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Opened 4 years ago
Last modified 4 years ago
#4829 assigned defect
multiple errors
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sequence | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-10.14.6-x86_64-i386-64bit
ChimeraX Version: 1.2.2 (2021-05-08 05:48:20 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.2.2 (2021-05-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open
> /Users/avisinger/Desktop/Keating_lab/EVH1_crosstalk/paralog_comparison_pdb/chimera_sessions/chimeraX/mena_vs_homer_conservation_210527.cxs
Log from Thu May 27 14:25:09 2021UCSF ChimeraX version: 1.2.2 (2021-05-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open
> /Users/avisinger/Desktop/Keating_lab/masstitr_project/paralog_comparison_pdb/chimera_sessions/chimeraX/mena_homer.cxs
Log from Wed May 12 14:02:08 2021UCSF ChimeraX version: 1.2.2 (2021-05-08)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/avisinger/Desktop/Keating_lab/masstitr_project/amy/chimera_sessions/mena_homer.py
Traceback (most recent call last):
File
"/Users/avisinger/Desktop/Keating_lab/masstitr_project/amy/chimera_sessions/mena_homer.py",
line 1, in <module>
import cPickle, base64
ModuleNotFoundError: No module named 'cPickle'
Error opening python file
/Users/avisinger/Desktop/Keating_lab/masstitr_project/amy/chimera_sessions/mena_homer.py
> open
> /Users/avisinger/Desktop/Keating_lab/masstitr_project/amy/chimera_sessions/mena_homer.pyc
Python code was compiled for a different version of Python
> open
> /Users/avisinger/Desktop/Keating_lab/masstitr_project/amy/chimera_sessions/mena_homer.py
Traceback (most recent call last):
File
"/Users/avisinger/Desktop/Keating_lab/masstitr_project/amy/chimera_sessions/mena_homer.py",
line 1, in <module>
import cPickle, base64
ModuleNotFoundError: No module named 'cPickle'
Error opening python file
/Users/avisinger/Desktop/Keating_lab/masstitr_project/amy/chimera_sessions/mena_homer.py
> open
> /Users/avisinger/Desktop/Keating_lab/masstitr_project/amy/chimera_sessions/mena_homer.py
Traceback (most recent call last):
File
"/Users/avisinger/Desktop/Keating_lab/masstitr_project/amy/chimera_sessions/mena_homer.py",
line 1, in <module>
import cPickle, base64
ModuleNotFoundError: No module named 'cPickle'
Error opening python file
/Users/avisinger/Desktop/Keating_lab/masstitr_project/amy/chimera_sessions/mena_homer.py
> open 5zz9 format mmcif fromDatabase pdb
5zz9 title:
Crystal structure of Homer2 EVH1/Drebrin PPXXF complex [more info...]
Chain information for 5zz9 #1
---
Chain | Description
A B C | Homer protein homolog 2
D E F | Peptide from Drebrin
5zz9 mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
3| author_and_software_defined_assembly
> open
> /Users/avisinger/Desktop/Keating_lab/dTERMen_score_prediction/Mena_EVH1/pdb_files/Mena_Abi1_refine_8_TH_PR.pdb
Summary of feedback from opening
/Users/avisinger/Desktop/Keating_lab/dTERMen_score_prediction/Mena_EVH1/pdb_files/Mena_Abi1_refine_8_TH_PR.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK Date 2020-02-14 Time 17:13:37 EST -0500 (1581718417.48 s)
Ignored bad PDB record found on line 2
REMARK PHENIX refinement
Ignored bad PDB record found on line 4
REMARK ****************** INPUT FILES AND LABELS
******************************
Ignored bad PDB record found on line 5
REMARK Reflections:
Ignored bad PDB record found on line 6
REMARK file name :
/cove/a0/usr1/theresa/projects/MenaAbi1/phenix/Refine_4/Mena-
Abi1_refine_data.mtz
39 messages similar to the above omitted
Chain information for Mena_Abi1_refine_8_TH_PR.pdb #2
---
Chain | Description
A | No description available
B | No description available
> ui tool show Matchmaker
> 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 5zz9, chain C (#1) with Mena_Abi1_refine_8_TH_PR.pdb, chain A (#2),
sequence alignment score = 205.9
RMSD between 77 pruned atom pairs is 1.053 angstroms; (across all 107 pairs:
2.208)
> hide atoms
> show cartoons
> split
Split 5zz9 (#1) into 6 models
Split Mena_Abi1_refine_8_TH_PR.pdb (#2) into 2 models
Chain information for 5zz9 A #1.1
---
Chain | Description
A | No description available
Chain information for 5zz9 B #1.2
---
Chain | Description
B | No description available
Chain information for 5zz9 C #1.3
---
Chain | Description
C | No description available
Chain information for 5zz9 D #1.4
---
Chain | Description
D | No description available
Chain information for 5zz9 E #1.5
---
Chain | Description
E | No description available
Chain information for 5zz9 F #1.6
---
Chain | Description
F | No description available
Chain information for Mena_Abi1_refine_8_TH_PR.pdb A #2.1
---
Chain | Description
A | No description available
Chain information for Mena_Abi1_refine_8_TH_PR.pdb B #2.2
---
Chain | Description
B | No description available
> hide #1.2 models
> hide #1.4 models
> hide #1.1 models
> hide #1.5 models
> ui tool show "Color Actions"
> color maroon
> select #1.3
878 atoms, 889 bonds, 122 residues, 1 model selected
> ~select #1.3
Nothing selected
> select #1.3
878 atoms, 889 bonds, 122 residues, 1 model selected
> color sel goldenrod
> select #1.6
80 atoms, 84 bonds, 12 residues, 1 model selected
> color sel gold
> select #2.2
143 atoms, 151 bonds, 10 residues, 1 model selected
> color sel lime
Alignment identifier is 2.2/B
> select #2.2/B:1000
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2.2/B:1000-1009
143 atoms, 151 bonds, 10 residues, 1 model selected
> select #2.2/B:1001
20 atoms, 20 bonds, 1 residue, 1 model selected
> select #2.2/B:1001-1009
132 atoms, 140 bonds, 9 residues, 1 model selected
> style sel stick
Changed 132 atom styles
> style sel stick
Changed 132 atom styles
> style sel stick
Changed 132 atom styles
> show sel atoms
> select H
901 atoms, 122 residues, 2 models selected
> delete atoms sel
> delete bonds sel
> select #2.2/B:1001
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #2.2/B:1001-1009
67 atoms, 75 bonds, 9 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #2.2/B
Alignment identifier is 2.2/B
> color sel byhetero
> ui tool show "Blast Protein"
> ui tool show "Modeller Comparative"
> select clear
> select clear
> select #2.1
867 atoms, 887 bonds, 112 residues, 1 model selected
> ~select #2.1
Nothing selected
> select #2
942 atoms, 970 bonds, 122 residues, 3 models selected
> ~select #2
Nothing selected
> select #2.2
75 atoms, 83 bonds, 10 residues, 1 model selected
> color sel byhetero
> mlp sel
Map values for surface "Mena_Abi1_refine_8_TH_PR.pdb B_B SES surface": minimum
-18.55, mean -2.144, maximum 21.97
To also show corresponding color key, enter the above mlp command and add key
true
> undo
> undo
> hide sel surfaces
> color sel byhetero
Destroying pre-existing alignment with identifier 2.2/B
Alignment identifier is 2.2/B
> ~select #2.2
1 model selected
> select #2.1
867 atoms, 887 bonds, 112 residues, 1 model selected
> select #1.3
878 atoms, 889 bonds, 122 residues, 1 model selected
> select #2.1
867 atoms, 887 bonds, 112 residues, 1 model selected
> ui tool show "Modeller Comparative"
> select #1.6
80 atoms, 84 bonds, 12 residues, 1 model selected
Alignment identifier is 1.6/F
> select #1.6/F:999
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1.6/F:999-1010
80 atoms, 84 bonds, 12 residues, 1 model selected
> style sel stick
Changed 80 atom styles
> style sel stick
Changed 80 atom styles
> hide sel atoms
> show sel atoms
> color sel byhetero
Color zone shortcut requires 1 displayed atomic model and 1 map, got 4 atomic
models, 0 maps.
Color zone shortcut requires 1 displayed atomic model and 1 map, got 4 atomic
models, 0 maps.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/toolbar/tool.py", line 202, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/toolshed/info.py", line 379, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/toolshed/__init__.py", line 1285, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/shortcuts/__init__.py", line 52, in run_provider
shortcuts.run_provider(session, name)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/shortcuts/shortcuts.py", line 1333, in run_provider
keyboard_shortcuts(session).try_shortcut(name)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/shortcuts/shortcuts.py", line 389, in try_shortcut
self.run_shortcut(keys)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/shortcuts/shortcuts.py", line 407, in run_shortcut
sc.run(self.session, status = self._enabled)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/shortcuts/shortcuts.py", line 326, in run
f(s)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/shortcuts/shortcuts.py", line 869, in hide_dust
for map in maps:
UnboundLocalError: local variable 'maps' referenced before assignment
UnboundLocalError: local variable 'maps' referenced before assignment
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/shortcuts/shortcuts.py", line 869, in hide_dust
for map in maps:
See log for complete Python traceback.
