sulfur cluster
SO4 — sulfate ion
6di6.pdb title:
Crystal structure of eukaryotic DNA primase large subunit iron-sulfur cluster
domain [more info...]
Chain information for 6di6.pdb #4
---
Chain | Description
A | DNA primase large subunit
Non-standard residues in 6di6.pdb #4
---
MPD — (4S)-2-methyl-2,4-pentanediol
SF4 — iron/sulfur cluster
Drag select of
Drag select of
Drag select of
Drag select of
Drag select of
Drag select of
> hide #!4 models
> hide #!2 models
> hide #!1 models
> hide #!3 models
> show #!2 models
> show #!4 models
> show #!3 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!3 models
> hide #!1 models
> hide #!2 models
> show #!2 models
> show #!3 models
> show #!1 models
> hide #!2 models
> hide #!4 models
> show #!2 models
> show #!4 models
> hide #!3 models
> hide #!1 models
> hide #!2 models
> hide #!4 models
> show #!3 models
> show #!1 models
Drag select of 10 atoms, 2 residues, 8 bonds
> select clear
> mmaker #3 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3l9q.pdb, chain A (#1) with 6dhw.pdb, chain A (#3), sequence
alignment score = 982.7
RMSD between 170 pruned atom pairs is 0.221 angstroms; (across all 170 pairs:
0.221)
> hide #!3 models
> select #1:500
16 atoms, 24 bonds, 1 model selected
> toolshed show Distances
> select #1/B:500@FE1
1 atom, 1 model selected
Exactly two atoms must be selected!
> distance #1/B:367@SG #1/B:500@FE1
Distance between 3l9q.pdb #1/B CYS 367 SG and SF4 500 FE1: 2.343Å
> select #1/B:500@FE3
1 atom, 1 model selected
> distance #1/B:384@SG #1/B:500@FE3
Distance between 3l9q.pdb #1/B CYS 384 SG and SF4 500 FE3: 2.315Å
> select #1/B:500@FE2
1 atom, 1 model selected
> distance #1/B:424@SG #1/B:500@FE2
Distance between 3l9q.pdb #1/B CYS 424 SG and SF4 500 FE2: 2.319Å
> select #1/B:500@FE4
1 atom, 1 model selected
> distance #1/B:287@SG #1/B:500@FE4
Distance between 3l9q.pdb #1/B CYS 287 SG and SF4 500 FE4: 2.297Å
> select #1:500
16 atoms, 24 bonds, 1 model selected
> toolshed show H-Bonds
Invalid H-bond GUI 'slop_color' attrbute value, using default: Invalid color
name or specifier
Invalid H-bond GUI 'slop_color' attrbute value, using default: Invalid color
name or specifier
> hbonds sel interModel false distSlop 0.5 intraMol false intraRes false
> reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.5 angstroms and 20 degrees
Models used:
1 3l9q.pdb
0 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
0 hydrogen bonds found
> hbonds sel interModel false distSlop 0.5 intraMol false intraRes false
> reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.5 angstroms and 20 degrees
Models used:
1 3l9q.pdb
0 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
0 hydrogen bonds found
> toolshed show Contacts
> contacts sel distanceOnly 3.5 interModel false showDist true reveal true log
> true
Ignore distances between atoms separated by 4 bonds or less
Detect intra-residue distances: False
Detect intra-molecule distances: True
20 distances
atom1 atom2 overlap distance
3l9q.pdb #1/A SF4 500 FE4 3l9q.pdb #1/A CYS 287 SG 1.205 2.295
3l9q.pdb #1/B SF4 500 FE4 3l9q.pdb #1/B CYS 287 SG 1.203 2.297
3l9q.pdb #1/B SF4 500 FE3 3l9q.pdb #1/B CYS 384 SG 1.185 2.315
3l9q.pdb #1/A SF4 500 FE3 3l9q.pdb #1/A CYS 367 SG 1.184 2.316
3l9q.pdb #1/B SF4 500 FE2 3l9q.pdb #1/B CYS 424 SG 1.181 2.319
3l9q.pdb #1/A SF4 500 FE1 3l9q.pdb #1/A CYS 424 SG 1.165 2.335
3l9q.pdb #1/B SF4 500 FE1 3l9q.pdb #1/B CYS 367 SG 1.157 2.343
3l9q.pdb #1/A SF4 500 FE2 3l9q.pdb #1/A CYS 384 SG 1.156 2.344
3l9q.pdb #1/A SF4 500 FE1 3l9q.pdb #1/A CYS 424 CB 0.353 3.147
3l9q.pdb #1/B SF4 500 FE2 3l9q.pdb #1/B CYS 424 CB 0.346 3.154
