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Opened 3 years ago
Closed 3 years ago
#8839 closed defect (fixed)
Error while hovering mouse in VR
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | VR | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.19044
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
Was interacting with 3D object in VR meeting from Desktop. Getting mouse hover error. Others in meeting had same error. It seemed to still work ok, just getting the error prompt.
Log:
You can double click a model's Name or ID in the model panel to edit those
fields
UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> ui tool show Meeting
> meeting join andi name Kristen color #ff0000 faceImage "D:/National
> Institutes of Health/NIAID-NIH 3D - Documents/Testing/Images/download.jpg"
Joining meeting"andi" at chimeraxmeeting.net port 52203
Log from Fri Apr 14 09:17:41 2023UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open /Users/cruzp2/Desktop/Gordon_conference_session_AF_1umk_working_dd.cxs
> format session
Log from Thu Feb 2 11:36:33 2023UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open /Users/cruzp2/Desktop/Gordon_conference_session_AF_1umk_working.cxs
Log from Thu Feb 2 10:34:00 2023UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open /Users/cruzp2/Desktop/Gordon_conference_session_AF_1umk.cxs
Log from Wed Feb 1 14:51:18 2023UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open /Users/cruzp2/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/eNOS_Hba/Gordon_Conference/Gordon_conference_session.cxs
Log from Tue Jan 31 14:24:37 2023UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open "/Volumes/NO NAME/eNOS/enos_2Hb.cxs"
Log from Thu Jan 26 11:18:44 2023UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open /Users/cruzp2/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/eNOS_Hba/Gordon_Conference/cluster4_3_renumber_2Hb.cxs
Log from Tue Jan 24 12:31:18 2023UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open "/Users/cruzp2/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/eNOS_Hba/Steve_figure/cluster4_3 with color.cxs"
> format session
Log from Fri Jun 24 15:04:01 2022UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
> open "/Users/cruzp2/OneDrive - National Institutes of
> Health/eNOS_Hba/Steve_figure/cluster4_3 with color.cxs"
Log from Fri Jun 24 13:21:50 2022UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/cruzp2/OneDrive - National Institutes of
> Health/eNOS_Hba/Steve_figure/cluster4_3.pdb"
Summary of feedback from opening /Users/cruzp2/OneDrive - National Institutes
of Health/eNOS_Hba/Steve_figure/cluster4_3.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK FILENAME="complex_162w.pdb0"
Ignored bad PDB record found on line 2
REMARK ===============================================================
Ignored bad PDB record found on line 3
REMARK HADDOCK run for complex
Ignored bad PDB record found on line 4
REMARK initial structure: complex_162.pdb
Ignored bad PDB record found on line 5
REMARK ===============================================================
29 messages similar to the above omitted
Chain information for cluster4_3.pdb #1
---
Chain | Description
A | No description available
B | No description available
> select #1/A:1-999
3270 atoms, 3361 bonds, 9 pseudobonds, 403 residues, 3 models selected
> ui tool show "Color Actions"
> color sel dark slate gray
> color sel midnight blue
> color sel salmon
> select #1/A:2000=2999
Expected an objects specifier or a keyword
> select #1/A:2000-2999
3198 atoms, 3290 bonds, 400 residues, 1 model selected
> color sel sienna
> select clear
> select ::name="HEM"
252 atoms, 264 bonds, 36 pseudobonds, 6 residues, 2 models selected
> color sel byelement
> select clear
> select #1/B:1000-1999
1157 atoms, 1189 bonds, 6 pseudobonds, 146 residues, 2 models selected
> color sel forest green
> color sel sea green
> color sel medium sea green
> color sel medium spring green
> color sel light sea green
> select #1/B:3000-3999
1157 atoms, 1189 bonds, 6 pseudobonds, 146 residues, 2 models selected
> color sel sea green
> color sel olive drab
> color sel chartreuse
> color sel medium aquamarine
> select #1/B:1000-1999
1157 atoms, 1189 bonds, 6 pseudobonds, 146 residues, 2 models selected
> color sel cornflower blue
> select #1/B:3000-3999
1157 atoms, 1189 bonds, 6 pseudobonds, 146 residues, 2 models selected
> color sel cyan
> color sel green
> color sel turquoise
> color sel dark turquoise
> color sel medium aquamarine
> color sel light green
> color sel sky blue
> select clear
> select #1/B:2000-2999
1092 atoms, 1122 bonds, 6 pseudobonds, 140 residues, 2 models selected
> color sel medium aquamarine
> color sel cadet blue
> color sel teal
> color sel light sea green
> color sel turquoise
> color sel dark turquoise
> color sel lawn green
> color sel green yellow
> color sel pale green
> select #1/B:1-999
1092 atoms, 1122 bonds, 6 pseudobonds, 140 residues, 2 models selected
> color sel light sea green
> color sel medium aquamarine
> color sel turquoise
> color sel medium turquoise
> select clear
> select ::name="HEM"
252 atoms, 264 bonds, 36 pseudobonds, 6 residues, 2 models selected
> color sel byelement
> select clear
> select #1/B:1004-1017
106 atoms, 108 bonds, 14 residues, 1 model selected
> ui tool show "Color Actions"
