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Opened 2 years ago
Closed 2 years ago
#9857 closed defect (duplicate)
Problem installing ISOLDE
| Reported by: | Owned by: | Greg Couch | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Third Party | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-13.2.1-arm64-arm-64bit
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
Dear ChimeraX team,
Thank you very much for this great tool!
I am trying to install the ISOLDE plugin.
When I use the “Add more tools” menu, and click on the “Install” button of the ISOLDE page, and end up with the “500 server error” page.
I am trying to install version 1.6.0 of ISOLDE and I am using ChimeraX 1.6.1 on Mac OSX (Ventura 13.2.1).
It would be great if I could install that tool, since I will teach how to use ChimeraX to my students this Friday.
Thank you very much!
Have a nice day,
Vincent
Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 4obe
Summary of feedback from opening 4obe fetched from pdb
---
warning | Atom H1 is not in the residue template for GLY /B:0
notes | Fetching compressed mmCIF 4obe from
http://files.rcsb.org/download/4obe.cif
Fetching CCD MG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/MG/MG.cif
4obe title:
Crystal Structure of GDP-bound Human KRas [more info...]
Chain information for 4obe #1
---
Chain | Description | UniProt
A B | GTPase KRas | RASK_HUMAN 1-169
Non-standard residues in 4obe #1
---
GDP — guanosine-5'-diphosphate
MG — magnesium ion
4obe mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> open 6ut0
Summary of feedback from opening 6ut0 fetched from pdb
---
notes | Fetching compressed mmCIF 6ut0 from
http://files.rcsb.org/download/6ut0.cif
Fetching CCD M1X from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/X/M1X/M1X.cif
6ut0 title:
Identification of the Clinical Development Candidate MRTX849, a Covalent
KRASG12C Inhibitor for the Treatment of Cancer [more info...]
Chain information for 6ut0 #2
---
Chain | Description | UniProt
A B C D | GTPase KRas | RASK_HUMAN 1-169
Non-standard residues in 6ut0 #2
---
GDP — guanosine-5'-diphosphate
M1X —
{(2S)-4-[7-(8-chloronaphthalen-1-yl)-2-{[(2S)-1-methylpyrrolidin-2-yl]methoxy}-5,6,7,8-tetrahydropyrido[3,4-d]pyrimidin-4-yl]-1-[(2S)-2-fluoropropanoyl]piperazin-2-yl}acetonitrile
MG — magnesium ion
6ut0 mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
3| author_and_software_defined_assembly
4| author_and_software_defined_assembly
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A #1/B
Alignment identifier is 1
> ui tool show "Show Sequence Viewer"
> sequence chain #2/A #2/B #2/C #2/D
Alignment identifier is 1
> focus
Unknown command: focus
> view
> ui tool show "Color Actions"
> set bgColor white
> split
Split 4obe (#1) into 2 models
Split 6ut0 (#2) into 4 models
Chain information for 4obe A #1.1
---
Chain | Description
A | No description available
Chain information for 4obe B #1.2
---
Chain | Description
B | No description available
Chain information for 6ut0 A #2.1
---
Chain | Description
A | No description available
Chain information for 6ut0 B #2.2
---
Chain | Description
B | No description available
Chain information for 6ut0 C #2.3
---
Chain | Description
C | No description available
Chain information for 6ut0 D #2.4
---
Chain | Description
D | No description available
> select #1
5725 atoms, 5414 bonds, 12 pseudobonds, 698 residues, 5 models selected
> select #1.1
2862 atoms, 2708 bonds, 6 pseudobonds, 347 residues, 2 models selected
> select clear
> select
> ::name="ALA"::name="ARG"::name="ASN"::name="ASP"::name="CYS"::name="GLN"::name="GLU"::name="GLY"::name="HIS"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TYR"::name="VAL"
16079 atoms, 16205 bonds, 1016 residues, 6 models selected
> hide sel target a
> select ::name="HOH"
801 atoms, 801 residues, 6 models selected
> hide sel target a
> select #2.3/C:12
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel target ab
> hide sel target a
> select clear
> ui tool show Matchmaker
> matchmaker #!1.2#!2.1-4 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 4obe A, chain A (#1.1) with 4obe B, chain B (#1.2), sequence
alignment score = 872.9
RMSD between 168 pruned atom pairs is 0.298 angstroms; (across all 169 pairs:
0.347)
Matchmaker 4obe A, chain A (#1.1) with 6ut0 A, chain A (#2.1), sequence
alignment score = 845
RMSD between 158 pruned atom pairs is 0.630 angstroms; (across all 169 pairs:
1.209)
Matchmaker 4obe A, chain A (#1.1) with 6ut0 B, chain B (#2.2), sequence
alignment score = 829
RMSD between 155 pruned atom pairs is 0.678 angstroms; (across all 167 pairs:
1.233)
Matchmaker 4obe A, chain A (#1.1) with 6ut0 C, chain C (#2.3), sequence
alignment score = 842.6
RMSD between 158 pruned atom pairs is 0.655 angstroms; (across all 169 pairs:
1.226)
Matchmaker 4obe A, chain A (#1.1) with 6ut0 D, chain D (#2.4), sequence
alignment score = 842
RMSD between 161 pruned atom pairs is 0.682 angstroms; (across all 169 pairs:
1.179)
> ui tool show Matchmaker
> ui tool show "Render By Attribute"
> open /Users/vzoete/Desktop/kyte-doolittle_hydrophobicity_cartoon.cxc
> setattr :asp res kdh -3.5 create true
Assigning kdh attribute to 90 items