3l9q.pdb #1/B SF4 500 FE4 3l9q.pdb #1/B CYS 287 CB 0.342 3.158
3l9q.pdb #1/A SF4 500 FE4 3l9q.pdb #1/A CYS 287 CB 0.334 3.166
3l9q.pdb #1/A SF4 500 FE3 3l9q.pdb #1/A CYS 367 CB 0.260 3.240
3l9q.pdb #1/B SF4 500 FE1 3l9q.pdb #1/B CYS 367 CB 0.258 3.242
3l9q.pdb #1/B SF4 500 FE3 3l9q.pdb #1/B CYS 384 CB 0.234 3.266
3l9q.pdb #1/A SF4 500 FE2 3l9q.pdb #1/A CYS 384 CB 0.208 3.292
3l9q.pdb #1/A SF4 500 S3 3l9q.pdb #1/A CYS 287 N 0.069 3.431
3l9q.pdb #1/B SF4 500 S1 3l9q.pdb #1/B CYS 287 N 0.059 3.441
3l9q.pdb #1/A SF4 500 S4 3l9q.pdb #1/A CYS 424 CB 0.051 3.449
3l9q.pdb #1/B SF4 500 S4 3l9q.pdb #1/B CYS 424 CB 0.041 3.459
20 distances
> contacts sel distanceOnly 3.0 interModel false showDist true reveal true log
> true
Ignore distances between atoms separated by 4 bonds or less
Detect intra-residue distances: False
Detect intra-molecule distances: True
8 distances
atom1 atom2 overlap distance
3l9q.pdb #1/A SF4 500 FE4 3l9q.pdb #1/A CYS 287 SG 0.705 2.295
3l9q.pdb #1/B SF4 500 FE4 3l9q.pdb #1/B CYS 287 SG 0.703 2.297
3l9q.pdb #1/B SF4 500 FE3 3l9q.pdb #1/B CYS 384 SG 0.685 2.315
3l9q.pdb #1/A SF4 500 FE3 3l9q.pdb #1/A CYS 367 SG 0.684 2.316
3l9q.pdb #1/B SF4 500 FE2 3l9q.pdb #1/B CYS 424 SG 0.681 2.319
3l9q.pdb #1/A SF4 500 FE1 3l9q.pdb #1/A CYS 424 SG 0.665 2.335
3l9q.pdb #1/B SF4 500 FE1 3l9q.pdb #1/B CYS 367 SG 0.657 2.343
3l9q.pdb #1/A SF4 500 FE2 3l9q.pdb #1/A CYS 384 SG 0.656 2.344
8 distances
> select #1:500
16 atoms, 24 bonds, 1 model selected
> contacts sel distanceOnly 3.0 interModel false showDist true reveal true log
> true
Ignore distances between atoms separated by 4 bonds or less
Detect intra-residue distances: False
Detect intra-molecule distances: True
8 distances
atom1 atom2 overlap distance
3l9q.pdb #1/A SF4 500 FE4 3l9q.pdb #1/A CYS 287 SG 0.705 2.295
3l9q.pdb #1/B SF4 500 FE4 3l9q.pdb #1/B CYS 287 SG 0.703 2.297
3l9q.pdb #1/B SF4 500 FE3 3l9q.pdb #1/B CYS 384 SG 0.685 2.315
3l9q.pdb #1/A SF4 500 FE3 3l9q.pdb #1/A CYS 367 SG 0.684 2.316
3l9q.pdb #1/B SF4 500 FE2 3l9q.pdb #1/B CYS 424 SG 0.681 2.319
3l9q.pdb #1/A SF4 500 FE1 3l9q.pdb #1/A CYS 424 SG 0.665 2.335
3l9q.pdb #1/B SF4 500 FE1 3l9q.pdb #1/B CYS 367 SG 0.657 2.343
3l9q.pdb #1/A SF4 500 FE2 3l9q.pdb #1/A CYS 384 SG 0.656 2.344
8 distances
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
Missing or invalid "atoms" argument: invalid atom-pair specifier
> ~distance
Drag select of 1 atoms, 5 residues
> hide hbonds
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
Unknown command: ~labels
> ~label
> ~distance
> select clear
> hide #!1 models
> show #!2 models
> select #2:514
16 atoms, 24 bonds, 1 model selected
> contacts sel distanceOnly 3.0 interModel false showDist true reveal true log
> true
Ignore distances between atoms separated by 4 bonds or less
Detect intra-residue distances: False
Detect intra-molecule distances: True
8 distances
atom1 atom2 overlap distance
3lgb.pdb #2/B SF4 514 FE3 3lgb.pdb #2/B CYS 417 SG 0.751 2.249
3lgb.pdb #2/A SF4 514 FE1 3lgb.pdb #2/A CYS 417 SG 0.743 2.257
3lgb.pdb #2/B SF4 514 FE1 3lgb.pdb #2/B CYS 336 SG 0.715 2.285
3lgb.pdb #2/B SF4 514 FE4 3lgb.pdb #2/B CYS 474 SG 0.706 2.294
3lgb.pdb #2/A SF4 514 FE3 3lgb.pdb #2/A CYS 474 SG 0.702 2.298
3lgb.pdb #2/A SF4 514 FE4 3lgb.pdb #2/A CYS 336 SG 0.697 2.303
3lgb.pdb #2/B SF4 514 FE2 3lgb.pdb #2/B CYS 434 SG 0.690 2.310
3lgb.pdb #2/A SF4 514 FE2 3lgb.pdb #2/A CYS 434 SG 0.686 2.314
8 distances
> hide #!2 models
> close #3
> close #1
> show #!2 models
> open2 /Users/fengwei.zheng/Downloads/6dhw.pdb
6dhw.pdb title:
Crystal structure of primase iron-sulfur domain (266-457) [more info...]