> color sel orchid
> color sel pale violet red
> color sel medium orchid
> color sel orchid
> color sel violet
> color sel plum
[Repeated 1 time(s)]
> color sel violet
> select clear
> save "/Users/cruzp2/OneDrive - National Institutes of
> Health/eNOS_Hba/Steve_figure/cluster4_3 with color.cxs"
> select #1/A
6540 atoms, 6723 bonds, 18 pseudobonds, 806 residues, 3 models selected
> show sel surfaces
> close #1.2
> close #1.3
> select clear
> select #1/A
6540 atoms, 6723 bonds, 16 pseudobonds, 806 residues, 2 models selected
> surface sel
> close #1.2
> select clear
> select #1/A:2000-2999
3198 atoms, 3290 bonds, 400 residues, 1 model selected
> color sel light coral
> select clear
> select #1/A:2000-2999
3198 atoms, 3290 bonds, 400 residues, 1 model selected
> color sel light pink
> select clear
> save "/Users/cruzp2/OneDrive - National Institutes of
> Health/eNOS_Hba/Steve_figure/cluster4_3 with color.cxs"
> select #1/B:3087-3097
89 atoms, 90 bonds, 11 residues, 1 model selected
> color sel midnight blue
> color sel hot pink
> color sel pale violet red
> color sel hot pink
> color sel dark violet
> color sel antique white
> color sel light pink
> color sel dark blue
> color sel navajo white
[Repeated 1 time(s)]
> color sel orchid
> color sel hot pink
> 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="TRP"::name="TYR"::name="VAL"
10726 atoms, 11025 bonds, 1368 residues, 1 model selected
> hide sel atoms
> select clear
> select ::name="HEM"
252 atoms, 264 bonds, 36 pseudobonds, 6 residues, 2 models selected
> style sel ball
Changed 252 atom styles
> style sel sphere
Changed 252 atom styles
> select clear
> select #1/B:1117-1126
82 atoms, 86 bonds, 10 residues, 1 model selected
> color sel deep pink
> select #1/B:3087-3097
89 atoms, 90 bonds, 11 residues, 1 model selected
> color sel light pink
> color sel pale violet red
> color sel thistle
> color sel light coral
> color sel pale violet red
> color sel orchid
> color sel purple
> color sel medium purple
> color sel pale violet red
> color sel rebecca purple
> color sel pink
> color sel violet
> color sel lavender
> color sel powder blue
> color sel pale violet red
> select clear
> select /A:2125
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
157 atoms, 160 bonds, 19 residues, 1 model selected
> select up
3198 atoms, 3290 bonds, 400 residues, 1 model selected
> color sel coral
> select clear
> select /A:2125
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:2125
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:2125
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:2125
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
157 atoms, 160 bonds, 19 residues, 1 model selected
> select up
3198 atoms, 3290 bonds, 400 residues, 1 model selected
> color sel dark salmon
> select clear
> save "/Users/cruzp2/OneDrive - National Institutes of
> Health/eNOS_Hba/Steve_figure/cluster4_3 with color.cxs"
> help help:user
> select /A:432
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
143 atoms, 146 bonds, 18 residues, 1 model selected
> select up
2874 atoms, 2957 bonds, 359 residues, 1 model selected
> surface sel enclose sel
> select /A:2130
12 atoms, 12 bonds, 1 residue, 1 model selected
> select up
157 atoms, 160 bonds, 19 residues, 1 model selected
> select up
3198 atoms, 3290 bonds, 400 residues, 1 model selected
> surface sel enclose sel
> select clear
> select add #1.2
2874 atoms, 359 residues, 1 model selected
> hide #1.2 models
> show #1.2 models
> color sel salmon target s
> select subtract #1.2
1 model selected
> select add #1.2
2874 atoms, 359 residues, 1 model selected
> hide #1.2 models
> show #1.2 models
> hide #1.2 models
> show #1.2 models
> hide #1.3 models
> show #1.3 models
> select add #1.3
6072 atoms, 759 residues, 2 models selected
> select subtract #1.2
3198 atoms, 400 residues, 3 models selected
> color sel sandy brown target s
> color sel light salmon target s
> hide #1.3 models
> show #1.3 models
> hide #1.3 models
> show #1.3 models
> select clear
> save "/Users/cruzp2/OneDrive - National Institutes of
> Health/eNOS_Hba/Steve_figure/cluster4_3 with color.cxs"
> hide #1.2 models
> select clear
> select /A:220
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
157 atoms, 160 bonds, 19 residues, 2 models selected
> select up
2874 atoms, 2957 bonds, 359 residues, 2 models selected
> select up
3053 atoms, 3140 bonds, 382 residues, 2 models selected
> select up
6396 atoms, 6579 bonds, 800 residues, 3 models selected
> select down
3053 atoms, 3140 bonds, 382 residues, 3 models selected
> select up
6396 atoms, 6579 bonds, 800 residues, 3 models selected
> select down
3053 atoms, 3140 bonds, 382 residues, 3 models selected
> select up
6396 atoms, 6579 bonds, 800 residues, 3 models selected
> select up
6540 atoms, 6723 bonds, 806 residues, 3 models selected
> select up
11038 atoms, 11345 bonds, 1378 residues, 3 models selected
> select up
11038 atoms, 11345 bonds, 40 pseudobonds, 1378 residues, 4 models selected
> select up
11038 atoms, 11345 bonds, 40 pseudobonds, 1378 residues, 4 models selected
> select up
11038 atoms, 11345 bonds, 40 pseudobonds, 1378 residues, 4 models selected
> select up
11038 atoms, 11345 bonds, 40 pseudobonds, 1378 residues, 4 models selected
> select up
11038 atoms, 11345 bonds, 40 pseudobonds, 1378 residues, 4 models selected