> setattr :glu res kdh -3.5 create true
Assigning kdh attribute to 77 items
> setattr :asn res kdh -3.5 create true
Assigning kdh attribute to 24 items
> setattr :gln res kdh -3.5 create true
Assigning kdh attribute to 54 items
> setattr :lys res kdh -3.9 create true
Assigning kdh attribute to 71 items
> setattr :arg res kdh -4.5 create true
Assigning kdh attribute to 60 items
> setattr :his res kdh -3.2 create true
Assigning kdh attribute to 24 items
> setattr :gly res kdh -0.4 create true
Assigning kdh attribute to 66 items
> setattr :pro res kdh -1.6 create true
Assigning kdh attribute to 24 items
> setattr :ser res kdh -0.8 create true
Assigning kdh attribute to 56 items
> setattr :thr res kdh -0.7 create true
Assigning kdh attribute to 72 items
> setattr :cys res kdh 2.5 create true
Assigning kdh attribute to 10 items
> setattr :met res kdh 1.9 create true
Assigning kdh attribute to 24 items
> setattr :mse res kdh 1.9 create true
Assigning kdh attribute to 0 items
> setattr :ala res kdh 1.8 create true
Assigning kdh attribute to 54 items
> setattr :val res kdh 4.2 create true
Assigning kdh attribute to 90 items
> setattr :ile res kdh 4.5 create true
Assigning kdh attribute to 66 items
> setattr :leu res kdh 3.8 create true
Assigning kdh attribute to 70 items
> setattr :phe res kdh 2.8 create true
Assigning kdh attribute to 36 items
> setattr :trp res kdh -0.9 create true
Assigning kdh attribute to 0 items
> setattr :tyr res kdh -1.3 create true
Assigning kdh attribute to 48 items
> color byattribute kdh protein target r palette dodgerblue:white:orangered
> noValueColor gray
1016 residues, atom kdh range -4.5 to 4.5
executed kyte-doolittle_hydrophobicity_cartoon.cxc
> ui tool show "Scale Bar"
> scalebar
> scalebar off
> ui tool show "Scale Bar"
> ui tool show "Selection Inspector"
> select
> ::name="ALA"::name="ARG"::name="ASN"::name="ASP"::name="CYS"::name="GLN"::name="GLU"::name="GLY"::name="HIS"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TYR"::name="VAL"
16079 atoms, 16205 bonds, 1016 residues, 6 models selected
> ui tool show "Scale Bar"
> ui tool show "Color Key"
> ui mousemode right "color key"
> ui tool show "Render By Attribute"
> key blue-white-red :-4.5 :0.0 :4.5 showTool true
> ui mousemode right translate
> close session
> open 4obe format mmcif fromDatabase pdb
Summary of feedback from opening 4obe fetched from pdb
---
warning | Atom H1 is not in the residue template for GLY /B:0
4obe title:
Crystal Structure of GDP-bound Human KRas [more info...]
Chain information for 4obe #1
---
Chain | Description | UniProt
A B | GTPase KRas | RASK_HUMAN 1-169
Non-standard residues in 4obe #1
---
GDP — guanosine-5'-diphosphate
MG — magnesium ion
4obe mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> open 6uto
Summary of feedback from opening 6uto fetched from pdb
---
notes | Fetching compressed mmCIF 6uto from
http://files.rcsb.org/download/6uto.cif
Fetching CCD GLC from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/C/GLC/GLC.cif
Fetching CCD NA from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/NA/NA.cif
Fetching CCD G3P from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/G3P/G3P.cif
Fetching CCD ACT from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/T/ACT/ACT.cif
6uto title:
Native E. coli Glyceraldehyde 3-phosphate dehydrogenase [more info...]
Chain information for 6uto #2
---
Chain | Description | UniProt
A B | Glyceraldehyde-3-phosphate dehydrogenase | A0A0U4BD45_ECOLX 1-330
Non-standard residues in 6uto #2
---
ACT — acetate ion
G3P — Sn-glycerol-3-phosphate
GLC — alpha-D-glucopyranose
NA — sodium ion
6uto mmCIF Assemblies
---
1| author_and_software_defined_assembly
> split
Split 4obe (#1) into 2 models
Split 6uto (#2) into 4 models
Chain information for 4obe A #1.1
---
Chain | Description
A | No description available
Chain information for 4obe B #1.2
---
Chain | Description
B | No description available
Chain information for 6uto A #2.1
---
Chain | Description
A | No description available
Chain information for 6uto B #2.2
---
Chain | Description
B | No description available
> select
> ::name="ALA"::name="ARG"::name="ASN"::name="ASP"::name="CYS"::name="GLN"::name="GLU"::name="GLY"::name="HIS"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="MSE"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TRP"::name="TYR"::name="VAL"
10228 atoms, 10348 bonds, 999 residues, 4 models selected
> hide sel target a
> ui tool show Matchmaker
> matchmaker #2.2-4#!1.2#!2.1 to #1.1
No matrix compatible with both reference structure and all match structures
> matchmaker #2.2-4#!1.2#!2.1 to #1.1
No matrix compatible with both reference structure and all match structures
> matchmaker #2.2-4#!1.2#!2.1 to #1.1
No matrix compatible with both reference structure and all match structures
> select clear
> ui tool show Matchmaker
> matchmaker #2.2-4#!1.2#!2.1 to #1.1
No matrix compatible with both reference structure and all match structures
> ui tool show Matchmaker
> matchmaker #2.2-4#!1.2#!2.1 to #1.1/A pairing bs
Reference and/or match model contains no nucleic or amino acid chains.
Use the command-line 'align' command to superimpose small molecules/ligands.