Chain information for 6dhw.pdb #1
---
Chain | Description
A B | DNA primase large subunit
Non-standard residues in 6dhw.pdb #1
---
SF4 — iron/sulfur cluster
SO4 — sulfate ion
> hide #!1 models
> hide #!2 models
> show #!1 models
> select #1:501
16 atoms, 24 bonds, 1 model selected
> contacts sel distanceOnly 3.0 interModel false showDist true reveal true log
> true
Ignore distances between atoms separated by 4 bonds or less
Detect intra-residue distances: False
Detect intra-molecule distances: True
8 distances
atom1 atom2 overlap distance
6dhw.pdb #1/B SF4 501 FE1 6dhw.pdb #1/B CYS 367 SG 0.457 2.543
6dhw.pdb #1/B SF4 501 FE4 6dhw.pdb #1/B CYS 424 SG 0.455 2.545
6dhw.pdb #1/B SF4 501 FE2 6dhw.pdb #1/B CYS 287 SG 0.453 2.547
6dhw.pdb #1/A SF4 501 FE1 6dhw.pdb #1/A CYS 287 SG 0.445 2.555
6dhw.pdb #1/A SF4 501 FE4 6dhw.pdb #1/A CYS 424 SG 0.436 2.564
6dhw.pdb #1/A SF4 501 FE2 6dhw.pdb #1/A CYS 384 SG 0.422 2.578
6dhw.pdb #1/B SF4 501 FE3 6dhw.pdb #1/B CYS 384 SG 0.421 2.579
6dhw.pdb #1/A SF4 501 FE3 6dhw.pdb #1/A CYS 367 SG 0.393 2.607
8 distances
> hide #!1 models
> show #!4 models
> select #4/A:601@FE2
1 atom, 1 model selected
> select up
8 atoms, 12 bonds, 1 model selected
> contacts sel distanceOnly 3.0 interModel false showDist true reveal true log
> true
Ignore distances between atoms separated by 4 bonds or less
Detect intra-residue distances: False
Detect intra-molecule distances: True
4 distances
atom1 atom2 overlap distance
6di6.pdb #4/A SF4 601 FE2 6di6.pdb #4/A CYS 417 SG 0.724 2.276
6di6.pdb #4/A SF4 601 FE1 6di6.pdb #4/A CYS 336 SG 0.701 2.299
6di6.pdb #4/A SF4 601 FE3 6di6.pdb #4/A CYS 474 SG 0.690 2.310
6di6.pdb #4/A SF4 601 FE4 6di6.pdb #4/A CYS 434 SG 0.690 2.310
4 distances
> close #1
> close session
> open /Users/fengwei.zheng/Documents/Draft_PolD/Session/Fig4/Fig4a_v2.cxs
opened ChimeraX session
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/nucleotides/_data.py", line 525, in rebuild
_rebuild_molecule('internal', mol)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/nucleotides/_data.py", line 652, in _rebuild_molecule
hide_residues = make_ladder(nd, residues, mol._ladder_params)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/nucleotides/_data.py", line 1237, in make_ladder
va, na, ta = get_cylinder(params.rung_radius, ep0, ep1)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/nucleotides/_data.py", line 733, in get_cylinder
h = distance(p0, p1)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/geometry/vector.py", line 71, in distance
return sqrt(distance_squared(p, q))
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/geometry/vector.py", line 63, in distance_squared
if len(p) == 3:
TypeError: object of type 'NoneType' has no len()
Error processing trigger "new frame":
TypeError: object of type 'NoneType' has no len()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/geometry/vector.py", line 63, in distance_squared
if len(p) == 3:
See log for complete Python traceback.
> close session
> open
> /Users/fengwei.zheng/Documents/Phenix/PolD/409-ystPolDcplx_rpFG_163_3.pdb
Summary of feedback from opening
/Users/fengwei.zheng/Documents/Phenix/PolD/409-ystPolDcplx_rpFG_163_3.pdb
---
warnings | Start residue of secondary structure not found: HELIX 9 9 ALA H 9
LYS H 20 1 12
Start residue of secondary structure not found: HELIX 10 10 VAL H 54 ALA H 56
5 3
Start residue of secondary structure not found: HELIX 11 11 LEU H 72 CYS H 81
1 10
Start residue of secondary structure not found: HELIX 12 12 SER H 141 LEU H
154 1 14
Start residue of secondary structure not found: HELIX 13 13 ALA H 209 LYS H
217 1 9
15 messages similar to the above omitted
Chain information for 409-ystPolDcplx_rpFG_163_3.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
E | No description available
F | No description available
G | No description available
P | No description available
T | No description available
> open /Users/fengwei.zheng/Documents/Structures/PolD/409-humPolDcplx.pdb
409-humPolDcplx.pdb title:
Processive human polymerase δ holoenzyme [more info...]