> select #1/A:1-999
3270 atoms, 3361 bonds, 8 pseudobonds, 403 residues, 2 models selected
> surface sel enclose sel
> color sel salmon target s
> select clear
> select /A:2042
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:2390@CB
1 atom, 1 residue, 1 model selected
> select /A:2041
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /A:2042
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:2041
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /A:2041
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /A:2042
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:2023@NE2
1 atom, 1 residue, 1 model selected
> select /A:439@CA
1 atom, 1 residue, 1 model selected
> select clear
> save "/Users/cruzp2/OneDrive - National Institutes of
> Health/eNOS_Hba/Steve_figure/cluster4_3 with color.cxs"
——— End of log from Fri Jun 24 13:21:50 2022 ———
opened ChimeraX session
> swapaa mousemode /A:139 MET
> swapaa mousemode /A:438 TRP
> swapaa mousemode /A:412 PRO
> swapaa mousemode /A:2310 PHE
> ui tool show "Show Sequence Viewer"
> sequence chain /B
Alignment identifier is 1/B
> help help:user
> swapaa mousemode /A:2015 TYR
> select /B:36
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #1/B:36-50
131 atoms, 138 bonds, 15 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain /B
Alignment identifier is 1/B
> select /B:34-36
25 atoms, 25 bonds, 3 residues, 1 model selected
> select /B:34-43
85 atoms, 88 bonds, 10 residues, 1 model selected
swapaa cannot align to residues /B HEM 201 which has fewer than 3 backbone
atoms (N, C, CA)
> color sel red
> select clear
> swapaa mousemode /A:83 SER
> swapaa mousemode /A:68 PRO
> swapaa mousemode /A:435 TRP
> swapaa mousemode /A:84 VAL
> swapaa mousemode /A:81 GLY
[Repeated 1 time(s)]
> swapaa mousemode /A:70 GLY
> swapaa mousemode /A:140 LEU
> swapaa mousemode /A:439 MET
> swapaa mousemode /A:81 MET
> swapaa mousemode /A:79 ILE
> select
> ::name="ALA"::name="ARG"::name="ASN"::name="ASP"::name="CYS"::name="GLN"::name="GLU"::name="GLY"::name="HAR"::name="HIS"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TRP"::name="TYR"::name="VAL"
10746 atoms, 11044 bonds, 4 pseudobonds, 1370 residues, 2 models selected
> hide sel atoms
> select clear
> save "/Users/cruzp2/OneDrive - National Institutes of
> Health/eNOS_Hba/Steve_figure/cluster4_3 with color.cxs"
——— End of log from Fri Jun 24 15:04:01 2022 ———
opened ChimeraX session
> hide #1.2 models
> hide #1.3 models
> hide #1.1 models
> show #1.1 models
> hide #1.1 models
> close session
> open /Users/cruzp2/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/eNOS_Hba/Gordon_Conference/cluster4_3_sym_copy.pdb
Summary of feedback from opening /Users/cruzp2/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/eNOS_Hba/Gordon_Conference/cluster4_3_sym_copy.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK FILENAME="complex_162w.pdb0"
Ignored bad PDB record found on line 2
REMARK ===============================================================
Ignored bad PDB record found on line 3
REMARK HADDOCK run for complex
Ignored bad PDB record found on line 4
REMARK initial structure: complex_162.pdb
Ignored bad PDB record found on line 5
REMARK ===============================================================
29 messages similar to the above omitted
Start residue of secondary structure not found: HELIX 1 1 SER A 85 GLN A 87 1
3
Start residue of secondary structure not found: HELIX 2 2 LEU A 123 SER A 137
1 15
Start residue of secondary structure not found: HELIX 3 3 GLN A 144 THR A 160
1 17
Start residue of secondary structure not found: HELIX 4 4 GLU A 167 ASN A 180
1 14
Start residue of secondary structure not found: HELIX 5 5 ALA A 204 GLY A 222
1 19
282 messages similar to the above omitted
End residue of secondary structure not found: HELIX 30 30 ALA B 53 ALA B 71 1
19
Start residue of secondary structure not found: HELIX 31 31 VAL B 73 ALA B 79
1 7
Start residue of secondary structure not found: HELIX 32 32 SER B 81 LYS B 90
1 10
Start residue of secondary structure not found: HELIX 33 33 PRO B 95 HIS B 112
1 18
Start residue of secondary structure not found: HELIX 34 34 PRO B 119 LEU B
136 1 18
Start residue of secondary structure not found: HELIX 35 35 PRO B 1005 LYS B
1017 1 13
80 messages similar to the above omitted
End residue of secondary structure not found: HELIX 30 30 ALA B 53 ALA B 71 1
19
Start residue of secondary structure not found: HELIX 31 31 VAL B 73 ALA B 79
1 7
Start residue of secondary structure not found: HELIX 32 32 SER B 81 LYS B 90
1 10
Start residue of secondary structure not found: HELIX 33 33 PRO B 95 HIS B 112
1 18
Start residue of secondary structure not found: HELIX 34 34 PRO B 119 LEU B
136 1 18
Start residue of secondary structure not found: HELIX 35 35 PRO B 1005 LYS B
1017 1 13
51 messages similar to the above omitted
Chain information for cluster4_3_sym_copy.pdb
---
Chain | Description
1.1/A 1.2/A 1.4/A 1.6/A | No description available
1.8/A 1.9/A | No description available
1.1/B 1.2/B 1.5/B 1.6/B | No description available
1.8/B 1.9/B | No description available
> hide #!1.9 models
> hide #!1.8 models
> hide #!1.7 models
> hide #!1.6 models
> hide #!1.5 models
> hide #!1.4 models
> hide #!1.3 models
> hide #!1.2 models
> hide #!1.1 models
> show #!1.1 models
> close session