> volume style surface
No volumes specified
> volume style mesh
No volumes specified
> view sel
> ui tool show "Side View"
> view sel
> select clear
> view
> select 2.1
Expected an objects specifier or a keyword
> sel: 2.1
Unknown command: sel: 2.1
> select: 2.1
Unknown command: select: 2.1
> select 2.1
Expected an objects specifier or a keyword
> lighting flat
> lighting shadows true intensity 0.5
> lighting full
> lighting simple
> preset "overall look" publication
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
> select #2.2
75 atoms, 83 bonds, 10 residues, 1 model selected
> view sel
> view sel
> view
> select #1.6/F:1006-1007
17 atoms, 17 bonds, 2 residues, 1 model selected
> select #1.6/F:1006-1007
17 atoms, 17 bonds, 2 residues, 1 model selected
> select #1.6/F:1006
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #1.6/F:1006
11 atoms, 11 bonds, 1 residue, 1 model selected
> view sel
Destroying pre-existing alignment with identifier 1.6/F
Alignment identifier is 1.6/F
> select #2.2
75 atoms, 83 bonds, 10 residues, 1 model selected
Alignment identifier is 2.2/B
> select #2.2/B:1008
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #2.2/B:1008
7 atoms, 7 bonds, 1 residue, 1 model selected
> view sel
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true
> lighting shadows false
> lighting flat
> lighting flat
> lighting flat
> lighting full
> lighting simple
> lighting simple
> select clear
> view
> select #1.6/F:1003-1005
19 atoms, 19 bonds, 3 residues, 1 model selected
> select #1.6/F:1003-1007
36 atoms, 37 bonds, 5 residues, 1 model selected
> view sel
> select #2.1
867 atoms, 887 bonds, 112 residues, 1 model selected
Alignment identifier is 2.1/A
> select #1.3
878 atoms, 889 bonds, 122 residues, 1 model selected
Alignment identifier is 1.3/C
> select #2.1/A:23
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #2.1/A:23
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #1.3/C:93
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #2.1/A:14
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2.1/A:23
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #2.1/A:23
14 atoms, 15 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1.3/C:30
14 atoms, 15 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 14 atom styles
> select #1.3/C:30
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #1.3/C:30
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #1.6/F:999-1007
60 atoms, 63 bonds, 9 residues, 1 model selected
> select #1.6/F:1002-1003
14 atoms, 15 bonds, 2 residues, 1 model selected
> select #1.6/F:999-1003
31 atoms, 33 bonds, 5 residues, 1 model selected
> select #1.3/C:30
14 atoms, 15 bonds, 1 residue, 1 model selected
> view sel
> show sel surfaces
> select #2.1
867 atoms, 887 bonds, 112 residues, 1 model selected
> show sel surfaces
> ui tool show "Color Actions"
> color sel maroon target s
> select clear
> select #2.1
867 atoms, 887 bonds, 112 residues, 3 models selected
> transparency (#!2.1 & sel) 90
> select clear
> select #2.1/A:23@CD1
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select #2.1
867 atoms, 887 bonds, 112 residues, 3 models selected
> select #2
942 atoms, 970 bonds, 122 residues, 5 models selected
> ~select #2
2 models selected
> select #2.1
867 atoms, 887 bonds, 112 residues, 3 models selected
> hide sel surfaces
> show sel surfaces
> select #2.1/A:23@CD1
1 atom, 1 residue, 1 model selected
> select #2.1.1
867 atoms, 112 residues, 3 models selected
> ~select #2.1.1
1 model selected
> select
3905 atoms, 3975 bonds, 540 residues, 12 models selected
> surface hidePatches (#1.6#!1.3#!2.1-2 & sel)
> ~select #2.1
3038 atoms, 3088 bonds, 428 residues, 12 models selected
> select #2.1
867 atoms, 887 bonds, 112 residues, 3 models selected
> show sel surfaces
> select clear
> select #2.1/A:23@N
1 atom, 1 residue, 1 model selected
> hide #!1.3 models
> hide #1.6 models
> select #2.1/A:23
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #2.1/A:23
14 atoms, 15 bonds, 1 residue, 1 model selected
> view sel
> view sel
> view sel
> view sel
> view sel
> view
> view sel
> select #2.1
867 atoms, 887 bonds, 112 residues, 1 model selected
> ~select #2.1
1 model selected
> select #2.1/A:23
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #2.1/A:23
14 atoms, 15 bonds, 1 residue, 1 model selected
> view sel
> select #2.1/A:23
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #2.1/A:23
14 atoms, 15 bonds, 1 residue, 1 model selected
> color sel indian red target s
> color sel indian red target as
> color sel salmon target as
> color sel dark salmon target as
> color sel dark turquoise target as
> color sel maroon target s
> select clear
> select #2.2/B:1000-1004
40 atoms, 43 bonds, 5 residues, 1 model selected
> select #2.2/B:1000-1009
75 atoms, 83 bonds, 10 residues, 1 model selected
> color sel lime target as
> color sel lime target acs
> color sel chartreuse target acs
> color sel lawn green target acs
> color sel byhetero
> color sel purple target acs
> color sel midnight blue target acs
> color sel byhetero
> color sel sky blue target acs
> color sel light sky blue target acs
> color sel aquamarine target acs
> color sel byhetero
> select #2.1/A:23
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #2.1/A:23
14 atoms, 15 bonds, 1 residue, 1 model selected
> color sel deep pink target acs
> color sel maroon target ac
> color sel maroon target acs
> color sel orchid target ac
> color sel deep pink target ac
> color sel magenta target ac
> color sel deep pink target ac
> color sel mint cream target ac
> color sel ghost white target ac
> color sel indigo target ac
> color sel royal blue target ac
> color sel tomato target ac
> color sel medium slate blue target ac
> color sel slate blue target ac
> select clear
> select #2.1/A:23
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #2.1/A:23
14 atoms, 15 bonds, 1 residue, 1 model selected
> view sel
> select clear
> select
3905 atoms, 3975 bonds, 540 residues, 10 models selected
> surface hidePatches (#!2.1-2 & sel)
> select clear
> select #2.1/A:23
14 atoms, 15 bonds, 1 residue, 1 model selected
> color sel maroon target c
> select clear
> select #2.1/A:23
14 atoms, 15 bonds, 1 residue, 1 model selected
> view sel
> select clear
> hide #!2 models
> show #!1.3 models
> show #1.6 models
> select #1.3/C:30
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #1.3/C:30
14 atoms, 15 bonds, 1 residue, 1 model selected
> color sel dark turquoise target c
> color sel goldenrod target a
> color sel goldenrod target ac
> color sel dodger blue target a
> color sel aquamarine target a
> color sel aquamarine target a
> select clear
> select #2.2
75 atoms, 83 bonds, 10 residues, 1 model selected
> ~select #2.2
1 model selected
> select #1.3
878 atoms, 889 bonds, 122 residues, 1 model selected
> ~select #1.3
1 model selected
> select #2.2
75 atoms, 83 bonds, 10 residues, 1 model selected
> ~select #2.2
1 model selected
> show #!2 models
> select #2.2
75 atoms, 83 bonds, 10 residues, 1 model selected
> ~select #2.2
1 model selected
> select #2.1/A:23@CD1
1 atom, 1 residue, 1 model selected
> select #2.1/A:22
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> select #1.3/C:30
14 atoms, 15 bonds, 1 residue, 1 model selected
> color sel medium slate blue target a
> color sel slate blue target a
> select clear
> hide #!2 models
> hide #!2.2 models
> select #1.3/C:30
14 atoms, 15 bonds, 1 residue, 1 model selected
> view sel
> show #!2.2 models
> select #1.3/C:30
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #1.3/C:30
14 atoms, 15 bonds, 1 residue, 1 model selected
> view sel
> select #2.1/A:23-24
21 atoms, 22 bonds, 2 residues, 1 model selected
> select #2.1/A:23-24
21 atoms, 22 bonds, 2 residues, 1 model selected
> select #2.1/A:23
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #2.1/A:23
14 atoms, 15 bonds, 1 residue, 1 model selected
> view sel
> select #1.3/C:30
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #1.3/C:30
14 atoms, 15 bonds, 1 residue, 1 model selected
> view sel
> select #2.1/A:23
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #2.1/A:23
14 atoms, 15 bonds, 1 residue, 1 model selected
> view sel
> hide #!1.3 models
> hide #1.6 models
> select clear
> select #2.1/A:22
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2.1/A:23
14 atoms, 15 bonds, 1 residue, 1 model selected
> label (#!2.1 & sel) attribute name
> ~label (#!2.1 & sel) residues
> select clear
> select #2.2
75 atoms, 83 bonds, 10 residues, 1 model selected
> color (#!2.2 & sel) byhetero
> select clear
> select clear
> save /Users/avisinger/Desktop/Mena_W.tif width 1337 height 858 supersample 3
> transparentBackground true
> show #!1.3 models
> show #1.6 models
> hide #!2 models
> save /Users/avisinger/Desktop/Homer_W.tif width 1337 height 858 supersample
> 3 transparentBackground true
> save /Users/avisinger/Desktop/mena_Vs_homer.cxs
——— End of log from Wed May 12 14:02:08 2021 ———
opened ChimeraX session
> {color sequential chains palette spectral-5} - Color sequentially by
> selected pallet.
Unknown command: {color sequential chains palette spectral-5} - Color
sequentially by selected pallet.