Chain information for 409-humPolDcplx.pdb #2
---
Chain | Description
A | DNA polymerase subunit δ P125
B | DNA polymerase δ subunit P50
C | DNA polymerase δ subunit 3
D | DNA polymerase δ subunit P12
E F G | proliferating cell nuclear antigen
P | DNA primer
T | DNA template
Non-standard residues in 409-humPolDcplx.pdb #2
---
DOC — 2',3'-dideoxycytidine-5'-monophosphate
SF4 — iron/sulfur cluster
TTP — thymidine-5'-triphosphate
ZN — zinc ion
> open2
> /Users/fengwei.zheng/Documents/Structures/PolD/templates/Pri2/hum_Pri2_3l9q.pdb
> /Users/fengwei.zheng/Documents/Structures/PolD/templates/Pri2/yst_Pri2_6di6.pdb
hum_Pri2_3l9q.pdb title:
Crystal structure of human polymerase α-primase P58 iron-sulfur cluster domain
[more info...]
Chain information for hum_Pri2_3l9q.pdb #3
---
Chain | Description
A B | DNA primase large subunit
Non-standard residues in hum_Pri2_3l9q.pdb #3
---
SF4 — iron/sulfur cluster
SO4 — sulfate ion
yst_Pri2_6di6.pdb title:
Crystal structure of eukaryotic DNA primase large subunit iron-sulfur cluster
domain [more info...]
Chain information for yst_Pri2_6di6.pdb #4
---
Chain | Description
A | DNA primase large subunit
Non-standard residues in yst_Pri2_6di6.pdb #4
---
MPD — (4S)-2-methyl-2,4-pentanediol
SF4 — iron/sulfur cluster
> hide
> show cartoons
> view #1
> dssp
> mmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 409-ystPolDcplx_rpFG_163_3.pdb, chain A (#1) with
409-humPolDcplx.pdb, chain A (#2), sequence alignment score = 2863.1
RMSD between 724 pruned atom pairs is 1.309 angstroms; (across all 981 pairs:
2.341)
> cartoon style xsection barbell
> cartoon style nucleic xsection oval width 1 thickness 1
> mmaker #3-4 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 409-ystPolDcplx_rpFG_163_3.pdb, chain A (#1) with
hum_Pri2_3l9q.pdb, chain A (#3), sequence alignment score = 81.8
RMSD between 4 pruned atom pairs is 1.088 angstroms; (across all 142 pairs:
24.772)
Matchmaker 409-ystPolDcplx_rpFG_163_3.pdb, chain A (#1) with
yst_Pri2_6di6.pdb, chain A (#4), sequence alignment score = 82.3
RMSD between 7 pruned atom pairs is 1.171 angstroms; (across all 155 pairs:
22.326)
> hide #!2 models
> hide #!3 models
> show #!3 models
> hide #!4 models
> select ::name="SF4"
40 atoms, 48 bonds, 18 pseudobonds, 5 models selected
> show sel atoms
> style sel stick
Changed 40 atom styles
> select clear
> select ::name="SF4"
40 atoms, 48 bonds, 18 pseudobonds, 5 models selected
> show sel atoms
> style sel sphere
Changed 40 atom styles
> color sel byhetero
> select #1/A:1101@S1
1 atom, 1 model selected
> select #1/A:1101@FE4
1 atom, 1 model selected
> select clear
> select ::name="SF4"
40 atoms, 48 bonds, 18 pseudobonds, 5 models selected
> style sel stick
Changed 40 atom styles
> select clear
> hide #!3 models
> hide #!1 models
> show #!2 models
> show #!1 models
> hide #!2 models
> select clear
> ui mousemode rightMode "link markers"
> ui mousemode rightMode "link markers"
> ui mousemode rightMode "mark plane"
> ui mousemode rightMode "mark plane"
> ui mousemode rightMode "mark surface"
> marker #5 177.2,188.2,152.2 color yellow radius 1
> marker #5 176.5,188.5,151.7 color yellow radius 1
> ui mousemode rightMode "delete markers"
> marker delete #5:2
> ui mousemode rightMode "mark plane"
> ui mousemode rightMode "mark surface"
> marker #5 183.1,185.3,155.7 color yellow radius 1
> ui mousemode rightMode "move markers"
> marker change #5:3 position 181.8,181.9,152.9
> marker change #5 radius 0.3
> marker change #5:3 position 182.4,181,150.7
> marker change #5:3 position 182.3,182.8,151.5
> mmaker #5 to #1/A:1101@S1
Reference and/or match model contains no nucleic or amino acid chains.