> close session
> open 4obe format mmcif fromDatabase pdb
Summary of feedback from opening 4obe fetched from pdb
---
warning | Atom H1 is not in the residue template for GLY /B:0
4obe title:
Crystal Structure of GDP-bound Human KRas [more info...]
Chain information for 4obe #1
---
Chain | Description | UniProt
A B | GTPase KRas | RASK_HUMAN 1-169
Non-standard residues in 4obe #1
---
GDP — guanosine-5'-diphosphate
MG — magnesium ion
4obe mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> open 6uto
6uto title:
Native E. coli Glyceraldehyde 3-phosphate dehydrogenase [more info...]
Chain information for 6uto #2
---
Chain | Description | UniProt
A B | Glyceraldehyde-3-phosphate dehydrogenase | A0A0U4BD45_ECOLX 1-330
Non-standard residues in 6uto #2
---
ACT — acetate ion
G3P — Sn-glycerol-3-phosphate
GLC — alpha-D-glucopyranose
NA — sodium ion
6uto mmCIF Assemblies
---
1| author_and_software_defined_assembly
> split
Split 4obe (#1) into 2 models
Split 6uto (#2) into 4 models
Chain information for 4obe A #1.1
---
Chain | Description
A | No description available
Chain information for 4obe B #1.2
---
Chain | Description
B | No description available
Chain information for 6uto A #2.1
---
Chain | Description
A | No description available
Chain information for 6uto B #2.2
---
Chain | Description
B | No description available
> ui tool show Matchmaker
> matchmaker #2.2-4#!1.2#!2.1 to #1.1/A pairing bs
Reference and/or match model contains no nucleic or amino acid chains.
Use the command-line 'align' command to superimpose small molecules/ligands.
> matchmaker #2.2-4#!1.2#!2.1 to #1.1/A pairing bs
Reference and/or match model contains no nucleic or amino acid chains.
Use the command-line 'align' command to superimpose small molecules/ligands.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 72, in refresh
self._items_change()
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 169, in _items_change
item_names = self._item_names()
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 47, in _item_names
values = [v for v in self.list_func() if self.filter_func(v)]
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 47, in <listcomp>
values = [v for v in self.list_func() if self.filter_func(v)]
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 22, in <lambda>
filter_func = lambda x, ff=filter_func, cf=class_filter: ff(x) and
isinstance(x, cf)
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/tool.py", line 313, in _filter_bring_models
ref_structures = [ref_value.structure]
AttributeError: 'NoneType' object has no attribute 'structure'
AttributeError: 'NoneType' object has no attribute 'structure'
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/match_maker/tool.py", line 313, in _filter_bring_models
ref_structures = [ref_value.structure]
See log for complete Python traceback.
> matchmaker #2.2-4#!1.2#!2.1 to #1.1
No matrix compatible with both reference structure and all match structures
> select
> ::name="ALA"::name="ARG"::name="ASN"::name="ASP"::name="CYS"::name="GLN"::name="GLU"::name="GLY"::name="HIS"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="MSE"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TRP"::name="TYR"::name="VAL"
10228 atoms, 10348 bonds, 999 residues, 4 models selected
> hide sel target a
> select ::name="HOH"
983 atoms, 983 residues, 4 models selected
> hide sel target a
> select add #2.3
1006 atoms, 24 bonds, 985 residues, 5 models selected
> select add #2.4
1029 atoms, 48 bonds, 987 residues, 6 models selected
> select clear
> ui tool show Matchmaker
> matchmaker #2.2-4#!1.2#!2.1 to #1.1
No matrix compatible with both reference structure and all match structures
> close session
> open 4obe format mmcif fromDatabase pdb
Summary of feedback from opening 4obe fetched from pdb
---
warning | Atom H1 is not in the residue template for GLY /B:0
4obe title:
Crystal Structure of GDP-bound Human KRas [more info...]
Chain information for 4obe #1
---
Chain | Description | UniProt
A B | GTPase KRas | RASK_HUMAN 1-169
Non-standard residues in 4obe #1
---
GDP — guanosine-5'-diphosphate
MG — magnesium ion
4obe mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> open 6ut0
6ut0 title:
Identification of the Clinical Development Candidate MRTX849, a Covalent
KRASG12C Inhibitor for the Treatment of Cancer [more info...]