> color sequential chains palette spectral-5
> color sequential chains spectral-5
Expected a keyword
> color sequential chains palette spectral-5
> show #!2 models
> color sequential palette spectral-5
> view
> lighting flat
> lighting shadows true intensity 0.5
> select #1.3
878 atoms, 889 bonds, 122 residues, 1 model selected
> ~select #1.3
1 model selected
> select #1.6
80 atoms, 84 bonds, 12 residues, 1 model selected
> ui tool show "Color Actions"
> color sel midnight blue
> select #2
942 atoms, 970 bonds, 122 residues, 3 models selected
> ~select #2
2 models selected
> select #2.2/B:1000
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2.2/B:1000-1009
75 atoms, 83 bonds, 10 residues, 1 model selected
> color sel midnight blue
> color (#!2.2 & sel) byelement
> select #1.6
80 atoms, 84 bonds, 12 residues, 1 model selected
> color sel byelement
> select clear
> hide #!2 models
Alignment identifier is 1
Alignment identifier is 1.3/C
Alignment identifier is 1.4/D
Alignment identifier is 1.5/E
Destroying pre-existing alignment with identifier 1.6/F
Alignment identifier is 1.6/F
Alignment identifier is 2.1/A
Destroying pre-existing alignment with identifier 2.2/B
Alignment identifier is 2.2/B
Alignment identifier is 1
Alignment identifier is 1.3/C
Alignment identifier is 1.4/D
Alignment identifier is 1.5/E
Alignment identifier is 1.6/F
Alignment identifier is 2.1/A
Alignment identifier is 2.2/B
> undo
> select #2
942 atoms, 970 bonds, 122 residues, 3 models selected
> ~select #2
2 models selected
> hide #!2 models
> select #1.6
80 atoms, 84 bonds, 12 residues, 1 model selected
> ~select #1.6
Nothing selected
> select #1.3
878 atoms, 889 bonds, 122 residues, 1 model selected
Alignment identifier is 1.3/C
> select #1.6
80 atoms, 84 bonds, 12 residues, 1 model selected
Alignment identifier is 1.6/F
> ~select #1.6
Nothing selected
> select #2.1
867 atoms, 887 bonds, 112 residues, 1 model selected
> select #2.2
75 atoms, 83 bonds, 10 residues, 1 model selected
> select #2.1
867 atoms, 887 bonds, 112 residues, 1 model selected
Alignment identifier is 2.1/A
> select #2.2
75 atoms, 83 bonds, 10 residues, 1 model selected
Alignment identifier is 2.2/B
> select #1.6/F:999
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1.6/F:999
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1.3/C:39
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1.3/C:39
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1.3/C:68
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1.3/C:68
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> show sel atoms
> hide sel atoms
> select #1.3/C:72
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1.3/C:72
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 7 atom styles
> style sel sphere
Changed 7 atom styles
> hide sel atoms
> select #1.3
878 atoms, 889 bonds, 122 residues, 1 model selected
> show sel surfaces
> select clear
> select #2.2
75 atoms, 83 bonds, 10 residues, 1 model selected
> show #1.6#!1.3 surfaces
> show #!1.3,6 surfaces
> hide #!1.3,6 surfaces
> ~select #2.2
1 model selected
> select #2.1
867 atoms, 887 bonds, 112 residues, 1 model selected
> show #!1.3,6 surfaces
> select #2.2/B:1000
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2.2/B:1000-1009
75 atoms, 83 bonds, 10 residues, 1 model selected
> hide #!1.3,6 surfaces
> select #2.2/B:1000
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2.2/B:1000-1009
75 atoms, 83 bonds, 10 residues, 1 model selected
> show #!1.3,6 surfaces
> select #2
942 atoms, 970 bonds, 122 residues, 3 models selected
> ~select #2
2 models selected
> select #2.1
867 atoms, 887 bonds, 112 residues, 1 model selected
> hide #!1.3,6 surfaces
> ~select #2.1
1 model selected
> select #2.1/A:113
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #2.1/A:2-113
867 atoms, 887 bonds, 112 residues, 1 model selected
> show #!1.3,6 surfaces
> hide #!1.3,6 surfaces
> select #2.1/A:113
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #2.1/A:2-113
867 atoms, 887 bonds, 112 residues, 1 model selected
> surface #1.3,6#!1
> select #2.2/B:1000
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2.2/B:1000-1009
75 atoms, 83 bonds, 10 residues, 1 model selected
> surface hidePatches #1.3,6#!1
> select #1.6
80 atoms, 84 bonds, 12 residues, 1 model selected
> ~select #1.6
1 model selected
> select #1.3
878 atoms, 889 bonds, 122 residues, 1 model selected
> show sel surfaces
> select #1.3/C:22@CD1
1 atom, 1 residue, 1 model selected
> select #1.6/F:999
5 atoms, 4 bonds, 1 residue, 1 model selected
> view sel
> view
> select clear
> select #2.1
867 atoms, 887 bonds, 112 residues, 1 model selected
> select #2.2
75 atoms, 83 bonds, 10 residues, 1 model selected
> select #2.1
867 atoms, 887 bonds, 112 residues, 1 model selected
> ~select #2.1
1 model selected
> select #2
942 atoms, 970 bonds, 122 residues, 3 models selected
> ~select #2
2 models selected
> show #!2 models
> hide #!2.1 models
> hide #!2.2 models
> hide #!2 models
> hide #!1.3,6 surfaces
> show #!2 models
> hide #!2 models
> show #!2.1 models
> show #!2.2 models
> hide #!2.2 models
> hide #!2.1 models
> hide #!2 models
> show #!2.1 models
> hide #!2.1 models
> show #!2.2 models
> show #!2.1 models
> hide #!2.2 models
> show #!1.3,6#!2.1 surfaces
> hide #!2.1 models
> show #!2.1 models
> show #!2.2 models
> hide #!2 models
> show #!2 models
> hide #!1.3,6#!2.1-2 surfaces
> split
Did not split 5zz9 A, has only one piece
Did not split 5zz9 B, has only one piece
Did not split 5zz9 C, has only one piece
Did not split 5zz9 D, has only one piece
Did not split 5zz9 E, has only one piece
Did not split 5zz9 F, has only one piece
Did not split Mena_Abi1_refine_8_TH_PR.pdb A, has only one piece
Did not split Mena_Abi1_refine_8_TH_PR.pdb B, has only one piece
> select 1
Expected an objects specifier or a keyword
> select 1.1:1
Expected an objects specifier or a keyword
> select 1.6:1
Expected an objects specifier or a keyword
> select 1:1.6
Expected an objects specifier or a keyword
> hide #!1 models
> select #2.1/A:2
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2.1/A:2-113
867 atoms, 887 bonds, 112 residues, 1 model selected
> surface (#!2.1 & sel)
> lighting full
> select clear
> save /Users/avisinger/Desktop/mena_F.tif width 1338 height 858 supersample 3
> save /Users/avisinger/Desktop/mena_fpocket.tif width 1338 height 858
> supersample 3 transparentBackground true
> hide #!2 models
> show #!1 models
> select #1.3
878 atoms, 889 bonds, 122 residues, 1 model selected
> show sel surfaces
> select clear
> save /Users/avisinger/Desktop/homer_fpocket.tif width 1338 height 858
> supersample 3 transparentBackground true
> hide #!1 models
> show #!2 models
> select #2.1/A:81@NH2
1 atom, 1 residue, 1 model selected
> select #2.1/A:81
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2.1/A:81
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel surfaces
> style sel sphere
Changed 11 atom styles
> style sel sphere
Changed 11 atom styles
> show sel atoms
> style sel sphere
Changed 11 atom styles
> color (#!2.1 & sel) byelement
> select #2.1/A:86@CG1
1 atom, 1 residue, 1 model selected
> select clear
> save /Users/avisinger/Desktop/mena_fpocket2.tif width 1338 height 858
> supersample 3 transparentBackground true
> hide #!2 models
> select #1.3
878 atoms, 889 bonds, 122 residues, 1 model selected
> select #1.6
80 atoms, 84 bonds, 12 residues, 1 model selected
> show #!1 models
> select #1.3
878 atoms, 889 bonds, 122 residues, 1 model selected
> select #1.3/C:22@CG2
1 atom, 1 residue, 1 model selected
> select clear
> select #1.3/C:88
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1.3/C:88
5 atoms, 4 bonds, 1 residue, 1 model selected
> hide sel surfaces
> hide sel surfaces
> hide sel surfaces
> show sel atoms
> hide sel atoms
> show sel surfaces
> hide #!1.3 models
> show #!1.3 models
> select #1.6
80 atoms, 84 bonds, 12 residues, 1 model selected
> ~select #1.6
1 model selected
> select #1.3/C:88
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1.3/C:88
5 atoms, 4 bonds, 1 residue, 1 model selected
> hide sel surfaces
> surface hidePatches (#!1.3 & sel)
> select #1.3
878 atoms, 889 bonds, 122 residues, 1 model selected
> ~select #1.3
1 model selected
> select #1.6
80 atoms, 84 bonds, 12 residues, 1 model selected
> ~select #1.6
1 model selected
> select #1.3
878 atoms, 889 bonds, 122 residues, 1 model selected
> select #1