Use the command-line 'align' command to superimpose small molecules/ligands.
> align #5 toAtoms #1/A:1101@S1
RMSD between 1 atom pairs is 0.000 angstroms
> marker change #5 radius 0.2
> hide #!1 models
> show #!1 models
> ui mousemode rightMode "mark surface"
> marker #5 186.7,184,153.6 color yellow radius 0.2
> ui mousemode rightMode "move markers"
> marker change #5:4 position 183.1,183.9,150.5
> marker change #5:4 radius 0.3
> hide #!1 models
> show #1/A:1101
> select #1/A:1101
8 atoms, 18 pseudobonds, 2 models selected
> show sel atoms
> show sel cartoons
> style sel sphere
Changed 8 atom styles
> style sel stick
Changed 8 atom styles
> show #!1 models
> show sel atoms
> hide sel atoms
> show sel atoms
> style sel stick
Changed 8 atom styles
> style sel sphere
Changed 8 atom styles
> style sel ball
Changed 8 atom styles
> show #!2 models
> hide #!1 models
> select #2/A:1202
8 atoms, 12 bonds, 1 model selected
> hide sel atoms
> show sel atoms
> hide sel atoms
> show sel cartoons
> show sel cartoons
> hide sel cartoons
> show sel atoms
> style sel stick
Changed 8 atom styles
> style sel stick
Changed 8 atom styles
> style sel sphere
Changed 8 atom styles
> style sel ball
Changed 8 atom styles
> style sel stick
Changed 8 atom styles
> hide #1-2 cartoons
> select #1/A:1101
8 atoms, 18 pseudobonds, 2 models selected
> show sel atoms
> show sel cartoons
> style sel stick
Changed 8 atom styles
> style sel sphere
Changed 8 atom styles
> style sel ball
Changed 8 atom styles
> show sel atoms
> show #!1 models
> style sel stick
Changed 8 atom styles
> hide #!2 models
> show #!2 models
> open /Users/fengwei.zheng/Documents/Structures/PolD/409-humPolDcplx.pdb
409-humPolDcplx.pdb title:
Processive human polymerase δ holoenzyme [more info...]
Chain information for 409-humPolDcplx.pdb #6
---
Chain | Description
A | DNA polymerase subunit δ P125
B | DNA polymerase δ subunit P50
C | DNA polymerase δ subunit 3
D | DNA polymerase δ subunit P12
E F G | proliferating cell nuclear antigen
P | DNA primer
T | DNA template
Non-standard residues in 409-humPolDcplx.pdb #6
---
DOC — 2',3'-dideoxycytidine-5'-monophosphate
SF4 — iron/sulfur cluster
TTP — thymidine-5'-triphosphate
ZN — zinc ion
> hide #6 & ~:1202
> mmaker #6/A:1202 to #1/A:1101
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 409-ystPolDcplx_rpFG_163_3.pdb, chain A (#1) with
409-humPolDcplx.pdb, chain A (#6), sequence alignment score = 0
Fewer than 3 residues aligned; cannot match 409-ystPolDcplx_rpFG_163_3.pdb,
chain A with 409-humPolDcplx.pdb, chain A
> align #6/A:1202 toAtoms #1/A:1101
RMSD between 8 atom pairs is 0.022 angstroms
> hide #!2 models
> hide #5 models
> hide #!6 models
> show #!6 models
> show #!2 models
> select #2
19722 atoms, 20206 bonds, 26 pseudobonds, 3 models selected
> ui mousemode rightMode "translate selected models"
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> ui mousemode rightMode "rotate selected models"
> close #5
> ~select #2
Nothing selected
> hide #!2 models
> show #!2 models
> mmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 409-ystPolDcplx_rpFG_163_3.pdb, chain A (#1) with
409-humPolDcplx.pdb, chain A (#2), sequence alignment score = 2863.1
RMSD between 724 pruned atom pairs is 1.309 angstroms; (across all 981 pairs:
2.341)
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #1
> show #1
> hide #1 & ~:1102
> undo
> hide #1 & ~:1101
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #1
> show #!2 models
> show #!3 models
> show #!4 models
> hide #!6 models
> show #!6 models
> show #1-4 cartoons
> dssp
> mmaker #2-4 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 409-ystPolDcplx_rpFG_163_3.pdb, chain A (#1) with
409-humPolDcplx.pdb, chain A (#2), sequence alignment score = 2863.1
RMSD between 724 pruned atom pairs is 1.309 angstroms; (across all 981 pairs:
2.341)
Matchmaker 409-ystPolDcplx_rpFG_163_3.pdb, chain A (#1) with
hum_Pri2_3l9q.pdb, chain A (#3), sequence alignment score = 81.8
RMSD between 4 pruned atom pairs is 1.088 angstroms; (across all 142 pairs:
24.772)
Matchmaker 409-ystPolDcplx_rpFG_163_3.pdb, chain A (#1) with