> open /Users/cruzp2/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/eNOS_Hba/Gordon_Conference/cluster4_3.pdb_cluster4_3_sym_copy.pdb
Summary of feedback from opening /Users/cruzp2/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/eNOS_Hba/Gordon_Conference/cluster4_3.pdb_cluster4_3_sym_copy.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK FILENAME="complex_162w.pdb0"
Ignored bad PDB record found on line 2
REMARK ===============================================================
Ignored bad PDB record found on line 3
REMARK HADDOCK run for complex
Ignored bad PDB record found on line 4
REMARK initial structure: complex_162.pdb
Ignored bad PDB record found on line 5
REMARK ===============================================================
29 messages similar to the above omitted
Chain information for cluster4_3.pdb_cluster4_3_sym_copy.pdb #1
---
Chain | Description
A | No description available
B | No description available
> help help:user
> combine #1 name enos_A
> combine #1 enos_B
Expected a keyword
> combine #1 name enos_B
> combine #1 name HB_A
> combine #1 name HB_B
> combine #1 name HB_C
> combine #1 name HB_D
> hide #!1 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> hide #!7 models
> select #2/B
4498 atoms, 4622 bonds, 26 pseudobonds, 572 residues, 3 models selected
> delete atoms (#!2 & sel)
> delete bonds (#!2 & sel)
> select #2/A:1000-2000
3270 atoms, 3362 bonds, 8 pseudobonds, 403 residues, 2 models selected
> delete atoms (#!2 & sel)
> delete bonds (#!2 & sel)
> show #!3 models
> hide #!2 models
> select #3/B
4498 atoms, 4622 bonds, 26 pseudobonds, 572 residues, 3 models selected
> delete atoms (#!3 & sel)
> delete bonds (#!3 & sel)
> select #2/A:0-999
3270 atoms, 3361 bonds, 9 pseudobonds, 403 residues, 3 models selected
> select #3/A:0-999
3270 atoms, 3361 bonds, 9 pseudobonds, 403 residues, 3 models selected
> delete atoms (#!3 & sel)
> delete bonds (#!3 & sel)
> show #!2 models
> combine #2-3 name enos_AB
Remapping chain ID 'A' in enos_B #3 to 'B'
> hide #!3 models
> hide #!2 models
> show #!2 models
> show #!3 models
> close #8
> combine #2-3 name enos_AB
Remapping chain ID 'A' in enos_B #3 to 'B'
> hide #!2 models
> hide #!3 models
> hide #!8 models
> show #!2 models
> show #!3 models
> hide #!2 models
> close #8
> show #!2 models
> hide #!2 models
> ui tool show "Change Chain IDs"
> select add #3
3270 atoms, 3362 bonds, 8 pseudobonds, 403 residues, 2 models selected
> select subtract #3
Nothing selected
> select add #3
3270 atoms, 3362 bonds, 8 pseudobonds, 403 residues, 2 models selected
> show #!1 models
> hide #!3 models
> select #1/A:1000-1999
3270 atoms, 3362 bonds, 8 pseudobonds, 403 residues, 2 models selected
> ui tool show "Change Chain IDs"
> changechains sel B
Cannot reassign chain ID to only part of polymeric chain
(cluster4_3.pdb_cluster4_3_sym_copy.pdb #1/A)
> select #1/B
4498 atoms, 4622 bonds, 26 pseudobonds, 572 residues, 3 models selected
> ui tool show "Change Chain IDs"
> changechains sel Z
Chain IDs of 572 residues changed
> select #1/A:1000-1999
3270 atoms, 3362 bonds, 8 pseudobonds, 403 residues, 2 models selected
> ui tool show "Change Chain IDs"
> changechains sel B
Cannot reassign chain ID to only part of polymeric chain
(cluster4_3.pdb_cluster4_3_sym_copy.pdb #1/A)
> select add #3
6540 atoms, 6724 bonds, 16 pseudobonds, 806 residues, 4 models selected
> ui tool show "Change Chain IDs"
> changechains sel B
Cannot reassign chain ID to only part of polymeric chain
(cluster4_3.pdb_cluster4_3_sym_copy.pdb #1/A)
> select add #1
14308 atoms, 14707 bonds, 52 pseudobonds, 1781 residues, 5 models selected
> select subtract #1
3270 atoms, 3362 bonds, 8 pseudobonds, 403 residues, 2 models selected
> hide #!1 models
> show #!3 models
> ui tool show "Change Chain IDs"
> changechains sel B
Chain IDs of 403 residues changed
> show #!2 models
> ui tool show "Renumber Residues"
> renumber #3/B:1067-1466 seqStart 67
400 residues renumbered
> select #2:67
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3:67
Nothing selected
> renumber #3/B:467-866 start 67
400 residues renumbered
> select #3:67
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide #!2 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!5 models
> show #!6 models
> show #!7 models
> hide #!6 models
> hide #!5 models
> show #!6 models
> hide #!7 models
> hide #!6 models
> show #!4 models
> select #4:1-1000
4362 atoms, 4483 bonds, 15 pseudobonds, 543 residues, 3 models selected
> select #4/A:1-1000
3270 atoms, 3361 bonds, 9 pseudobonds, 403 residues, 3 models selected
> select #4/B:1-1000
1092 atoms, 1122 bonds, 6 pseudobonds, 140 residues, 2 models selected
> select ~sel
60638 atoms, 62326 bonds, 230 pseudobonds, 7556 residues, 20 models selected
> show #!2 models
> hide #!4 models
> show #!4 models
> select add #4
61730 atoms, 63448 bonds, 237 pseudobonds, 7696 residues, 20 models selected
> select clear
> select #4/A
6540 atoms, 6723 bonds, 18 pseudobonds, 806 residues, 3 models selected
> hide #!2 models
> select
61730 atoms, 63448 bonds, 237 pseudobonds, 7696 residues, 20 models selected
> select clear
> select #4/A
6540 atoms, 6723 bonds, 18 pseudobonds, 806 residues, 3 models selected
> delete atoms (#!4 & sel)
> delete bonds (#!4 & sel)
> select #4/B,C,D
4498 atoms, 4622 bonds, 26 pseudobonds, 572 residues, 3 models selected
> select #4/B:1000-7000