Chain information for 6ut0 #2
---
Chain | Description | UniProt
A B C D | GTPase KRas | RASK_HUMAN 1-169
Non-standard residues in 6ut0 #2
---
GDP — guanosine-5'-diphosphate
M1X —
{(2S)-4-[7-(8-chloronaphthalen-1-yl)-2-{[(2S)-1-methylpyrrolidin-2-yl]methoxy}-5,6,7,8-tetrahydropyrido[3,4-d]pyrimidin-4-yl]-1-[(2S)-2-fluoropropanoyl]piperazin-2-yl}acetonitrile
MG — magnesium ion
6ut0 mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
3| author_and_software_defined_assembly
4| author_and_software_defined_assembly
> ui tool show "Color Actions"
> set bgColor white
> select ::name="HOH"
801 atoms, 801 residues, 2 models selected
> hide sel target a
> select
> ::name="ALA"::name="ARG"::name="ASN"::name="ASP"::name="CYS"::name="GLN"::name="GLU"::name="GLY"::name="HIS"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TYR"::name="VAL"
16079 atoms, 16205 bonds, 1016 residues, 2 models selected
> hide sel target a
> select clear
> ui tool show Matchmaker
> split
Split 4obe (#1) into 2 models
Split 6ut0 (#2) into 4 models
Chain information for 4obe A #1.1
---
Chain | Description
A | No description available
Chain information for 4obe B #1.2
---
Chain | Description
B | No description available
Chain information for 6ut0 A #2.1
---
Chain | Description
A | No description available
Chain information for 6ut0 B #2.2
---
Chain | Description
B | No description available
Chain information for 6ut0 C #2.3
---
Chain | Description
C | No description available
Chain information for 6ut0 D #2.4
---
Chain | Description
D | No description available
> ui tool show Matchmaker
> matchmaker #!1.2#!2.1-4 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 4obe A, chain A (#1.1) with 4obe B, chain B (#1.2), sequence
alignment score = 872.9
RMSD between 168 pruned atom pairs is 0.298 angstroms; (across all 169 pairs:
0.347)
Matchmaker 4obe A, chain A (#1.1) with 6ut0 A, chain A (#2.1), sequence
alignment score = 845
RMSD between 158 pruned atom pairs is 0.630 angstroms; (across all 169 pairs:
1.209)
Matchmaker 4obe A, chain A (#1.1) with 6ut0 B, chain B (#2.2), sequence
alignment score = 829
RMSD between 155 pruned atom pairs is 0.678 angstroms; (across all 167 pairs:
1.233)
Matchmaker 4obe A, chain A (#1.1) with 6ut0 C, chain C (#2.3), sequence
alignment score = 842.6
RMSD between 158 pruned atom pairs is 0.655 angstroms; (across all 169 pairs:
1.226)
Matchmaker 4obe A, chain A (#1.1) with 6ut0 D, chain D (#2.4), sequence
alignment score = 842
RMSD between 161 pruned atom pairs is 0.682 angstroms; (across all 169 pairs:
1.179)
> ui tool show "Render By Attribute"
> open /Users/vzoete/Desktop/kyte-doolittle_hydrophobicity.cxc
> setattr :asp res kdh -3.5 create true
Assigning kdh attribute to 90 items
> setattr :glu res kdh -3.5 create true
Assigning kdh attribute to 77 items
> setattr :asn res kdh -3.5 create true
Assigning kdh attribute to 24 items
> setattr :gln res kdh -3.5 create true
Assigning kdh attribute to 54 items
> setattr :lys res kdh -3.9 create true
Assigning kdh attribute to 71 items
> setattr :arg res kdh -4.5 create true
Assigning kdh attribute to 60 items
> setattr :his res kdh -3.2 create true
Assigning kdh attribute to 24 items
> setattr :gly res kdh -0.4 create true
Assigning kdh attribute to 66 items
> setattr :pro res kdh -1.6 create true
Assigning kdh attribute to 24 items
> setattr :ser res kdh -0.8 create true
Assigning kdh attribute to 56 items
> setattr :thr res kdh -0.7 create true
Assigning kdh attribute to 72 items
> setattr :cys res kdh 2.5 create true
Assigning kdh attribute to 10 items
> setattr :met res kdh 1.9 create true
Assigning kdh attribute to 24 items
> setattr :mse res kdh 1.9 create true
Assigning kdh attribute to 0 items
> setattr :ala res kdh 1.8 create true
Assigning kdh attribute to 54 items
> setattr :val res kdh 4.2 create true
Assigning kdh attribute to 90 items
> setattr :ile res kdh 4.5 create true
Assigning kdh attribute to 66 items
> setattr :leu res kdh 3.8 create true
Assigning kdh attribute to 70 items
> setattr :phe res kdh 2.8 create true
Assigning kdh attribute to 36 items
> setattr :trp res kdh -0.9 create true
Assigning kdh attribute to 0 items
> setattr :tyr res kdh -1.3 create true
Assigning kdh attribute to 48 items
> color byattribute kdh protein target r palette dodgerblue:white:orangered
> noValueColor gray
1016 residues, atom kdh range -4.5 to 4.5
executed kyte-doolittle_hydrophobicity.cxc
> close session
> open 4obe format mmcif fromDatabase pdb
Summary of feedback from opening 4obe fetched from pdb
---
warning | Atom H1 is not in the residue template for GLY /B:0
4obe title:
Crystal Structure of GDP-bound Human KRas [more info...]
Chain information for 4obe #1
---
Chain | Description | UniProt
A B | GTPase KRas | RASK_HUMAN 1-169
Non-standard residues in 4obe #1
---
GDP — guanosine-5'-diphosphate
MG — magnesium ion
4obe mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> open 6uto
6uto title:
Native E. coli Glyceraldehyde 3-phosphate dehydrogenase [more info...]
Chain information for 6uto #2
---
Chain | Description | UniProt
A B | Glyceraldehyde-3-phosphate dehydrogenase | A0A0U4BD45_ECOLX 1-330
Non-standard residues in 6uto #2
---
ACT — acetate ion
G3P — Sn-glycerol-3-phosphate
GLC — alpha-D-glucopyranose
NA — sodium ion
6uto mmCIF Assemblies
---
1| author_and_software_defined_assembly
> close #2
> open 6ut0
6ut0 title:
Identification of the Clinical Development Candidate MRTX849, a Covalent
KRASG12C Inhibitor for the Treatment of Cancer [more info...]