yst_Pri2_6di6.pdb, chain A (#4), sequence alignment score = 82.3
RMSD between 7 pruned atom pairs is 1.171 angstroms; (across all 155 pairs:
22.326)
> hide #!4 models
> hide #!3 models
> show #3-4 cartoons
> show #!4 models
> show #!3 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> hide #!3 models
> color #1/A:984-1030 blue
> color #2/A:990-1032 blue
> color #1/A:1031-1097 magenta
> color #2/A:1033-1107 magenta
Drag select of
> hide #!2 models
> hide #!1 models
> show #!2 models
> show #!1 models
> hide #!2 models
> show #!2 models
> name cysB2 #2/A:1033-1107
> name cysA2 #2/A:990-1032
> name cysA1 #2/A:984-1030
> name cysA1 #1/A:984-1030
> name cysB1 #1/A:1031-1097
> hide #1-2 cartoons
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show cysA1 & cysB1 cartoons
> show cysA1 cartoons
> show cysA1 | cysB1 cartoons
> show cysA2 | cysB2 cartoons
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> select ::name="ZN"
3 atoms, 3 models selected
> show @Zn
> hide #!6 models
> show #!6 models
> show #!3 models
> hide #!3 models
> show #!3 models
> show #!4 models
> hide #!4 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> ui mousemode rightMode select
> select clear
> select #6/A:1201@ZN
1 atom, 1 model selected
> hide sel atoms
> select #1/A:1105@ZN
1 atom, 1 model selected
> color sel red
> select clear
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> mmaker #2/A:990-1107 to #1/A:984-1097
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 409-ystPolDcplx_rpFG_163_3.pdb, chain A (#1) with
409-humPolDcplx.pdb, chain A (#2), sequence alignment score = 261.5
RMSD between 92 pruned atom pairs is 1.111 angstroms; (across all 105 pairs:
2.157)
> show #!3 models
> mmaker #3 to #1/A:984-1097
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 409-ystPolDcplx_rpFG_163_3.pdb, chain A (#1) with
hum_Pri2_3l9q.pdb, chain A (#3), sequence alignment score = 37
RMSD between 14 pruned atom pairs is 0.320 angstroms; (across all 89 pairs:
25.866)
> select #3
3233 atoms, 2870 bonds, 16 pseudobonds, 3 models selected
> ui mousemode rightMode translate
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
Drag select of 8 residues
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> hide #!3 models
> show #!4 models
> hide #3-4/B cartoons
> show #!3 models
> hide #3-4/B
> select #3
3233 atoms, 2870 bonds, 16 pseudobonds, 3 models selected
> hide #!4 models
> hide #!2 models
> hide #!1 models
> show #!1 models
> select clear
> select #3
3233 atoms, 2870 bonds, 16 pseudobonds, 3 models selected
Drag select of
> show #!2 models
> mmaker #3/A:500 to #1/A:984-1097
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 409-ystPolDcplx_rpFG_163_3.pdb, chain A (#1) with
hum_Pri2_3l9q.pdb, chain A (#3), sequence alignment score = 0
Fewer than 3 residues aligned; cannot match 409-ystPolDcplx_rpFG_163_3.pdb,
chain A with hum_Pri2_3l9q.pdb, chain A
> align #3/A:500 toAtoms #1/A:984-1097
Unequal number of atoms to pair, 8 and 900
> hide #!2 models
> align #3/A:500 toAtoms #1/A:1102
Unequal number of atoms to pair, 8 and 28
> align #3/A:500 toAtoms #6/A:1202
RMSD between 8 atom pairs is 2.245 angstroms
> align #3/A toAtoms cysB1
Unequal number of atoms to pair, 1639 and 562
> mmaker #3/A to cysB1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 409-ystPolDcplx_rpFG_163_3.pdb, chain A (#1) with
hum_Pri2_3l9q.pdb, chain A (#3), sequence alignment score = 39.2
RMSD between 13 pruned atom pairs is 0.681 angstroms; (across all 58 pairs:
18.756)
> select #3
3233 atoms, 2870 bonds, 16 pseudobonds, 3 models selected
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> show #!2 models
> show #!4 models
> mmaker #3/A to #4
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker yst_Pri2_6di6.pdb, chain A (#4) with hum_Pri2_3l9q.pdb, chain A
(#3), sequence alignment score = 428.5
RMSD between 106 pruned atom pairs is 0.865 angstroms; (across all 161 pairs:
5.202)
> hide #!2 models
> hide #!1 models
> ui mousemode rightMode select
> select clear
> hide #!4 models
> show #!4 models
> show #!2 models
> show #!1 models
> select #4
1718 atoms, 1576 bonds, 6 pseudobonds, 3 models selected
> select #3