2963 atoms, 3005 bonds, 418 residues, 7 models selected
> ~select #1
2 models selected
> select #1.3
878 atoms, 889 bonds, 122 residues, 1 model selected
> hide sel surfaces
> select #1.3/C:88
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1.3/C:88
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel atoms
> show sel atoms
> undo
> undo
> undo
> undo
> undo
> lighting full
> lighting flat
> lighting full
> lighting shadows false
> lighting shadows true
> select #1.3/C:84
5 atoms, 4 bonds, 1 residue, 1 model selected
> show (#!1.3 & sel) target ab
> style sel stick
Changed 5 atom styles
> hide #!1.3 models
> show #!1.3 models
> select #1.3
878 atoms, 889 bonds, 122 residues, 1 model selected
> ~select #1.3
1 model selected
> hide #!1.3 models
> show #!1.3 models
> select #1.3
878 atoms, 889 bonds, 122 residues, 1 model selected
> show sel surfaces
> hide #!1 models
> show #!1 models
> select #1
2963 atoms, 3005 bonds, 418 residues, 7 models selected
> ~select #1
2 models selected
> hide #!1 models
> hide #!1.6 models
> show #!1.6 models
> show #!2 models
> hide #!1 models
> save /Users/avisinger/Desktop/mena_fpocket2.tif width 1338 height 858
> supersample 3 transparentBackground true
> save /Users/avisinger/Desktop/mena_fpocket3.tif width 1338 height 858
> supersample 3 transparentBackground true
> select #2.1/A:81
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2.1/A:81
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel surfaces
> color sequential palette spectral-5
> select #2.2
75 atoms, 83 bonds, 10 residues, 1 model selected
> ui tool show "Color Actions"
> color sel midnight blue
> color (#!2.2 & sel) byelement
> select clear
> save /Users/avisinger/Desktop/mena_fpocket3.tif width 1338 height 858
> supersample 3 transparentBackground true
> hide #!2 models
> select #1.6
80 atoms, 84 bonds, 12 residues, 1 model selected
> ~select #1.6
1 model selected
> show #!1 models
> select #1.6
80 atoms, 84 bonds, 12 residues, 1 model selected
> ui tool show "Color Actions"
> color sel midnight blue
> color (#!1.6 & sel) byelement
> select clear
> save /Users/avisinger/Desktop/homer_fpocket2.tif width 1338 height 858
> supersample 3 transparentBackground true
> select #1.3/C:88
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1.3/C:88
5 atoms, 4 bonds, 1 residue, 1 model selected
> hide sel surfaces
> hide sel surfaces
> show sel atoms
> select #1.3
878 atoms, 889 bonds, 122 residues, 1 model selected
> ~select #1.3
1 model selected
> select #1.3
878 atoms, 889 bonds, 122 residues, 1 model selected
> hide sel surfaces
> select #1.3/C:84@CA
1 atom, 1 residue, 1 model selected
> style sel sphere
Changed 1 atom style
> select #1.3
878 atoms, 889 bonds, 122 residues, 1 model selected
> ~select #1.3
1 model selected
> select #1.3
878 atoms, 889 bonds, 122 residues, 1 model selected
> show sel surfaces
> select clear
> select #1.3/C:88
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1.3/C:88
5 atoms, 4 bonds, 1 residue, 1 model selected
> hide sel surfaces
> hide sel surfaces
> color (#!1.3 & sel) byelement
> select #1.3/C:88
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1.3/C:88
5 atoms, 4 bonds, 1 residue, 1 model selected
> surface hidePatches (#!1.3 & sel)
> select #1.3
878 atoms, 889 bonds, 122 residues, 1 model selected
> select #1.3/C:88
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1.3/C:88
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1.3/C:88
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1.3/C:88-95
54 atoms, 54 bonds, 8 residues, 1 model selected
> select #1.3/C:89
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1.3/C:88-89
13 atoms, 12 bonds, 2 residues, 1 model selected
> hide sel surfaces
> hide sel surfaces
> select #1.3/C:86-87
11 atoms, 10 bonds, 2 residues, 1 model selected
> select #1.3/C:86-94
61 atoms, 61 bonds, 9 residues, 1 model selected
> hide sel surfaces
> hide sel surfaces
> select #1.3/C:10-22,30-32,38-45,50-57,60-67,73-75,80-85,90-95
450 atoms, 458 bonds, 55 residues, 1 model selected
> select #1.3/C:89
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1.3/C:89-95
49 atoms, 49 bonds, 7 residues, 1 model selected
> show sel surfaces
> select #1.3/C:87-88
10 atoms, 9 bonds, 2 residues, 1 model selected
> select #1.3/C:87-88
10 atoms, 9 bonds, 2 residues, 1 model selected
> show sel surfaces
> show sel surfaces
> select #1.3/C:88
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1.3/C:88
5 atoms, 4 bonds, 1 residue, 1 model selected
> hide sel surfaces
> select #1.3/C:87
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1.3/C:87-89
18 atoms, 17 bonds, 3 residues, 1 model selected
> hide sel surfaces
> hide sel surfaces
> hide sel surfaces
> select #1.3/C:90
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1.3/C:90-95
41 atoms, 41 bonds, 6 residues, 1 model selected
> select #1.3/C:89
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1.3/C:86-89
24 atoms, 23 bonds, 4 residues, 1 model selected
> select #1.3/C:84-85
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #1.3/C:31-85
417 atoms, 426 bonds, 55 residues, 1 model selected
> select #1.3/C:85
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1.3/C:84-85
13 atoms, 12 bonds, 2 residues, 1 model selected
> hide sel surfaces
> select #1.3/C:37@O
1 atom, 1 residue, 1 model selected
> select #1.3/C:57@OD1
1 atom, 1 residue, 1 model selected
> select clear
> save /Users/avisinger/Desktop/homer_fpocket3.tif width 1338 height 858
> supersample 3 transparentBackground true
> select #1.3/C:84@CA
1 atom, 1 residue, 1 model selected
> color (#!1.3 & sel) byelement
> select clear
> save /Users/avisinger/Desktop/homer_fpocket3.tif width 1338 height 858
> supersample 3 transparentBackground true
> select #1.3
878 atoms, 889 bonds, 122 residues, 1 model selected
> show sel surfaces
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> ui tool show "Blast Protein"
Window position QRect(1365,-189 54x38) outside any known screen, using primary
screen
Window position QRect(1150,-189 67x145) outside any known screen, using
primary screen
Window position QRect(1154,-161 100x163) outside any known screen, using
primary screen
> ui tool show "Modeller Comparative"
Window position QRect(676,-532 100x30) outside any known screen, using primary
screen
Back buffer dpr of 1 doesn't match <_NSViewBackingLayer: 0x6000002c9920>
contents scale of 2 - updating layer to match.
Back buffer dpr of 2 doesn't match <_NSViewBackingLayer: 0x6000002c9920>
contents scale of 1 - updating layer to match.
> modeller comparative 1.3/C:1 multichain true numModels 5 fast false
> hetPreserve false hydrogens false waterPreserve false
Window position QRect(676,-532 100x30) outside any known screen, using primary
screen
No Modeller license key provided. Get a license key by registering at the
Modeller web site.
> ui tool show Matchmaker
Window position QRect(676,-532 100x30) outside any known screen, using primary
screen
Back buffer dpr of 1 doesn't match <_NSViewBackingLayer: 0x6000005276f0>
contents scale of 2 - updating layer to match.
Back buffer dpr of 2 doesn't match <_NSViewBackingLayer: 0x6000005276f0>
contents scale of 1 - updating layer to match.
> matchmaker #!1.3 to #2.1
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 Mena_Abi1_refine_8_TH_PR.pdb A, chain A (#2.1) with 5zz9 C, chain C
(#1.3), sequence alignment score = 201.1
RMSD between 77 pruned atom pairs is 1.053 angstroms; (across all 107 pairs:
2.208)
Window position QRect(676,-532 100x30) outside any known screen, using primary
screen
> ui tool show Matchmaker
Window position QRect(676,-532 100x30) outside any known screen, using primary
screen
> matchmaker #!1.3 to #2.1 showAlignment true
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 Mena_Abi1_refine_8_TH_PR.pdb A, chain A (#2.1) with 5zz9 C, chain C
(#1.3), sequence alignment score = 201.1
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: 5zz9 C #1.3/C,
Mena_Abi1_refine_8_TH_PR.pdb A #2.1/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 77 pruned atom pairs is 1.053 angstroms; (across all 107 pairs:
2.208)
Window position QRect(676,-548 100x62) outside any known screen, using primary
screen
Back buffer dpr of 1 doesn't match <_NSViewBackingLayer: 0x6000002d57d0>
contents scale of 2 - updating layer to match.
Back buffer dpr of 2 doesn't match <_NSViewBackingLayer: 0x6000002d57d0>
contents scale of 1 - updating layer to match.