3406 atoms, 3500 bonds, 19 pseudobonds, 432 residues, 3 models selected
> delete atoms (#!4 & sel)
> delete bonds (#!4 & sel)
> show #!5 models
> hide #!4 models
> select #5/A
6540 atoms, 6723 bonds, 18 pseudobonds, 806 residues, 3 models selected
> delete atoms (#!5 & sel)
> delete bonds (#!5 & sel)
> select #4/B:0-999,2000-7000
1092 atoms, 1122 bonds, 6 pseudobonds, 140 residues, 2 models selected
> select subtract #4
Nothing selected
> show #!4 models
> hide #!5 models
> show #!5 models
> hide #!4 models
> select #5/B:0-999,2000-7000
3341 atoms, 3433 bonds, 19 pseudobonds, 426 residues, 3 models selected
> delete atoms (#!5 & sel)
> delete bonds (#!5 & sel)
> show #!4 models
> show #!6 models
> hide #!5 models
> hide #!4 models
> select #5/A
Nothing selected
> select #6/A
6540 atoms, 6723 bonds, 18 pseudobonds, 806 residues, 3 models selected
> delete atoms (#!6 & sel)
> delete bonds (#!6 & sel)
> select #6/B:0-1999,3000-7000
3448 atoms, 3544 bonds, 25 pseudobonds, 433 residues, 3 models selected
> delete atoms (#!6 & sel)
> delete bonds (#!6 & sel)
> show #!5 models
> show #!4 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> show #!7 models
> select #7/A
6540 atoms, 6723 bonds, 18 pseudobonds, 806 residues, 3 models selected
> delete atoms (#!7 & sel)
> delete bonds (#!7 & sel)
> select #7/B:0-2999
3299 atoms, 3389 bonds, 13 pseudobonds, 425 residues, 3 models selected
> delete atoms (#!7 & sel)
> delete bonds (#!7 & sel)
Drag select of 42 atoms, 44 bonds, 6 pseudobonds
> delete atoms (#!7 & sel)
> delete bonds (#!7 & sel)
> show #!6 models
> show #!5 models
> show #!4 models
> select add #4
1092 atoms, 1122 bonds, 6 pseudobonds, 140 residues, 2 models selected
> select subtract #4
Nothing selected
> select add #4
1092 atoms, 1122 bonds, 6 pseudobonds, 140 residues, 2 models selected
> changechains sel A
Chain IDs of 140 residues changed
> select #4/A:109
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #4
1092 atoms, 1122 bonds, 6 pseudobonds, 140 residues, 2 models selected
> select subtract #4
Nothing selected
> select add #6
1050 atoms, 1078 bonds, 139 residues, 1 model selected
> changechains sel C
Chain IDs of 139 residues changed
> changechains sel C
Chain IDs of 0 residues changed
> select add #7
2207 atoms, 2267 bonds, 6 pseudobonds, 285 residues, 3 models selected
> select subtract #6
1157 atoms, 1189 bonds, 6 pseudobonds, 146 residues, 2 models selected
> select add #6
2207 atoms, 2267 bonds, 6 pseudobonds, 285 residues, 3 models selected
> select subtract #6
1157 atoms, 1189 bonds, 6 pseudobonds, 146 residues, 2 models selected
> changechains sel D
Chain IDs of 146 residues changed
> select subtract #7
Nothing selected
> hide #!7 models
> hide #!6 models
> hide #!5 models
> show #!6 models
> select add #6
1050 atoms, 1078 bonds, 139 residues, 1 model selected
> renumber #6/C start 2
139 residues renumbered
> show #!5 models
> select subtract #6
Nothing selected
> hide #!6 models
> hide #!4 models
> show #!7 models
> hide #!7 models
> show #!7 models
> show #!2 models
> show #!3 models
> hide #!2 models
> hide #!3 models
> select add #7
1157 atoms, 1189 bonds, 6 pseudobonds, 146 residues, 2 models selected
> renumber #7/D:3002-3146 start 2
145 residues renumbered
> show #!6 models
> show #!4 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> select subtract #7
Nothing selected
> show #!2 models
> show #!3 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> select ::name="HEM"
462 atoms, 484 bonds, 66 pseudobonds, 11 residues, 12 models selected
> select ::name="H4B"::name="HAR"::name="HEM"
582 atoms, 596 bonds, 74 pseudobonds, 19 residues, 12 models selected
> select ::name="HAR"
52 atoms, 40 bonds, 8 pseudobonds, 4 residues, 6 models selected
> select clear
> select add #4
1092 atoms, 1122 bonds, 6 pseudobonds, 140 residues, 2 models selected
> changechains sel AH
Chain IDs of 140 residues changed
> select add #5
2249 atoms, 2311 bonds, 12 pseudobonds, 286 residues, 4 models selected
> select subtract #4
1157 atoms, 1189 bonds, 6 pseudobonds, 146 residues, 2 models selected
> changechains sel BH
Chain IDs of 146 residues changed
> changechains sel BH
Chain IDs of 0 residues changed
> select add #6
2207 atoms, 2267 bonds, 6 pseudobonds, 285 residues, 3 models selected
> select subtract #5
1050 atoms, 1078 bonds, 139 residues, 1 model selected
> changechains sel CH
Chain IDs of 139 residues changed
> select add #7
2207 atoms, 2267 bonds, 6 pseudobonds, 285 residues, 3 models selected
> select subtract #6
1157 atoms, 1189 bonds, 6 pseudobonds, 146 residues, 2 models selected
> changechains sel DH
Chain IDs of 146 residues changed
> select clear
> save /Users/cruzp2/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/eNOS_Hba/Gordon_Conference/cluster4_3_renumber.cxs
> select clear
> hide #!3 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> hide #!7 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!4 models
> select #4/AH:201@NB
1 atom, 1 residue, 1 model selected
> ui tool show "Build Structure"
> build modify #4/AH:201@NB N 3 geometry trigonal resName UNL
> select #4/AH:201@HB1
1 atom, 1 residue, 1 model selected
> help help:credits.html
> hide sel atoms
> delete atoms sel
> delete bonds sel
> select #4/AH:201@HB2
1 atom, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
You must select exactly one atom to modify.