Chain information for 6ut0 #2
---
Chain | Description | UniProt
A B C D | GTPase KRas | RASK_HUMAN 1-169
Non-standard residues in 6ut0 #2
---
GDP — guanosine-5'-diphosphate
M1X —
{(2S)-4-[7-(8-chloronaphthalen-1-yl)-2-{[(2S)-1-methylpyrrolidin-2-yl]methoxy}-5,6,7,8-tetrahydropyrido[3,4-d]pyrimidin-4-yl]-1-[(2S)-2-fluoropropanoyl]piperazin-2-yl}acetonitrile
MG — magnesium ion
6ut0 mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
3| author_and_software_defined_assembly
4| author_and_software_defined_assembly
> split
Split 4obe (#1) into 2 models
Split 6ut0 (#2) into 4 models
Chain information for 4obe A #1.1
---
Chain | Description
A | No description available
Chain information for 4obe B #1.2
---
Chain | Description
B | No description available
Chain information for 6ut0 A #2.1
---
Chain | Description
A | No description available
Chain information for 6ut0 B #2.2
---
Chain | Description
B | No description available
Chain information for 6ut0 C #2.3
---
Chain | Description
C | No description available
Chain information for 6ut0 D #2.4
---
Chain | Description
D | No description available
> select
> ::name="ALA"::name="ARG"::name="ASN"::name="ASP"::name="CYS"::name="GLN"::name="GLU"::name="GLY"::name="HIS"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TYR"::name="VAL"
16079 atoms, 16205 bonds, 1016 residues, 6 models selected
> hide sel target a
> select ::name="HOH"
801 atoms, 801 residues, 6 models selected
> hide sel target a
> ui tool show "Color Actions"
> set bgColor white
> ui tool show Matchmaker
> matchmaker #!1.2#!2.1-4 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 4obe A, chain A (#1.1) with 4obe B, chain B (#1.2), sequence
alignment score = 872.9
RMSD between 168 pruned atom pairs is 0.298 angstroms; (across all 169 pairs:
0.347)
Matchmaker 4obe A, chain A (#1.1) with 6ut0 A, chain A (#2.1), sequence
alignment score = 845
RMSD between 158 pruned atom pairs is 0.630 angstroms; (across all 169 pairs:
1.209)
Matchmaker 4obe A, chain A (#1.1) with 6ut0 B, chain B (#2.2), sequence
alignment score = 829
RMSD between 155 pruned atom pairs is 0.678 angstroms; (across all 167 pairs:
1.233)
Matchmaker 4obe A, chain A (#1.1) with 6ut0 C, chain C (#2.3), sequence
alignment score = 842.6
RMSD between 158 pruned atom pairs is 0.655 angstroms; (across all 169 pairs:
1.226)
Matchmaker 4obe A, chain A (#1.1) with 6ut0 D, chain D (#2.4), sequence
alignment score = 842
RMSD between 161 pruned atom pairs is 0.682 angstroms; (across all 169 pairs:
1.179)
> save /Users/vzoete/Desktop/Exo01-Session02.cxs
> open /Users/vzoete/Desktop/kyte-doolittle_hydrophobicity.cxc
> setattr :asp res kdh -3.5 create true
Assigning kdh attribute to 90 items
> setattr :glu res kdh -3.5 create true
Assigning kdh attribute to 77 items
> setattr :asn res kdh -3.5 create true
Assigning kdh attribute to 24 items
> setattr :gln res kdh -3.5 create true
Assigning kdh attribute to 54 items
> setattr :lys res kdh -3.9 create true
Assigning kdh attribute to 71 items
> setattr :arg res kdh -4.5 create true
Assigning kdh attribute to 60 items
> setattr :his res kdh -3.2 create true
Assigning kdh attribute to 24 items
> setattr :gly res kdh -0.4 create true
Assigning kdh attribute to 66 items
> setattr :pro res kdh -1.6 create true
Assigning kdh attribute to 24 items
> setattr :ser res kdh -0.8 create true
Assigning kdh attribute to 56 items
> setattr :thr res kdh -0.7 create true
Assigning kdh attribute to 72 items
> setattr :cys res kdh 2.5 create true
Assigning kdh attribute to 10 items
> setattr :met res kdh 1.9 create true
Assigning kdh attribute to 24 items
> setattr :mse res kdh 1.9 create true
Assigning kdh attribute to 0 items
> setattr :ala res kdh 1.8 create true
Assigning kdh attribute to 54 items
> setattr :val res kdh 4.2 create true
Assigning kdh attribute to 90 items
> setattr :ile res kdh 4.5 create true
Assigning kdh attribute to 66 items
> setattr :leu res kdh 3.8 create true
Assigning kdh attribute to 70 items
> setattr :phe res kdh 2.8 create true
Assigning kdh attribute to 36 items
> setattr :trp res kdh -0.9 create true
Assigning kdh attribute to 0 items
> setattr :tyr res kdh -1.3 create true
Assigning kdh attribute to 48 items
executed kyte-doolittle_hydrophobicity.cxc
> ui tool show "Render By Attribute"
> color byattribute r:kdh #!1.1-2#!2.1-4 target cabs palette
> -4.5,blue:0,white:4.5,red
17292 atoms, 1833 residues, atom kdh range -4.5 to 4.5
> select
> ::name="ALA"::name="ARG"::name="ASN"::name="ASP"::name="CYS"::name="GLN"::name="GLU"::name="GLY"::name="HIS"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TYR"::name="VAL"
16079 atoms, 16205 bonds, 1016 residues, 6 models selected
> show sel target ab
> hide sel target a
> ui tool show "Render By Attribute"
> key blue-white-red :-4.5 :0.0 :4.5 showTool true
> ui mousemode right "color key"
> key blue-white-red :-4.5 :0.0 :4.