> sequence header consensus show
Showing consensus header ("seq_consensus" residue attribute) for alignment 1
> sequence header conservation show
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
> sequence header consensus hide
Hiding consensus header for alignment 1
> sequence header rmsd hide
Hiding rmsd header for alignment 1
> select #1.3/C:27 #2.1/A:20
13 atoms, 11 bonds, 2 residues, 2 models selected
> select #1.3/C:28 #2.1/A:21
14 atoms, 12 bonds, 2 residues, 2 models selected
> select #2.1/A:3-17,22-26,31-40,45-50,59-65,67-74,76-82,86-91,93,97,100-110
> #1.3/C:9-23,29-33,36-45,50-55,62-68,70-77,79-85,91-96,98,102,105-115
1242 atoms, 1259 bonds, 154 residues, 2 models selected
Window position QRect(396,-747 659x459) outside any known screen, using
primary screen
> save
> /Users/avisinger/Desktop/Keating_lab/masstitr_project/paralog_comparison_pdb/chimera_sessions/chimeraX/mena_vs_homer_210527.cxs
> hide sel & #!1.3 surfaces
> show sel & #!1.3 surfaces
> hide #!1 models
> show #!1 models
> select #1
2963 atoms, 3005 bonds, 418 residues, 7 models selected
> ~select #1
2 models selected
> select #1
2963 atoms, 3005 bonds, 418 residues, 7 models selected
> ~select #1
2 models selected
> select #1.3
878 atoms, 889 bonds, 122 residues, 1 model selected
> select #1.6
80 atoms, 84 bonds, 12 residues, 1 model selected
> select #2.1
867 atoms, 887 bonds, 112 residues, 1 model selected
> select #2.2
75 atoms, 83 bonds, 10 residues, 1 model selected
> hide #!1.3,6 surfaces
> hide #!1.3,6 atoms
> select #1.6
80 atoms, 84 bonds, 12 residues, 1 model selected
> show sel atoms
> select #1
2963 atoms, 3005 bonds, 418 residues, 7 models selected
> ~select #1
2 models selected
> hide #!1 models
> show #!2 models
> select #2
942 atoms, 970 bonds, 122 residues, 3 models selected
> hide sel surfaces
> ~select #2.1
75 atoms, 83 bonds, 10 residues, 4 models selected
> ~select #2.2
2 models selected
> select #2.1
867 atoms, 887 bonds, 112 residues, 1 model selected
> hide sel atoms
> select clear
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
Window position QRect(676,-532 100x30) outside any known screen, using primary
screen
> color byattribute seq_conservation protein palette cyanmaroon range -1.4,1.4
> noValueColor yellow
3874 atoms, 509 residues, 4 surfaces, atom seq_conservation range -0.679 to
100
> select #1.3/C:25 #2.1/A:18
14 atoms, 12 bonds, 2 residues, 2 models selected
> select #1.3/C:29 #2.1/A:22
17 atoms, 15 bonds, 2 residues, 2 models selected
> select #1.3/C:30 #2.1/A:23
28 atoms, 30 bonds, 2 residues, 2 models selected
> select #1.3/C:32 #2.1/A:25
14 atoms, 14 bonds, 2 residues, 2 models selected
> select #2.1/A:27
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #2.1/A:27-28
8 atoms, 7 bonds, 2 residues, 1 model selected
> select #2.1
867 atoms, 887 bonds, 112 residues, 1 model selected
> ~select #2.1
1 model selected
> select #2.2
75 atoms, 83 bonds, 10 residues, 1 model selected
> ui tool show "Color Actions"
> color sel midnight blue
> color sel byelement
> select clear
Window position QRect(396,-747 659x459) outside any known screen, using
primary screen
> save
> /Users/avisinger/Desktop/Keating_lab/masstitr_project/paralog_comparison_pdb/chimera_sessions/chimeraX/mena_vs_homer_conservation_210527.cxs
> select #1.3
878 atoms, 889 bonds, 122 residues, 1 model selected
> ~select #1.3
1 model selected
> show #!1 models
> hide #!2 models
> select #1.6
80 atoms, 84 bonds, 12 residues, 1 model selected
> color sel midnight blue
> color sel byelement
> select clear
Window position QRect(396,-747 659x459) outside any known screen, using
primary screen
> save
> /Users/avisinger/Desktop/Keating_lab/masstitr_project/paralog_comparison_pdb/chimera_sessions/chimeraX/mena_vs_homer_conservation_210527.cxs
——— End of log from Thu May 27 14:25:09 2021 ———
opened ChimeraX session
> close session
> open
> /Users/avisinger/Desktop/Keating_lab/dTERMen_score_prediction/Mena_EVH1/pdb_files/Mena_Abi1_refine_8_TH_PR.pdb
> format pdb
Summary of feedback from opening
/Users/avisinger/Desktop/Keating_lab/dTERMen_score_prediction/Mena_EVH1/pdb_files/Mena_Abi1_refine_8_TH_PR.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK Date 2020-02-14 Time 17:13:37 EST -0500 (1581718417.48 s)
Ignored bad PDB record found on line 2
REMARK PHENIX refinement
Ignored bad PDB record found on line 4
REMARK ****************** INPUT FILES AND LABELS
******************************
Ignored bad PDB record found on line 5
REMARK Reflections:
Ignored bad PDB record found on line 6
REMARK file name :
/cove/a0/usr1/theresa/projects/MenaAbi1/phenix/Refine_4/Mena-
Abi1_refine_data.mtz
39 messages similar to the above omitted
Chain information for Mena_Abi1_refine_8_TH_PR.pdb #1
---
Chain | Description
A | No description available
B | No description available
> open 5zz9
5zz9 title:
Crystal structure of Homer2 EVH1/Drebrin PPXXF complex [more info...]
Chain information for 5zz9 #2
---
Chain | Description
A B C | Homer protein homolog 2
D E F | Peptide from Drebrin
5zz9 mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
3| author_and_software_defined_assembly
> select #2
2963 atoms, 3005 bonds, 418 residues, 1 model selected
> hide sel atoms
> show sel cartoons
Alignment identifier is 1
Alignment identifier is 2
> select #2/E:993
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/D:997-1005/E:993-1005/F:999-1005
201 atoms, 208 bonds, 29 residues, 1 model selected
> select #2/E:993
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/D:997-1011/E:993-1011/F:999-1010
330 atoms, 343 bonds, 46 residues, 1 model selected
> style sel stick
Changed 330 atom styles
> style sel stick
Changed 330 atom styles
> show sel atoms
> split
Split Mena_Abi1_refine_8_TH_PR.pdb (#1) into 2 models
Split 5zz9 (#2) into 6 models
Chain information for Mena_Abi1_refine_8_TH_PR.pdb A #1.1
---
Chain | Description
A | No description available
Chain information for Mena_Abi1_refine_8_TH_PR.pdb B #1.2
---
Chain | Description
B | No description available
Chain information for 5zz9 A #2.1
---
Chain | Description
A | No description available
Chain information for 5zz9 B #2.2
---
Chain | Description
B | No description available
Chain information for 5zz9 C #2.3
---
Chain | Description
C | No description available
Chain information for 5zz9 D #2.4
---
Chain | Description
D | No description available
Chain information for 5zz9 E #2.5
---
Chain | Description
E | No description available
Chain information for 5zz9 F #2.6
---
Chain | Description
F | No description available
> select #2.1
877 atoms, 888 bonds, 123 residues, 1 model selected
> select #2.5
154 atoms, 157 bonds, 21 residues, 1 model selected
> select #2.1
877 atoms, 888 bonds, 123 residues, 1 model selected
> select #2.2
875 atoms, 885 bonds, 124 residues, 1 model selected
> select #2.1
877 atoms, 888 bonds, 123 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> undo
Undo failed, probably because structures have been modified.
> close session
> open
> /Users/avisinger/Desktop/Keating_lab/dTERMen_score_prediction/Mena_EVH1/pdb_files/Mena_Abi1_refine_8_TH_PR.pdb
> format pdb
Summary of feedback from opening
/Users/avisinger/Desktop/Keating_lab/dTERMen_score_prediction/Mena_EVH1/pdb_files/Mena_Abi1_refine_8_TH_PR.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK Date 2020-02-14 Time 17:13:37 EST -0500 (1581718417.48 s)
Ignored bad PDB record found on line 2
REMARK PHENIX refinement
Ignored bad PDB record found on line 4
REMARK ****************** INPUT FILES AND LABELS
******************************
Ignored bad PDB record found on line 5
REMARK Reflections:
Ignored bad PDB record found on line 6
REMARK file name :
/cove/a0/usr1/theresa/projects/MenaAbi1/phenix/Refine_4/Mena-
Abi1_refine_data.mtz
39 messages similar to the above omitted
Chain information for Mena_Abi1_refine_8_TH_PR.pdb #1
---
Chain | Description
A | No description available
B | No description available
> open 5zz9
5zz9 title:
Crystal structure of Homer2 EVH1/Drebrin PPXXF complex [more info...]
Chain information for 5zz9 #2
---
Chain | Description
A B C | Homer protein homolog 2
D E F | Peptide from Drebrin
5zz9 mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
3| author_and_software_defined_assembly
> split
Split Mena_Abi1_refine_8_TH_PR.pdb (#1) into 2 models
Split 5zz9 (#2) into 6 models
Chain information for Mena_Abi1_refine_8_TH_PR.pdb A #1.1
---
Chain | Description
A | No description available
Chain information for Mena_Abi1_refine_8_TH_PR.pdb B #1.2
---
Chain | Description
B | No description available
Chain information for 5zz9 A #2.1
---
Chain | Description
A | No description available
Chain information for 5zz9 B #2.2
---
Chain | Description
B | No description available
Chain information for 5zz9 C #2.3
---
Chain | Description
C | No description available
Chain information for 5zz9 D #2.4
---
Chain | Description
D | No description available
Chain information for 5zz9 E #2.5
---
Chain | Description
E | No description available
Chain information for 5zz9 F #2.6
---
Chain | Description
F | No description available
> delete atoms
> delete bonds
> close session
> open
> /Users/avisinger/Desktop/Keating_lab/dTERMen_score_prediction/Mena_EVH1/pdb_files/Mena_Abi1_refine_8_TH_PR.pdb
> format pdb
Summary of feedback from opening
/Users/avisinger/Desktop/Keating_lab/dTERMen_score_prediction/Mena_EVH1/pdb_files/Mena_Abi1_refine_8_TH_PR.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK Date 2020-02-14 Time 17:13:37 EST -0500 (1581718417.48 s)
Ignored bad PDB record found on line 2
REMARK PHENIX refinement
Ignored bad PDB record found on line 4
REMARK ****************** INPUT FILES AND LABELS
******************************
Ignored bad PDB record found on line 5
REMARK Reflections:
Ignored bad PDB record found on line 6
REMARK file name :
/cove/a0/usr1/theresa/projects/MenaAbi1/phenix/Refine_4/Mena-
Abi1_refine_data.mtz
39 messages similar to the above omitted
Chain information for Mena_Abi1_refine_8_TH_PR.pdb #1
---
Chain | Description
A | No description available
B | No description available
> open 5zz9
5zz9 title:
Crystal structure of Homer2 EVH1/Drebrin PPXXF complex [more info...]