[Repeated 1 time(s)]Drag select of 1 residues
> select #4/AH:201@NB
1 atom, 1 residue, 1 model selected
> build modify #4/AH:201@NB N 2 geometry trigonal
[Repeated 1 time(s)]
> style sel stick
Changed 1 atom style
> style sel stick
Changed 1 atom style
> select clear
No visible atoms or bonds selected
> select add #4.1
6 pseudobonds, 1 model selected
> select subtract #4.2
6 pseudobonds, 1 model selected
> select subtract #4.1
Nothing selected
> select add #4.1
6 pseudobonds, 1 model selected
> close #4.1
> hide #4.2 models
> show #!5 models
> hide #!4 models
> select add #5.1
6 pseudobonds, 1 model selected
> select subtract #5.2
6 pseudobonds, 1 model selected
> select subtract #5.1
Nothing selected
> select add #5.1
6 pseudobonds, 1 model selected
> select subtract #5.2
6 pseudobonds, 1 model selected
> close #5.1
> select #5/BH:1201@NB
1 atom, 1 residue, 1 model selected
> show sel cartoons
> ui tool show "Build Structure"
> build modify #5/BH:1201@NB N 2 geometry trigonal resName UNL
> build modify #5/BH:1201@NB N 2 geometry trigonal
> style sel stick
Changed 1 atom style
> select clear
> show #!6 models
> hide #!5 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!6 models
> select add #7.1
6 pseudobonds, 1 model selected
> select subtract #7.2
6 pseudobonds, 1 model selected
> close #7.1
> select #7/DH:3148@NB
1 atom, 1 residue, 1 model selected
> build modify #7/DH:3148@NB N 2 geometry trigonal
> select #7/DH:3148@HB1
1 atom, 1 residue, 1 model selected
> style sel stick
Changed 1 atom style
> undo
[Repeated 2 time(s)]
> select #7/DH:3148@HB1
1 atom, 1 residue, 1 model selected
> select #7/DH:3148@HB1
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #7/DH:3148@NB
1 atom, 1 residue, 1 model selected
> build modify #7/DH:3148@NB N 2 geometry trigonal
> style sel stick
Changed 1 atom style
> select clear
> show #!6 models
> hide #!7 models
> show #!5 models
> hide #!6 models
> select #5/BH:1201@C4A
1 atom, 1 residue, 1 model selected
> select #5/BH:1201@C4A
1 atom, 1 residue, 1 model selected
> select #5/BH:1201@C4A
1 atom, 1 residue, 1 model selected
> select up
42 atoms, 46 bonds, 1 residue, 1 model selected
> select clear
[Repeated 1 time(s)]
> select #5/BH:1201@ND
1 atom, 1 residue, 1 model selected
> build modify #5/BH:1201@ND N 3 geometry tetrahedral
> build modify #5/BH:1201@ND N 2 geometry tetrahedral
> build modify #5/BH:1201@ND N 2 geometry tetrahedral resName HEM
> show #!4 models
> hide #!5 models
> select #4/AH:201@NB
1 atom, 1 residue, 1 model selected
> build modify #4/AH:201@NB N 2 geometry tetrahedral resName HEM
> show #!5 models
> show #!7 models
> hide #!5 models
> hide #!4 models
> show #!6 models
> show #!5 models
> show #!4 models
> show #!3 models
> show #!2 models
> hide #!7 models
> hide #!5 models
> hide #!4 models
> hide #!3 models
> hide #!2 models
> show #!1 models
> combine #1
> hide #!1 models
> hide #!8 models
> show #!8 models
> select #7 \- #7:3147
Expected a keyword
> select #7! #7:3147
Expected an objects specifier or a keyword
> select #7!~#7:3147
Expected an objects specifier or a keyword
> select #7~#7:3147
Expected an objects specifier or a keyword
> select #7 &~ #7:3147
1157 atoms, 1191 bonds, 146 residues, 1 model selected
> select #8 &~ #8:3147
10996 atoms, 11301 bonds, 38 pseudobonds, 1377 residues, 3 models selected
> hide #!8 models
> show #!8 models
> save /Users/cruzp2/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/eNOS_Hba/Gordon_Conference/cluster4_3_renumber.cxs
> hide #!8 models
> show #!8 models
> delete atoms (#!8 & sel)
> delete bonds (#!8 & sel)
> hide #!8 models
> show #!8 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> save /Users/cruzp2/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/eNOS_Hba/Gordon_Conference/cluster4_3_renumber.cxs
> combine #6,8 close true modelId 6 name HB_C
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> select #6/Z:3147@NB
1 atom, 1 residue, 1 model selected
> build modify #6/Z:3147@NB N 2 geometry tetrahedral colorByElement false
> undo
> select #6/Z:3147@HB1
1 atom, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select add #6.1
6 pseudobonds, 1 model selected
> close #6.1
> select #6/Z:3147@NB
1 atom, 1 residue, 1 model selected
> build modify #6/Z:3147@NB N 2 geometry trigonal colorByElement false
> style sel stick
Changed 1 atom style
> color sel byelement
> select clear
> save /Users/cruzp2/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/eNOS_Hba/Gordon_Conference/cluster4_3_renumber.cxs
> show #!2 models
> show #!3 models
> show #!4 models
> show #!5 models
> show #!7 models
> combine #2-7 name culster4_3_renumber
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> hide #!7 models
> select #8/B:1010@NB
1 atom, 1 residue, 1 model selected
> build modify #8/B:1010@NB N 2 geometry trigonal colorByElement false
> select #8/B:1010@HB2
1 atom, 1 residue, 1 model selected
> undo
[Repeated 1 time(s)]
> select #8/B:1010@HB2
1 atom, 1 residue, 1 model selected
> select add #8/B:1010@HB1
2 atoms, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
You must select exactly one atom to modify.