> key blue-white-red :-4.5 :0.0 :4
> key blue-white-red :-4.5 :0.0 :
> key blue-white-red :-4.5 :0.0 :H
> key blue-white-red :-4.5 :0.0 :Hy
> key blue-white-red :-4.5 :0.0 :Hyd
> key blue-white-red :-4.5 :0.0 :Hydr
> key blue-white-red :-4.5 :0.0 :Hydro
> key blue-white-red :-4.5 :0.0 :Hydrop
> key blue-white-red :-4.5 :0.0 :Hydroph
> key blue-white-red :-4.5 :0.0 :Hydropho
> key blue-white-red :-4.5 :0.0 :Hydrophob
> key blue-white-red :-4.5 :0.0 :Hydrophobi
> key blue-white-red :-4.5 :0.0 :Hydrophobic
> key blue-white-red :H :0.0 :Hydrophobic
> key blue-white-red :Hy :0.0 :Hydrophobic
> key blue-white-red :Hyd :0.0 :Hydrophobic
> key blue-white-red :Hydr :0.0 :Hydrophobic
> key blue-white-red :Hydro :0.0 :Hydrophobic
> key blue-white-red :Hydrop :0.0 :Hydrophobic
> key blue-white-red :Hydroph :0.0 :Hydrophobic
> key blue-white-red :Hydrophy :0.0 :Hydrophobic
> key blue-white-red :Hydrophyl :0.0 :Hydrophobic
> key blue-white-red :Hydrophyli :0.0 :Hydrophobic
> key blue-white-red :Hydrophylic :0.0 :Hydrophobic
> key blue-white-red :Hydrophlic :0.0 :Hydrophobic
> key blue-white-red :Hydrophlici :0.0 :Hydrophobic
> key blue-white-red ":Hydrophlici\\\" :0.0 :Hydrophobic
> key blue-white-red ":Hydrophlici\\\\\\\" :0.0 :Hydrophobic
> key blue-white-red ":Hydrophlici\\\" :0.0 :Hydrophobic
> key blue-white-red :Hydrophlici :0.0 :Hydrophobic
> key blue-white-red :Hydrophlic :0.0 :Hydrophobic
> key blue-white-red :Hydrophli :0.0 :Hydrophobic
> key blue-white-red :Hydrophl :0.0 :Hydrophobic
> key blue-white-red :Hydroph :0.0 :Hydrophobic
> key blue-white-red :Hydrophi :0.0 :Hydrophobic
> key blue-white-red :Hydrophil :0.0 :Hydrophobic
> key blue-white-red :Hydrophili :0.0 :Hydrophobic
> key blue-white-red :Hydrophilic :0.0 :Hydrophobic
> ui mousemode right translate
> key blue-white-red :-4.5 :0.0 :4.5 showTool true
> ui mousemode right "color key"
> key blue-white-red :-4.5 :0.0 :H
> key blue-white-red :-4.5 :0.0 :Hy
> key blue-white-red :-4.5 :0.0 :Hyd
> key blue-white-red :-4.5 :0.0 :Hydr
> key blue-white-red :-4.5 :0.0 :Hydro
> key blue-white-red :-4.5 :0.0 :Hydrop
> key blue-white-red :-4.5 :0.0 :Hydroph
> key blue-white-red :-4.5 :0.0 :Hydropho
> key blue-white-red :-4.5 :0.0 :Hydrophoc
> key blue-white-red :-4.5 :0.0 :Hydropho
> key blue-white-red :-4.5 :0.0 :Hydroph
> key blue-white-red :-4.5 :0.0 :Hydropho
> key blue-white-red :-4.5 :0.0 :Hydrophob
> key blue-white-red :-4.5 :0.0 :Hydrophobi
> key blue-white-red :-4.5 :0.0 :Hydrophobic
> key blue-white-red :H :0.0 :Hydrophobic
> key blue-white-red :Hy :0.0 :Hydrophobic
> key blue-white-red :Hyd :0.0 :Hydrophobic
> key blue-white-red :Hydr :0.0 :Hydrophobic
> key blue-white-red :Hydro :0.0 :Hydrophobic
> key blue-white-red :Hydrop :0.0 :Hydrophobic
> key blue-white-red :Hydroph :0.0 :Hydrophobic
> key blue-white-red :Hydrophi :0.0 :Hydrophobic
> key blue-white-red :Hydrophil :0.0 :Hydrophobic
> key blue-white-red :Hydrophili :0.0 :Hydrophobic
> key blue-white-red :Hydrophilic :0.0 :Hydrophobic
> key pos 0.0000,0.08000
> key pos 0.6000,0.08000
> ui mousemode right translate
> select
> ::name="ALA"::name="ARG"::name="ASN"::name="ASP"::name="CYS"::name="GLN"::name="GLU"::name="GLY"::name="HIS"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TYR"::name="VAL"
16079 atoms, 16205 bonds, 1016 residues, 6 models selected
> show sel target ab
> select clear
> color byattribute a:bfactor #!1.1-2#!2.1-4 target cabs palette
> 6.71,blue:35.2908,white:55,red
17292 atoms, 1833 residues, atom bfactor range 6.71 to 101
> color byattribute a:bfactor #!1.1-2#!2.1-4 target cabs palette
> 6.71,blue:35,white:55,red
17292 atoms, 1833 residues, atom bfactor range 6.71 to 101
> color byattribute a:bfactor #!1.1-2#!2.1-4 target cabs palette
> 6.71,blue:30,white:55,red
17292 atoms, 1833 residues, atom bfactor range 6.71 to 101
> key blue-white-red :6.7 :30.0 :55.0 showTool true
> ui mousemode right "color key"
> key blue-white-red :6.7 :30.0 :f
> key blue-white-red :6.7 :30.0 :
> key blue-white-red :6.7 :30.0 :F
> key blue-white-red :6.7 :30.0 :Fl
> key blue-white-red :6.7 :30.0 :Fle
> key blue-white-red :6.7 :30.0 :Flex
> key blue-white-red :6.7 :30.0 :Flexi
> key blue-white-red :6.7 :30.0 :Flexib
> key blue-white-red :6.7 :30.0 :Flexibl
> key blue-white-red :6.7 :30.0 :Flexible
> key blue-white-red :R :30.0 :Flexible
> key blue-white-red :Ri :30.0 :Flexible
> key blue-white-red :Rig :30.0 :Flexible
> key blue-white-red :Rigi :30.0 :Flexible
> key blue-white-red :Rigid :30.0 :Flexible
> ui mousemode right translate
> tile
3 models tiled
> tile viewAll true
3 models tiled
> ~tile
> key blue-white-red :6.7 :30.0 :55.0 showTool true