Chain information for 5zz9 #2
---
Chain | Description
A B C | Homer protein homolog 2
D E F | Peptide from Drebrin
5zz9 mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
3| author_and_software_defined_assembly
> split
Split Mena_Abi1_refine_8_TH_PR.pdb (#1) into 2 models
Split 5zz9 (#2) into 6 models
Chain information for Mena_Abi1_refine_8_TH_PR.pdb A #1.1
---
Chain | Description
A | No description available
Chain information for Mena_Abi1_refine_8_TH_PR.pdb B #1.2
---
Chain | Description
B | No description available
Chain information for 5zz9 A #2.1
---
Chain | Description
A | No description available
Chain information for 5zz9 B #2.2
---
Chain | Description
B | No description available
Chain information for 5zz9 C #2.3
---
Chain | Description
C | No description available
Chain information for 5zz9 D #2.4
---
Chain | Description
D | No description available
Chain information for 5zz9 E #2.5
---
Chain | Description
E | No description available
Chain information for 5zz9 F #2.6
---
Chain | Description
F | No description available
> select #2.2
875 atoms, 885 bonds, 124 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #2.3
878 atoms, 889 bonds, 122 residues, 1 model selected
> select #2.4
99 atoms, 102 bonds, 16 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #2.3
878 atoms, 889 bonds, 122 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #2.6
80 atoms, 84 bonds, 12 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> show cartoons
> hide atoms
> ui tool show Matchmaker
> matchmaker #2.1 to #1.1
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 Mena_Abi1_refine_8_TH_PR.pdb A, chain A (#1.1) with 5zz9 A, chain A
(#2.1), sequence alignment score = 204.7
RMSD between 83 pruned atom pairs is 1.130 angstroms; (across all 108 pairs:
2.185)
> close session
> open
> /Users/avisinger/Desktop/Keating_lab/dTERMen_score_prediction/Mena_EVH1/pdb_files/Mena_Abi1_refine_8_TH_PR.pdb
> format pdb
Summary of feedback from opening
/Users/avisinger/Desktop/Keating_lab/dTERMen_score_prediction/Mena_EVH1/pdb_files/Mena_Abi1_refine_8_TH_PR.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK Date 2020-02-14 Time 17:13:37 EST -0500 (1581718417.48 s)
Ignored bad PDB record found on line 2
REMARK PHENIX refinement
Ignored bad PDB record found on line 4
REMARK ****************** INPUT FILES AND LABELS
******************************
Ignored bad PDB record found on line 5
REMARK Reflections:
Ignored bad PDB record found on line 6
REMARK file name :
/cove/a0/usr1/theresa/projects/MenaAbi1/phenix/Refine_4/Mena-
Abi1_refine_data.mtz
39 messages similar to the above omitted
Chain information for Mena_Abi1_refine_8_TH_PR.pdb #1
---
Chain | Description
A | No description available
B | No description available
> open 5zz9
5zz9 title:
Crystal structure of Homer2 EVH1/Drebrin PPXXF complex [more info...]
Chain information for 5zz9 #2
---
Chain | Description
A B C | Homer protein homolog 2
D E F | Peptide from Drebrin
5zz9 mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
3| author_and_software_defined_assembly
> show cartoons
> hide atoms
> select 5zz9
Expected an objects specifier or a keyword
> select 5zz9
Expected an objects specifier or a keyword
> select 1
Expected an objects specifier or a keyword
> select #1
1843 atoms, 1871 bonds, 122 residues, 1 model selected
> select #1
1843 atoms, 1871 bonds, 122 residues, 1 model selected
> select #2
2963 atoms, 3005 bonds, 418 residues, 1 model selected
> select #2/B
875 atoms, 885 bonds, 124 residues, 1 model selected
> select #2/BC
Nothing selected
> select #2/B,C
1753 atoms, 1774 bonds, 246 residues, 1 model selected
> select #2/B,C,D,F
1932 atoms, 1960 bonds, 274 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> ui tool show Matchmaker
> 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 Mena_Abi1_refine_8_TH_PR.pdb, chain A (#1) with 5zz9, chain A (#2),
sequence alignment score = 204.7
RMSD between 83 pruned atom pairs is 1.130 angstroms; (across all 108 pairs:
2.185)
> color byattribute seq_conservation protein palette cyanmaroon range -1.4,1.4
> noValueColor yellow
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 280, in execute
cmd.run(cmd_text)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/std_commands/color.py", line 1142, in color_by_attr
non_none_colors = _value_colors(palette, range, non_none_attr_vals)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/std_commands/color.py", line 1263, in _value_colors
min_val, max_val = min(values), max(values)
ValueError: min() arg is an empty sequence
ValueError: min() arg is an empty sequence
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/std_commands/color.py", line 1263, in _value_colors
min_val, max_val = min(values), max(values)
See log for complete Python traceback.
> color byattribute seq_conservation protein palette cyanmaroon range -1.4,1.4
> noValueColor yellow
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 280, in execute
cmd.run(cmd_text)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/std_commands/color.py", line 1142, in color_by_attr
non_none_colors = _value_colors(palette, range, non_none_attr_vals)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/std_commands/color.py", line 1263, in _value_colors
min_val, max_val = min(values), max(values)
ValueError: min() arg is an empty sequence
ValueError: min() arg is an empty sequence
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/std_commands/color.py", line 1263, in _value_colors
min_val, max_val = min(values), max(values)
See log for complete Python traceback.
> color byattribute seq_conservation -1.4,1.4 novalue yellow
Expected a collection of one of 'atoms', 'cartoons', 'ribbons', or 'surfaces'
or a keyword
> color byattribute seq_conservation
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 280, in execute
cmd.run(cmd_text)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/std_commands/color.py", line 1142, in color_by_attr
non_none_colors = _value_colors(palette, range, non_none_attr_vals)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/std_commands/color.py", line 1263, in _value_colors
min_val, max_val = min(values), max(values)
ValueError: min() arg is an empty sequence
ValueError: min() arg is an empty sequence
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/std_commands/color.py", line 1263, in _value_colors
min_val, max_val = min(values), max(values)
See log for complete Python traceback.
> ui tool show "Blast Protein"
> ui tool show "Modeller Comparative"
> select #1
1843 atoms, 1871 bonds, 122 residues, 1 model selected
> select #2
1031 atoms, 1045 bonds, 144 residues, 1 model selected
> select #1
1843 atoms, 1871 bonds, 122 residues, 1 model selected
> select #2
1031 atoms, 1045 bonds, 144 residues, 1 model selected
> select #1
1843 atoms, 1871 bonds, 122 residues, 1 model selected
> select #2
1031 atoms, 1045 bonds, 144 residues, 1 model selected
> select #1
1843 atoms, 1871 bonds, 122 residues, 1 model selected
> select #2
1031 atoms, 1045 bonds, 144 residues, 1 model selected
> hide #1 models
> hide #2 models
> show #2 models
> show #1 models
> select #1
1843 atoms, 1871 bonds, 122 residues, 1 model selected
> select #2
1031 atoms, 1045 bonds, 144 residues, 1 model selected
> select #1
1843 atoms, 1871 bonds, 122 residues, 1 model selected
> select #2
1031 atoms, 1045 bonds, 144 residues, 1 model selected
> select #1
1843 atoms, 1871 bonds, 122 residues, 1 model selected
> select #2
1031 atoms, 1045 bonds, 144 residues, 1 model selected
> select #1
1843 atoms, 1871 bonds, 122 residues, 1 model selected
> select #2
1031 atoms, 1045 bonds, 144 residues, 1 model selected
> select #1
1843 atoms, 1871 bonds, 122 residues, 1 model selected
> ~select #1
Nothing selected
> select #1
1843 atoms, 1871 bonds, 122 residues, 1 model selected
> ~select #1
Nothing selected
> select #1
1843 atoms, 1871 bonds, 122 residues, 1 model selected
> ~select #1
Nothing selected
> split
Split Mena_Abi1_refine_8_TH_PR.pdb (#1) into 2 models
Split 5zz9 (#2) into 2 models
Chain information for Mena_Abi1_refine_8_TH_PR.pdb A #1.1
---
Chain | Description
A | No description available
Chain information for Mena_Abi1_refine_8_TH_PR.pdb B #1.2
---
Chain | Description
B | No description available
Chain information for 5zz9 A #2.1
---
Chain | Description
A | No description available
Chain information for 5zz9 E #2.2
---
Chain | Description
E | No description available
> select #1
1843 atoms, 1871 bonds, 122 residues, 3 models selected
> select #2
1031 atoms, 1045 bonds, 144 residues, 3 models selected
> ui tool show "Show Sequence Viewer"
> ui tool show "Modeller Comparative"
No alignments chosen for modeling
> select #1
1843 atoms, 1871 bonds, 122 residues, 3 models selected
> select #2
1031 atoms, 1045 bonds, 144 residues, 3 models selected
> ui tool show "Blast Protein"
> ~select #2
Nothing selected
> select #2.1
877 atoms, 888 bonds, 123 residues, 1 model selected
> select #1.1
1700 atoms, 1720 bonds, 112 residues, 1 model selected
> view #2.1 clip false
> view #2.1 clip false
> select #2.1
877 atoms, 888 bonds, 123 residues, 1 model selected
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> ui tool show Matchmaker
> matchmaker #2.1 to #1.1
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 Mena_Abi1_refine_8_TH_PR.pdb A, chain A (#1.1) with 5zz9 A, chain A
(#2.1), sequence alignment score = 204.7
RMSD between 83 pruned atom pairs is 1.130 angstroms; (across all 108 pairs:
2.185)
> ui tool show Matchmaker
> matchmaker #1.2#2.1-2 to #1.1 showAlignment true
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 Mena_Abi1_refine_8_TH_PR.pdb A, chain A (#1.1) with
Mena_Abi1_refine_8_TH_PR.pdb B, chain B (#1.2), sequence alignment score = 3.6
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: Mena_Abi1_refine_8_TH_PR.pdb A
#1.1/A, Mena_Abi1_refine_8_TH_PR.pdb B #1.2/B
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 6 pruned atom pairs is 1.244 angstroms; (across all 10 pairs:
2.805)
Matchmaker Mena_Abi1_refine_8_TH_PR.pdb A, chain A (#1.1) with 5zz9 A, chain A
(#2.1), sequence alignment score = 204.7
Alignment identifier is 2
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2
Hiding conservation header for alignment 2
Chains used in RMSD evaluation for alignment 2: Mena_Abi1_refine_8_TH_PR.pdb A
#1.1/A, 5zz9 A #2.1/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2
RMSD between 83 pruned atom pairs is 1.130 angstroms; (across all 108 pairs:
2.185)
Matchmaker Mena_Abi1_refine_8_TH_PR.pdb A, chain A (#1.1) with 5zz9 E, chain E
(#2.2), sequence alignment score = 10.2
Alignment identifier is 3
Showing conservation header ("seq_conservation" residue attribute) for
alignment 3
Hiding conservation header for alignment 3
Chains used in RMSD evaluation for alignment 3: Mena_Abi1_refine_8_TH_PR.pdb A
#1.1/A, 5zz9 E #2.2/E
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 3
Iteration produces fewer than 3 residues aligned.