> select #8/B:1010@NB
1 atom, 1 residue, 1 model selected
> build modify #8/B:1010@NB N 2 geometry trigonal colorByElement false
> hide #8.1 models
> show #8.1 models
> select #8/B:1010@HB2
1 atom, 1 residue, 1 model selected
> select #8/B:1010@HB1
1 atom, 1 residue, 1 model selected
> select add #8/B:1010@HB2
2 atoms, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select #8/B:1010@NB
1 atom, 1 residue, 1 model selected
> style sel stick
Changed 1 atom style
> select clear
> select #8/B:1010@C1B
1 atom, 1 residue, 1 model selected
> select add #8/B:1010@NB
2 atoms, 1 residue, 1 model selected
> bond sel
Created 1 bond
> select clear
> select #8/B:1010@NB
1 atom, 1 residue, 1 model selected
> select add #8/B:1010@C4B
2 atoms, 1 residue, 1 model selected
> bond sel
Created 1 bond
> color sel byelement
> select #8/B:1010@C4B
1 atom, 1 residue, 1 model selected
> color sel byelement
> select #8/B:1010@C4B
1 atom, 1 residue, 1 model selected
> color sel byhetero
> select #8/A:510@NB
1 atom, 1 residue, 1 model selected
> build modify #8/A:510@NB N 2 geometry trigonal colorByElement false
> select #8/A:510@HB1
1 atom, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select #8/A:510@C4B
1 atom, 1 residue, 1 model selected
> select #8/A:510@NB
1 atom, 1 residue, 1 model selected
> select add #8/A:510@C4B
2 atoms, 1 residue, 1 model selected
> bond sel
Created 1 bond
> select clear
> select #8/A:510@NB
1 atom, 1 residue, 1 model selected
> style sel stick
Changed 1 atom style
> color sel byelement
> select #8/B:422
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel target ab
> hide sel target a
> select #8/B:424
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> save /Users/cruzp2/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/eNOS_Hba/Gordon_Conference/cluster4_3_renumber.cxs
> select clear
> save /Users/cruzp2/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/eNOS_Hba/Gordon_Conference/cluster4_3_renumber.cxs
> hide #!8 models
> show #!8 models
> combine #8 name cluster4_3_renumber_copy
> ui tool show Matchmaker
> matchmaker #9/B to #8/A pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker culster4_3_renumber, chain A (#8) with cluster4_3_renumber_copy,
chain B (#9), sequence alignment score = 3026.8
Fewer than 3 residues aligned; cannot match culster4_3_renumber, chain A with
cluster4_3_renumber_copy, chain B
> hide #!8 models
> show #!8 models
> ui tool show Matchmaker
> matchmaker #9/B to #8/A pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker culster4_3_renumber, chain A (#8) with cluster4_3_renumber_copy,
chain B (#9), sequence alignment score = 3026.8
Fewer than 3 residues aligned; cannot match culster4_3_renumber, chain A with
cluster4_3_renumber_copy, chain B
> select #8/A
3270 atoms, 3363 bonds, 9 pseudobonds, 403 residues, 3 models selected
> select #9/B
3270 atoms, 3364 bonds, 8 pseudobonds, 403 residues, 2 models selected
> matchmaker #9/A to #8/A pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker culster4_3_renumber, chain A (#8) with cluster4_3_renumber_copy,
chain A (#9), sequence alignment score = 3624.4
RMSD between 400 pruned atom pairs is 0.000 angstroms; (across all 400 pairs:
0.000)
> matchmaker #9/B to #8/A pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker culster4_3_renumber, chain A (#8) with cluster4_3_renumber_copy,
chain B (#9), sequence alignment score = 3026.8
Fewer than 3 residues aligned; cannot match culster4_3_renumber, chain A with
cluster4_3_renumber_copy, chain B
> hide #!8 models
> show #!1 models
> select clear
> select #1:1-999
4362 atoms, 4483 bonds, 15 pseudobonds, 543 residues, 3 models selected
> select #1/A:1-999
3270 atoms, 3361 bonds, 9 pseudobonds, 403 residues, 3 models selected
> hide #!9 models
> select #1/A:1000-1999
3270 atoms, 3362 bonds, 8 pseudobonds, 403 residues, 2 models selected
> matchmaker #1/A to #8/A pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker culster4_3_renumber, chain A (#8) with
cluster4_3.pdb_cluster4_3_sym_copy.pdb, chain A (#1), sequence alignment score
= 3624.4
RMSD between 400 pruned atom pairs is 0.000 angstroms; (across all 400 pairs:
0.000)
> show #!8 models
> show #!9 models
> hide #!8 models
> hide #!9 models
> show #!8 models
> show #!9 models
> hide #!9 models
> matchmaker #1/A & sel to #8/A pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker culster4_3_renumber, chain A (#8) with
cluster4_3.pdb_cluster4_3_sym_copy.pdb, chain A (#1), sequence alignment score
= 2078.6
RMSD between 400 pruned atom pairs is 0.240 angstroms; (across all 400 pairs:
0.240)
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!8 models
> show #!9 models
> select #9/B:254
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
91 atoms, 91 bonds, 12 residues, 1 model selected
> select up
3198 atoms, 3290 bonds, 400 residues, 1 model selected
> matchmaker #9/B & sel to #8/A pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker culster4_3_renumber, chain A (#8) with cluster4_3_renumber_copy,