> ui mousemode right "color key"
> key blue-white-red :6.7 :30.0 :H
> key blue-white-red :6.7 :30.0 :Hi
> key blue-white-red :6.7 :30.0 :Hig
> key blue-white-red :6.7 :30.0 :High
> key blue-white-red :6.7 :30.0 ":High "
> key blue-white-red :6.7 :30.0 ":High B"
> key blue-white-red :6.7 :30.0 ":High B-"
> key blue-white-red :6.7 :30.0 ":High B-f"
> key blue-white-red :6.7 :30.0 ":High B-fa"
> key blue-white-red :6.7 :30.0 ":High B-fac"
> key blue-white-red :6.7 :30.0 ":High B-fact"
> key blue-white-red :6.7 :30.0 ":High B-facto"
> key blue-white-red :6.7 :30.0 ":High B-factor"
> key blue-white-red :L :30.0 ":High B-factor"
> key blue-white-red :Lo :30.0 ":High B-factor"
> key blue-white-red :Low :30.0 ":High B-factor"
> key blue-white-red ":Low " :30.0 ":High B-factor"
> key blue-white-red ":Low B" :30.0 ":High B-factor"
> key blue-white-red ":Low B-" :30.0 ":High B-factor"
> key blue-white-red ":Low B-F" :30.0 ":High B-factor"
> key blue-white-red ":Low B-Fa" :30.0 ":High B-factor"
> key blue-white-red ":Low B-Fac" :30.0 ":High B-factor"
> key blue-white-red ":Low B-Fact" :30.0 ":High B-factor"
> key blue-white-red ":Low B-Facto" :30.0 ":High B-factor"
> key blue-white-red ":Low B-Factor" :30.0 ":High B-factor"
> key delete
> ui mousemode right translate
> color byattribute a:bfactor #!1.1-2#!2.1-4 target cabs palette
> 6.71,blue:30,white:55,red
17292 atoms, 1833 residues, atom bfactor range 6.71 to 101
> key blue-white-red :6.7 :30.0 :55.0 showTool true
> ui mousemode right "color key"
> key blue-white-red :6.7 :30.0 :H
> key blue-white-red :6.7 :30.0 :Hi
> key blue-white-red :6.7 :30.0 :Hig
> key blue-white-red :6.7 :30.0 :High
> key blue-white-red :6.7 :30.0 ":High "
> key blue-white-red :6.7 :30.0 ":High B"
> key blue-white-red :6.7 :30.0 ":High B-"
> key blue-white-red :6.7 :30.0 ":High B-F"
> key blue-white-red :6.7 :30.0 ":High B-Fa"
> key blue-white-red :6.7 :30.0 ":High B-Fac"
> key blue-white-red :6.7 :30.0 ":High B-Fact"
> key blue-white-red :6.7 :30.0 ":High B-Facto"
> key blue-white-red :6.7 :30.0 ":High B-Factor"
> key blue-white-red :L :30.0 ":High B-Factor"
> key blue-white-red :Lo :30.0 ":High B-Factor"
> key blue-white-red :Low :30.0 ":High B-Factor"
> key blue-white-red ":Low " :30.0 ":High B-Factor"
> key blue-white-red ":Low B" :30.0 ":High B-Factor"
> key blue-white-red ":Low B-" :30.0 ":High B-Factor"
> key blue-white-red ":Low B-F" :30.0 ":High B-Factor"
> key blue-white-red ":Low B-Fa" :30.0 ":High B-Factor"
> key blue-white-red ":Low B-Fac" :30.0 ":High B-Factor"
> key blue-white-red ":Low B-Fact" :30.0 ":High B-Factor"
> key blue-white-red ":Low B-Facto" :30.0 ":High B-Factor"
> key blue-white-red ":Low B-Factor" :30.0 ":High B-Factor"
> key pos 0.0000,0.08000
> key pos 0.6,0.08000
> ui mousemode right translate
> tile
3 models tiled
> tile columns 6
3 models tiled
> key blue-white-red :6.7 :30.0 :55.0 showTool true
> ui mousemode right "color key"
> key blue-white-red :6.7 :30.0 :H
> key blue-white-red :6.7 :30.0 :Hi
> key blue-white-red :6.7 :30.0 :Hig
> key blue-white-red :6.7 :30.0 :High
> key blue-white-red :6.7 :30.0 ":High "
> key blue-white-red :6.7 :30.0 ":High B"
> key blue-white-red :6.7 :30.0 ":High B-"
> key blue-white-red :6.7 :30.0 ":High B-f"
> key blue-white-red :6.7 :30.0 ":High B-fa"
> key blue-white-red :6.7 :30.0 ":High B-fac"
> key blue-white-red :6.7 :30.0 ":High B-fact"
> key blue-white-red :6.7 :30.0 ":High B-facto"
> key blue-white-red :6.7 :30.0 ":High B-factor"
> key blue-white-red :L :30.0 ":High B-factor"
> key blue-white-red :Lo :30.0 ":High B-factor"
> key blue-white-red :Loe :30.0 ":High B-factor"
> key blue-white-red :Lo :30.0 ":High B-factor"
> key blue-white-red :Low :30.0 ":High B-factor"
> key blue-white-red ":Low " :30.0 ":High B-factor"
> key blue-white-red ":Low B" :30.0 ":High B-factor"
> key blue-white-red ":Low B-" :30.0 ":High B-factor"
> key blue-white-red ":Low B-F" :30.0 ":High B-factor"
> key blue-white-red ":Low B-Fa" :30.0 ":High B-factor"
> key blue-white-red ":Low B-Fac" :30.0 ":High B-factor"
> key blue-white-red ":Low B-Fact" :30.0 ":High B-factor"
> key blue-white-red ":Low B-Facto" :30.0 ":High B-factor"
> key blue-white-red ":Low B-Factor" :30.0 ":High B-factor"
> key blue-white-red ":Low B-Factor" :30.0 ":High B-actor"
> key blue-white-red ":Low B-Factor" :30.0 ":High B-actorF"
> key blue-white-red ":Low B-Factor" :30.0 ":High B-actorF\\\"
> key blue-white-red ":Low B-Factor" :30.0 ":High B-actorF"
> key blue-white-red ":Low B-Factor" :30.0 ":High B-actorF\\\"
> key blue-white-red ":Low B-Factor" :30.0 ":High B-actorF\\\\\\\"
> key blue-white-red ":Low B-Factor" :30.0 ":High B-actorF\\\"