Cannot match Mena_Abi1_refine_8_TH_PR.pdb A, chain A with 5zz9 E, chain E
satisfying iteration threshold.
> select #2.2
154 atoms, 157 bonds, 21 residues, 1 model selected
> select #2.1
877 atoms, 888 bonds, 123 residues, 1 model selected
> hide #!2 models
> undo
> undo
> undo
> undo
> undo
> undo
> undo
> undo
> undo
> undo
> show #!1 models
> close session
> open
> /Users/avisinger/Desktop/Keating_lab/dTERMen_score_prediction/Mena_EVH1/pdb_files/Mena_Abi1_refine_8_TH_PR.pdb
> format pdb
Summary of feedback from opening
/Users/avisinger/Desktop/Keating_lab/dTERMen_score_prediction/Mena_EVH1/pdb_files/Mena_Abi1_refine_8_TH_PR.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK Date 2020-02-14 Time 17:13:37 EST -0500 (1581718417.48 s)
Ignored bad PDB record found on line 2
REMARK PHENIX refinement
Ignored bad PDB record found on line 4
REMARK ****************** INPUT FILES AND LABELS
******************************
Ignored bad PDB record found on line 5
REMARK Reflections:
Ignored bad PDB record found on line 6
REMARK file name :
/cove/a0/usr1/theresa/projects/MenaAbi1/phenix/Refine_4/Mena-
Abi1_refine_data.mtz
39 messages similar to the above omitted
Chain information for Mena_Abi1_refine_8_TH_PR.pdb #1
---
Chain | Description
A | No description available
B | No description available
> open 5zz9
5zz9 title:
Crystal structure of Homer2 EVH1/Drebrin PPXXF complex [more info...]
Chain information for 5zz9 #2
---
Chain | Description
A B C | Homer protein homolog 2
D E F | Peptide from Drebrin
5zz9 mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
3| author_and_software_defined_assembly
> select #2 /A
877 atoms, 888 bonds, 123 residues, 1 model selected
> select #2 /B,C,D,F
1932 atoms, 1960 bonds, 274 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> show cartoons
> hide atoms
> ui tool show Matchmaker
> matchmaker #2 to #1 showAlignment true
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 Mena_Abi1_refine_8_TH_PR.pdb, chain A (#1) with 5zz9, chain A (#2),
sequence alignment score = 204.7
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: Mena_Abi1_refine_8_TH_PR.pdb
#1/A, 5zz9 #2/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 83 pruned atom pairs is 1.130 angstroms; (across all 108 pairs:
2.185)
> save
> /Users/avisinger/Desktop/Keating_lab/EVH1_crosstalk/paralog_comparison_pdb/chimera_sessions/chimeraX/mena_homer_210626.cxs
> color byattribute seq_conservation protein palette cyanmaroon range -1.4,1.4
> noValueColor yellow
2863 atoms, 255 residues, atom seq_conservation range -0.675 to 1.47
> save
> /Users/avisinger/Desktop/Keating_lab/EVH1_crosstalk/paralog_comparison_pdb/chimera_sessions/chimeraX/mena_homer_210626.cxs
> split
Split Mena_Abi1_refine_8_TH_PR.pdb (#1) into 2 models
Split 5zz9 (#2) into 2 models
Chain information for Mena_Abi1_refine_8_TH_PR.pdb A #1.1
---
Chain | Description
A | No description available
Chain information for Mena_Abi1_refine_8_TH_PR.pdb B #1.2
---
Chain | Description
B | No description available
Chain information for 5zz9 A #2.1
---
Chain | Description
A | No description available
Chain information for 5zz9 E #2.2
---
Chain | Description
E | No description available
Associated Mena_Abi1_refine_8_TH_PR.pdb A (1.1) chain A to
Mena_Abi1_refine_8_TH_PR.pdb, chain A with 0 mismatches
Associated 5zz9 A (2.1) chain A to 5zz9, chain A with 0 mismatches
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 367, in <lambda>
self.associate([s for s in models if isinstance(s, AtomicStructure)],
force=False))
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 329, in associate
self._notify_observers(note_name, note_data)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seqalign/alignment.py", line 652, in _notify_observers
recipient.alignment_notification(note_name, note_data)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/alignment_headers/header_sequence.py", line 414, in
alignment_notification
prev_structs = len(set([x.structure
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/alignment_headers/header_sequence.py", line 414, in
<listcomp>
prev_structs = len(set([x.structure
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 57, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 85, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
AttributeError: 'Sequence' object has no attribute 'structure'
Error processing trigger "add models":
AttributeError: 'Sequence' object has no attribute 'structure'
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 85, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
Chains used in RMSD evaluation for alignment 1: Mena_Abi1_refine_8_TH_PR.pdb A
#1.1/A, 5zz9 A #2.1/A
> save
> /Users/avisinger/Desktop/Keating_lab/EVH1_crosstalk/paralog_comparison_pdb/chimera_sessions/chimeraX/mena_homer_210626.cxs
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 281, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/atomic/molobject.py", line 1143, in take_snapshot
'structure': self.structure,
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/atomic/molc.py", line 78, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
TypeError: Cannot instantiate Python class corresponding to C++
24QGraphicsRectItemPrivate
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 260, in discovery
self.processed[key] = self.process(obj, parents)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 284, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x11205ba60> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x13f292cd0> ->
<chimerax.atomic.molobject.StructureSeq object at 0x12b9fe700> '5zz9, chain A'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 877, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 607, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 262, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x11205ba60> -> <chimerax.seq-view.tool.SequenceViewer object at 0x13f292cd0>
-> <chimerax.atomic.molobject.StructureSeq object at 0x12b9fe700> '5zz9, chain
A': Error while saving session data for 'tools' -> <chimerax.core.tools.Tools
object at 0x11205ba60> -> <chimerax.seq-view.tool.SequenceViewer object at
0x13f292cd0> -> <chimerax.atomic.molobject.StructureSeq object at 0x12b9fe700>
'5zz9, chain A'
ValueError: error processing: 'tools' -> -> -> '5zz9, chain A': Error while
saving session data for 'tools' -> -> -> '5zz9, chain A'
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 262, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 281, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/atomic/molobject.py", line 1143, in take_snapshot
'structure': self.structure,
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/atomic/molc.py", line 78, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
TypeError: Cannot instantiate Python class corresponding to C++
24QGraphicsRectItemPrivate
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 260, in discovery
self.processed[key] = self.process(obj, parents)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 284, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x11205ba60> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x13f292cd0> ->
<chimerax.atomic.molobject.StructureSeq object at 0x12b9fe700> '5zz9, chain A'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 116, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 51, in display
run(session, cmd)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/cmd.py", line 87, in provider_save
provider_info.bundle_info.run_provider(session, provider_info.format_name,
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core_formats/__init__.py", line 79, in save
return cxs_save(session, path, **kw)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 877, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 607, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 262, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x11205ba60> -> <chimerax.seq-view.tool.SequenceViewer object at 0x13f292cd0>
-> <chimerax.atomic.molobject.StructureSeq object at 0x12b9fe700> '5zz9, chain
A': Error while saving session data for 'tools' -> <chimerax.core.tools.Tools
object at 0x11205ba60> -> <chimerax.seq-view.tool.SequenceViewer object at
0x13f292cd0> -> <chimerax.atomic.molobject.StructureSeq object at 0x12b9fe700>
'5zz9, chain A'
ValueError: error processing: 'tools' -> -> -> '5zz9, chain A': Error while
saving session data for 'tools' -> -> -> '5zz9, chain A'
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 262, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
> ui tool show Matchmaker
> select #2.2
154 atoms, 157 bonds, 21 residues, 1 model selected
> ~select #2.2
Nothing selected
> select #2.2
154 atoms, 157 bonds, 21 residues, 1 model selected
> ui tool show "Color Actions"
> color sel dark blue
> select #1.2
143 atoms, 151 bonds, 10 residues, 1 model selected
> color sel dark blue
> select clear
> select #1.2
143 atoms, 151 bonds, 10 residues, 1 model selected
> ~select #1.2
Nothing selected
> hide #!1 models
> select #2.2
154 atoms, 157 bonds, 21 residues, 1 model selected
> style sel stick
Changed 154 atom styles
> show sel cartoons
> style sel stick
Changed 154 atom styles
> show sel atoms
> ui tool show "Color Actions"
> color sel byhetero
> color sel byelement
> select ::name="HOH"
11 atoms, 11 residues, 2 models selected
> delete atoms sel
> delete bonds sel
> show #!1 models
> hide #!2 models
> select #2.2
152 atoms, 157 bonds, 19 residues, 1 model selected
> ~select #2.2
Nothing selected
> select #1.2
143 atoms, 151 bonds, 10 residues, 1 model selected
> style sel stick
Changed 143 atom styles
> show sel atoms
> color sel byelement
> save
> /Users/avisinger/Desktop/Keating_lab/EVH1_crosstalk/paralog_comparison_pdb/chimera_sessions/chimeraX/mena_homer_210626.cxs
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 281, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/atomic/molobject.py", line 1143, in take_snapshot
'structure': self.structure,
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/atomic/molc.py", line 78, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
TypeError: Cannot instantiate Python class corresponding to C++
30QGraphicsSimpleTextItemPrivate
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 260, in discovery
self.processed[key] = self.process(obj, parents)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 284, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x11205ba60> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x13f292cd0> ->
<chimerax.atomic.molobject.StructureSeq object at 0x12b9fe700> '5zz9, chain A'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 877, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 607, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 262, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x11205ba60> -> <chimerax.seq-view.tool.SequenceViewer object at 0x13f292cd0>
-> <chimerax.atomic.molobject.StructureSeq object at 0x12b9fe700> '5zz9, chain
A': Error while saving session data for 'tools' -> <chimerax.core.tools.Tools
object at 0x11205ba60> -> <chimerax.seq-view.tool.SequenceViewer object at
0x13f292cd0> -> <chimerax.atomic.molobject.StructureSeq object at 0x12b9fe700>
'5zz9, chain A'
ValueError: error processing: 'tools' -> -> -> '5zz9, chain A': Error while
saving session data for 'tools' -> -> -> '5zz9, chain A'
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 262, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 281, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/atomic/molobject.py", line 1143, in take_snapshot