3233 atoms, 2870 bonds, 16 pseudobonds, 3 models selected
> select #4
1718 atoms, 1576 bonds, 6 pseudobonds, 3 models selected
> select #3-4
4951 atoms, 4446 bonds, 22 pseudobonds, 6 models selected
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> hide #!4 models
> show #!4 models
> ~select #4
3233 atoms, 2870 bonds, 16 pseudobonds, 3 models selected
> ~select #3
Nothing selected
> ui mousemode rightMode select
> hide #!2 models
> select #1/A:1102
28 atoms, 29 bonds, 1 model selected
> show sel atoms
> hide sel atoms
> select #1/A:1101
8 atoms, 18 pseudobonds, 2 models selected
> show sel atoms
> select clear
> select #1/A:1101
8 atoms, 18 pseudobonds, 2 models selected
> hide sel atoms
> select #6/A:1202 :<2.5 & #1:cys
Nothing selected
> select #6/A:1202 :<2.5 & #1
8 atoms, 18 pseudobonds, 2 models selected
> show sel atoms
> hide sel atoms
> select #6/A:1202 :<3 & #1
43 atoms, 30 bonds, 22 pseudobonds, 2 models selected
> show sel atoms
> style sel stick
Changed 43 atom styles
> color sel byhetero
> hide sel atoms
> select #6/A:1202 :<3 & #1:cys
24 atoms, 20 bonds, 1 model selected
> show sel atoms
> ui mousemode rightMode distance
> ui mousemode rightMode select
> select #1/A:1059@SG
1 atom, 1 model selected
> select #6/A:1202@FE4
1 atom, 1 model selected
> ui mousemode rightMode distance
> distance #1/A:1059@SG #6/A:1202@FE4
Distance between 409-ystPolDcplx_rpFG_163_3.pdb #1/A CYS 1059 SG and
409-humPolDcplx.pdb #6/A SF4 1202 FE4: 2.994Å
> distance #6/A:1202@FE2 #1/A:1074@SG
Distance between 409-humPolDcplx.pdb #6/A SF4 1202 FE2 and
409-ystPolDcplx_rpFG_163_3.pdb #1/A CYS 1074 SG: 2.956Å
> distance #1/A:1056@SG #6/A:1202@FE3
Distance between 409-ystPolDcplx_rpFG_163_3.pdb #1/A CYS 1056 SG and
409-humPolDcplx.pdb #6/A SF4 1202 FE3: 2.931Å
> distance #6/A:1202@FE1 #1/A:1069@SG
Distance between 409-humPolDcplx.pdb #6/A SF4 1202 FE1 and
409-ystPolDcplx_rpFG_163_3.pdb #1/A CYS 1069 SG: 2.872Å
> hide #5.1 models
> close #5.1
> ui mousemode rightMode select
> select clear
Drag select of
> hide #!1 models
> hide #!6 models
> show #!1 models
> show #!6 models
> hide #!6 models
> hide #!1 models
> hide #5 models
> show #!2 models
> select #2/A:1202 :<3 & #2:cys
24 atoms, 20 bonds, 1 model selected
> show sel atoms
> style sel stick
Changed 24 atom styles
> color sel byhetero
> hide #2.1 models
> show #2.1 models
> select clear
> label #3.1
Missing or invalid "atoms" argument: Expected two atoms to be specified (0
specified)
> ui mousemode rightMode distance
> distance #2/A:1061@SG #2/A:1202@FE4
Distance between 409-humPolDcplx.pdb #2/A CYS 1061 SG and SF4 1202 FE4: 2.376Å
> distance #2/A:1061@SG #2/A:1202@FE4
Distance already exists; modify distance properties with 'distance style'
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> distance #2/A:1202@FE4 #2/A:1061@SG
Distance already exists; modify distance properties with 'distance style'
> distance #2/A:1202@FE2 #2/A:1076@SG
Distance between 409-humPolDcplx.pdb #2/A SF4 1202 FE2 and CYS 1076 SG: 2.252Å
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> distance #2/A:1202@FE2 #2/A:1076@SG
Distance already exists; modify distance properties with 'distance style'
> distance #2/A:1202@FE2 #2/A:1076@SG
Distance already exists; modify distance properties with 'distance style'
> hide #5.1 models
> show #5.1 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> distance #2/A:1202@FE1 #2/A:1071@SG
Distance between 409-humPolDcplx.pdb #2/A SF4 1202 FE1 and CYS 1071 SG: 2.252Å
> distance #2/A:1058@SG #2/A:1202@FE3
Distance between 409-humPolDcplx.pdb #2/A CYS 1058 SG and SF4 1202 FE3: 2.268Å
> close #5
> hide #!2 models
> show #!1 models
> show #!6 models
> distance #1/A:1059@SG #6/A:1202@FE4
Distance between 409-ystPolDcplx_rpFG_163_3.pdb #1/A CYS 1059 SG and
409-humPolDcplx.pdb #6/A SF4 1202 FE4: 2.994Å
> distance #1/A:1056@SG #6/A:1202@FE3
Distance between 409-ystPolDcplx_rpFG_163_3.pdb #1/A CYS 1056 SG and
409-humPolDcplx.pdb #6/A SF4 1202 FE3: 2.931Å
> distance #6/A:1202@FE2 #1/A:1074@SG
Distance between 409-humPolDcplx.pdb #6/A SF4 1202 FE2 and
409-ystPolDcplx_rpFG_163_3.pdb #1/A CYS 1074 SG: 2.956Å
> distance #6/A:1202@FE1 #1/A:1069@SG