> key blue-white-red ":Low B-Factor" :30.0 ":High B-actorF"
> key blue-white-red ":Low B-Factor" :30.0 ":High B-actor"
> key blue-white-red ":Low B-Factor" :30.0 ":High B-acto"
> key blue-white-red ":Low B-Factor" :30.0 ":High B-act"
> key blue-white-red ":Low B-Factor" :30.0 ":High B-ac"
> key blue-white-red ":Low B-Factor" :30.0 ":High B-a"
> key blue-white-red ":Low B-Factor" :30.0 ":High B-"
> key blue-white-red ":Low B-Factor" :30.0 ":High B-F"
> key blue-white-red ":Low B-Factor" :30.0 ":High B-Fa"
> key blue-white-red ":Low B-Factor" :30.0 ":High B-Fac"
> key blue-white-red ":Low B-Factor" :30.0 ":High B-Fact"
> key blue-white-red ":Low B-Factor" :30.0 ":High B-Facto"
> key blue-white-red ":Low B-Factor" :30.0 ":High B-Factor"
> key blue-white-red :6.7 :30.0 :55.0 showTool true
> ui mousemode right translate
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.2 models
> hide #!2.2 models
> hide #!2.3 models
> hide #!2.4 models
> hide #4 models
> show #4 models
> hide #4 models
> ~tile
> hide #!2 models
> hide #!2.1 models
> hide #!1 models
> hide #!1.1 models
> show #!2.1 models
> ui tool show "Render By Attribute"
> close session
> Clear file history
Unknown command: Clear file history
> toolshed show
[Repeated 2 time(s)]
OpenGL version: 4.1 Metal - 83
OpenGL renderer: Apple M2 Max
OpenGL vendor: Apple
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac14,6
Model Number: Z175001NUSM/A
Chip: Apple M2 Max
Total Number of Cores: 12 (8 performance and 4 efficiency)
Memory: 32 GB
System Firmware Version: 8419.80.7
OS Loader Version: 8419.80.7
Software:
System Software Overview:
System Version: macOS 13.2.1 (22D68)
Kernel Version: Darwin 22.3.0
Time since boot: 20 days, 22 hours, 49 minutes
Graphics/Displays:
Apple M2 Max:
Chipset Model: Apple M2 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 30
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
LG UltraFine:
Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus)
UI Looks like: 2560 x 1440 @ 60.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Automatically Adjust Brightness: No
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
build: 0.10.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 3.1.0
ChimeraX-AddCharge: 1.5.9.1
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.43.10
ChimeraX-AtomicLibrary: 10.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.8
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.6.1
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.1
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.0.12
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.9
ChimeraX-ModelPanel: 1.3.7
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.0
ChimeraX-NRRD: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.1
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.8.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Topography: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.28.4
ChimeraX-uniprot: 2.2.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.3
contourpy: 1.0.7
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7
decorator: 5.1.1
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.39.3
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.8.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.2.22
imagesize: 1.4.1
importlib-metadata: 6.6.0
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.6
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.0.2
jupyter-core: 5.3.0
jupyterlab-widgets: 3.0.7
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.2
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.23.5
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.3.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.5.0
prompt-toolkit: 3.0.38
psutil: 5.9.4
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.3
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.3
python-dateutil: 2.8.2
pytz: 2023.3
pyzmq: 25.0.2
qtconsole: 5.4.0
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.28.2
scipy: 1.9.3
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4.1
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tcia-utils: 1.2.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.1
traitlets: 5.9.0
typing-extensions: 4.5.0
tzdata: 2023.3
urllib3: 1.26.15
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.7
zipp: 3.15.0
Change History (2)
comment:1 by , 2 years ago
| Component: | Unassigned → Third Party |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Problem installing ISOLDE |
comment:2 by , 2 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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Duplicate of #9856