'structure': self.structure,
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/atomic/molc.py", line 78, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
TypeError: Cannot instantiate Python class corresponding to C++
30QGraphicsSimpleTextItemPrivate
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 260, in discovery
self.processed[key] = self.process(obj, parents)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 284, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x11205ba60> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x13f292cd0> ->
<chimerax.atomic.molobject.StructureSeq object at 0x12b9fe700> '5zz9, chain A'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 116, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 51, in display
run(session, cmd)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/cmd.py", line 87, in provider_save
provider_info.bundle_info.run_provider(session, provider_info.format_name,
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core_formats/__init__.py", line 79, in save
return cxs_save(session, path, **kw)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 877, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 607, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 262, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x11205ba60> -> <chimerax.seq-view.tool.SequenceViewer object at 0x13f292cd0>
-> <chimerax.atomic.molobject.StructureSeq object at 0x12b9fe700> '5zz9, chain
A': Error while saving session data for 'tools' -> <chimerax.core.tools.Tools
object at 0x11205ba60> -> <chimerax.seq-view.tool.SequenceViewer object at
0x13f292cd0> -> <chimerax.atomic.molobject.StructureSeq object at 0x12b9fe700>
'5zz9, chain A'
ValueError: error processing: 'tools' -> -> -> '5zz9, chain A': Error while
saving session data for 'tools' -> -> -> '5zz9, chain A'
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 262, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
> save
> /Users/avisinger/Desktop/Keating_lab/EVH1_crosstalk/paralog_comparison_pdb/chimera_sessions/chimeraX/mena_homer_210626_2.cxs
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 281, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/atomic/molobject.py", line 1143, in take_snapshot
'structure': self.structure,
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/atomic/molc.py", line 78, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
TypeError: Cannot instantiate Python class corresponding to C++
30QGraphicsSimpleTextItemPrivate
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 260, in discovery
self.processed[key] = self.process(obj, parents)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 284, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x11205ba60> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x13f292cd0> ->
<chimerax.atomic.molobject.StructureSeq object at 0x12b9fe700> '5zz9, chain A'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 877, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 607, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 262, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x11205ba60> -> <chimerax.seq-view.tool.SequenceViewer object at 0x13f292cd0>
-> <chimerax.atomic.molobject.StructureSeq object at 0x12b9fe700> '5zz9, chain
A': Error while saving session data for 'tools' -> <chimerax.core.tools.Tools
object at 0x11205ba60> -> <chimerax.seq-view.tool.SequenceViewer object at
0x13f292cd0> -> <chimerax.atomic.molobject.StructureSeq object at 0x12b9fe700>
'5zz9, chain A'
ValueError: error processing: 'tools' -> -> -> '5zz9, chain A': Error while
saving session data for 'tools' -> -> -> '5zz9, chain A'
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 262, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 281, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/atomic/molobject.py", line 1143, in take_snapshot
'structure': self.structure,
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/atomic/molc.py", line 78, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
TypeError: Cannot instantiate Python class corresponding to C++
30QGraphicsSimpleTextItemPrivate
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 260, in discovery
self.processed[key] = self.process(obj, parents)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 284, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x11205ba60> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x13f292cd0> ->
<chimerax.atomic.molobject.StructureSeq object at 0x12b9fe700> '5zz9, chain A'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 116, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 51, in display
run(session, cmd)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/cmd.py", line 87, in provider_save
provider_info.bundle_info.run_provider(session, provider_info.format_name,
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core_formats/__init__.py", line 79, in save
return cxs_save(session, path, **kw)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 877, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 607, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 262, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x11205ba60> -> <chimerax.seq-view.tool.SequenceViewer object at 0x13f292cd0>
-> <chimerax.atomic.molobject.StructureSeq object at 0x12b9fe700> '5zz9, chain
A': Error while saving session data for 'tools' -> <chimerax.core.tools.Tools
object at 0x11205ba60> -> <chimerax.seq-view.tool.SequenceViewer object at
0x13f292cd0> -> <chimerax.atomic.molobject.StructureSeq object at 0x12b9fe700>
'5zz9, chain A'
ValueError: error processing: 'tools' -> -> -> '5zz9, chain A': Error while
saving session data for 'tools' -> -> -> '5zz9, chain A'
File
"/Applications/ChimeraX-1.2.2.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 262, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
OpenGL version: 4.1 INTEL-12.10.22
OpenGL renderer: Intel(R) UHD Graphics 617
OpenGL vendor: Intel Inc.Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: MacBookAir8,2
Processor Name: Intel Core i5
Processor Speed: 1.6 GHz
Number of Processors: 1
Total Number of Cores: 2
L2 Cache (per Core): 256 KB
L3 Cache: 4 MB
Hyper-Threading Technology: Enabled
Memory: 8 GB
Boot ROM Version: 1037.147.4.0.0 (iBridge: 17.16.16610.0.0,0)
Software:
System Software Overview:
System Version: macOS 10.14.6 (18G6032)
Kernel Version: Darwin 18.7.0
Time since boot: 2 days 16:34
Graphics/Displays:
Intel UHD Graphics 617:
Chipset Model: Intel UHD Graphics 617
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x87c0
Revision ID: 0x0002
Metal: Supported, feature set macOS GPUFamily2 v1
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Automatically Adjust Brightness: No
DELL U2211H:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60 Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: XVV5807UC8KL
Mirror: Off
Online: Yes
Rotation: Supported
Automatically Adjust Brightness: No
Connection Type: DVI or HDMI
Adapter Firmware Version: 7.55
Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.2
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2020.12.5
cftime: 1.4.1
chardet: 3.0.4
ChimeraX-AddCharge: 1.0
ChimeraX-AddH: 2.1.6
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.13.3
ChimeraX-AtomicLibrary: 3.1.3
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 1.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.5.2
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.1
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.1
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.2.1
ChimeraX-CommandLine: 1.1.4
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.2.2
ChimeraX-CoreFormats: 1.0
ChimeraX-coulombic: 1.1.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.1
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.2
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.0
ChimeraX-Hbonds: 2.1
ChimeraX-Help: 1.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.0
ChimeraX-ImageFormats: 1.1
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-Label: 1.0
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.0.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.0
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 1.2.1
ChimeraX-MDcrds: 2.2
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.3
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.0.1
ChimeraX-ModelPanel: 1.0.1
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.1
ChimeraX-OpenCommand: 1.5
ChimeraX-PDB: 2.4.1
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.1
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.0.1
ChimeraX-ReadPbonds: 1.0
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.4
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SeqView: 2.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.0
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.0.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.3.1
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.0.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.7.4
ChimeraX-uniprot: 2.1
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.3
comtypes: 1.1.7
cxservices: 1.0
cycler: 0.10.0
Cython: 0.29.21
decorator: 5.0.7
distlib: 0.3.1
docutils: 0.16
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 2.10.0
html2text: 2020.1.16
idna: 2.10
ihm: 0.17
imagecodecs: 2020.5.30
imagesize: 1.2.0
ipykernel: 5.3.4
ipython: 7.18.1
ipython-genutils: 0.2.0
jedi: 0.17.2
Jinja2: 2.11.2
jupyter-client: 6.1.7
jupyter-core: 4.7.1
kiwisolver: 1.3.1
line-profiler: 2.1.2
lxml: 4.6.2
lz4: 3.1.0
MarkupSafe: 1.1.1
matplotlib: 3.3.2
matplotlib-inline: 0.1.2
msgpack: 1.0.0
netCDF4: 1.5.4
networkx: 2.5
numexpr: 2.7.3
numpy: 1.19.2
numpydoc: 1.1.0
openvr: 1.14.1501
packaging: 20.9
ParmEd: 3.2.0
parso: 0.7.1
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 7.2.0
pip: 21.0.1
pkginfo: 1.5.0.1
prompt-toolkit: 3.0.18
psutil: 5.7.2
ptyprocess: 0.7.0
pycollada: 0.7.1
pydicom: 2.0.0
Pygments: 2.7.1
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 2.4.7
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.1
pytz: 2021.1
pyzmq: 22.0.3
qtconsole: 4.7.7
QtPy: 1.9.0
RandomWords: 0.3.0
requests: 2.24.0
scipy: 1.5.2
setuptools: 50.3.2
sfftk-rw: 0.6.7.dev1
six: 1.15.0
snowballstemmer: 2.1.0
sortedcontainers: 2.2.2
Sphinx: 3.2.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 1.0.3
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.4
suds-jurko: 0.6
tables: 3.6.1
tifffile: 2020.9.3
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.0.5
urllib3: 1.25.11
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.36.0
wheel-filename: 1.3.0
Change History (4)
comment:1 by , 4 years ago
| Component: | Unassigned → Volume Data |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → multiple errors |
comment:2 by , 4 years ago
| Owner: | changed from to |
|---|
Fixed hide dust toolbar button error when no maps are opened.
Eric can look at subsequent errors, color byattr and sequences.
comment:3 by , 4 years ago
The empty sequence to min() was because all seq_conservation values were None. Added some code to handle that.
comment:4 by , 4 years ago
| Component: | Volume Data → Sequence |
|---|
Note:
See TracTickets
for help on using tickets.
The first actual ChimeraX error is:
so initially assigning to T.G. Once that's dealt with through whatever means, I guess reassign based on whatever the next error is.