Distance between 409-humPolDcplx.pdb #6/A SF4 1202 FE1 and
409-ystPolDcplx_rpFG_163_3.pdb #1/A CYS 1069 SG: 2.872Å
> show #!2 models
> hide #!2 models
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
Unknown command: ~distances
> ~label
> show #!2 models
> hide #!1 models
> hide #!6 models
> hide #!2 models
> show #!1 models
> show #!6 models
> hide #!4 models
> select #3/A:500 :<3 & #3:cys
24 atoms, 20 bonds, 1 model selected
> show sel atoms
> select clear
Drag select of 6 residues
Drag select of
> hide #!3 models
> show #!4 models
> select #4/A:601 :<3 & #4:cys
24 atoms, 20 bonds, 1 model selected
> show sel atoms
> select clear
> show #!3 models
> color #3-4 blue cartoons
> color #3-4 magenta cartoons
> color #3-4 magenta
> undo
> select #4/A:601 :<3 & #4:cys
24 atoms, 20 bonds, 1 model selected
> color sel magenta
> color sel byhetero
> hide #!3 models
> show #!3 models
> hide #!4 models
> select #4/A:601 :<3 & #4:cys
24 atoms, 20 bonds, 1 model selected
> select #3/A:500 :<3 & #3:cys
24 atoms, 20 bonds, 1 model selected
> color sel magenta
> color sel byhetero
> select clear
> ui mousemode rightMode select
> show #!4 models
> select #3-4
4951 atoms, 4446 bonds, 22 pseudobonds, 6 models selected
> ui mousemode rightMode "rotate selected models"
> ~select #4
3233 atoms, 2870 bonds, 16 pseudobonds, 3 models selected
> ~select #3
Nothing selected
> hide #!3 models
> show #!3 models
> dssp
> ~label
> show #!2 models
> hide #!4 models
> select #3
3233 atoms, 2870 bonds, 16 pseudobonds, 3 models selected
> select clear
> show #!4 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #!4 models
> show #!4 models
> show #!3 models
> mmaker #3 to #4
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker yst_Pri2_6di6.pdb, chain A (#4) with hum_Pri2_3l9q.pdb, chain B
(#3), sequence alignment score = 435.4
RMSD between 116 pruned atom pairs is 0.934 angstroms; (across all 157 pairs:
5.201)
> mmaker #3 to #4/A
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker yst_Pri2_6di6.pdb, chain A (#4) with hum_Pri2_3l9q.pdb, chain B
(#3), sequence alignment score = 435.4
RMSD between 116 pruned atom pairs is 0.934 angstroms; (across all 157 pairs:
5.201)
> mmaker #3/A to #4/A
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker yst_Pri2_6di6.pdb, chain A (#4) with hum_Pri2_3l9q.pdb, chain A
(#3), sequence alignment score = 428.5
RMSD between 106 pruned atom pairs is 0.865 angstroms; (across all 161 pairs:
5.202)
> hide #!4 models
> show #!4 models
> hide #!3 models
> show #!3 models
> hide #!2 models
> ~label
> select #3-4
4951 atoms, 4446 bonds, 22 pseudobonds, 6 models selected
> select clear
> select #3-4
4951 atoms, 4446 bonds, 22 pseudobonds, 6 models selected
> select #1-2
39256 atoms, 40187 bonds, 88 pseudobonds, 6 models selected
> ~label
> select clear
> show #!2 models
Empty filename passed to function
> save2 /Users/fengwei.zheng/Documents/Draft_PolD/Session/MK/MK3_Fe-
> S_comparison.cxs
Unable to save 'nucleotides' ->
<chimerax.atomic.nucleotides._data.NucleotideState object at 0x12f878f90>".
Session might not restore properly.
> save2 /Users/fengwei.zheng/Documents/Draft_PolD/Session/MK/MK3_Fe-
> S_comparison.cxs
Unable to save 'nucleotides' ->
<chimerax.atomic.nucleotides._data.NucleotideState object at 0x12f878f90>".
Session might not restore properly.
Unable to restore session, resetting.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 661, in restore
obj = sm.restore_snapshot(self, data)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/nucleotides/_data.py", line 477, in restore_snapshot
if data['version'] != 1:
TypeError: 'NoneType' object is not subscriptable
opened ChimeraX session
OpenGL version: 4.1 ATI-2.9.26
OpenGL renderer: AMD Radeon Pro 580 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
Change History (2)
comment:1 by , 5 years ago
| Component: | Unassigned → Sessions |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Problems both saving and restoring nucleotides |
comment:2 by , 5 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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duplicate of #3263