chain B (#9), sequence alignment score = 3026.8
Fewer than 3 residues aligned; cannot match culster4_3_renumber, chain A with
cluster4_3_renumber_copy, chain B
> select #9/A:219
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
157 atoms, 160 bonds, 19 residues, 1 model selected
> select up
2874 atoms, 2957 bonds, 359 residues, 1 model selected
> matchmaker #9/A & sel to #8/B pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker culster4_3_renumber, chain B (#8) with cluster4_3_renumber_copy,
chain A (#9), sequence alignment score = 1866.5
RMSD between 359 pruned atom pairs is 0.167 angstroms; (across all 359 pairs:
0.167)
> show #!8 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> select clear
> save /Users/cruzp2/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/eNOS_Hba/Gordon_Conference/cluster4_3_renumber_2Hb.cxs
——— End of log from Tue Jan 24 12:31:18 2023 ———
opened ChimeraX session
> select /AH
3276 atoms, 3372 bonds, 420 residues, 3 models selected
> ui tool show "Color Actions"
> show sel & #!8-9 surfaces
> color sel green target s
> color sel medium sea green target s
> color sel medium spring green target s
> color sel dark turquoise target s
> color sel medium aquamarine target s
> color sel light green target s
> color sel sea green target s
> color sel medium sea green target s
> select /CH
3150 atoms, 3234 bonds, 417 residues, 3 models selected
> show sel & #!8-9 surfaces
> color sel pale green target s
> color sel light green target s
> color sel medium sea green target s
> select /AH
3276 atoms, 3372 bonds, 420 residues, 3 models selected
> color sel pale green target s
> color sel light green target s
> select /BH
3471 atoms, 3573 bonds, 438 residues, 3 models selected
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> color sel medium turquoise target s
> show sel & #!8-9 surfaces
> select /BH
3471 atoms, 3573 bonds, 438 residues, 3 models selected
> show sel & #!8-9 surfaces
> color sel medium turquoise target s
> color sel light sea green target s
> color sel steel blue target s
> color sel light sea green target s
> color sel medium turquoise target s
> color sel turquoise target s
> color sel medium turquoise target s
> color sel light sea green target s
> hide sel & #!8-9 surfaces
> hide #!9 models
> hide #!8 models
> select add #8
13352 atoms, 13739 bonds, 17 pseudobonds, 1670 residues, 7 models selected
> select add #9
23233 atoms, 23905 bonds, 34 pseudobonds, 2902 residues, 11 models selected
> select subtract #8
12195 atoms, 12548 bonds, 17 pseudobonds, 1524 residues, 10 models selected
> select subtract #9
1157 atoms, 1191 bonds, 146 residues, 4 models selected
> select subtract #5
Nothing selected
> show #!1 models
> show #!7 models
> hide #!7 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> select add #8
11038 atoms, 11357 bonds, 17 pseudobonds, 1378 residues, 3 models selected
> hide sel surfaces
> select clear
> hide #!8 models
> show #!9 models
> select add #9
11038 atoms, 11357 bonds, 17 pseudobonds, 1378 residues, 3 models selected
> hide sel surfaces
> select clear
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> ui tool show Matchmaker
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!9 models
> show #!9 models
> show #!1 models
> hide #!1 models
> matchmaker #!9 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 cluster4_3.pdb_cluster4_3_sym_copy.pdb, chain A (#1) with
cluster4_3_renumber_copy, chain A (#9), sequence alignment score = 3624.4
RMSD between 400 pruned atom pairs is 0.000 angstroms; (across all 400 pairs:
0.000)
> select add #1
11038 atoms, 11345 bonds, 44 pseudobonds, 1378 residues, 3 models selected
> hide #!9 models
> show #!9 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> select clear
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!8 models
> hide #!9 models
> show #!1 models
> hide #!8 models
> select #1/A:1-999
3270 atoms, 3361 bonds, 9 pseudobonds, 403 residues, 3 models selected
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!8 models
> hide #!1 models
> select #8/B:165
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
115 atoms, 117 bonds, 14 residues, 1 model selected
> select up
3198 atoms, 3290 bonds, 400 residues, 1 model selected
> matchmaker #!8 & sel to #1 & sel
No 'to' model specified
> select add #8
11038 atoms, 11357 bonds, 17 pseudobonds, 1378 residues, 3 models selected
> select subtract #8
3 models selected
> select add #8
11038 atoms, 11357 bonds, 17 pseudobonds, 1378 residues, 3 models selected
> select #1/A:1-999
3270 atoms, 3361 bonds, 9 pseudobonds, 403 residues, 3 models selected
> select #8/B
3270 atoms, 3364 bonds, 8 pseudobonds, 403 residues, 2 models selected
> show #!1 models
> hide #!8 models
> select #1/A:1000-1999
3270 atoms, 3362 bonds, 8 pseudobonds, 403 residues, 2 models selected
> show #!8 models
> select #8/A
3270 atoms, 3363 bonds, 9 pseudobonds, 403 residues, 3 models selected
> matchmaker #!8 & sel to #1 & sel
No 'to' model specified
> help help:user
> hide #!1 models
> hide #!8 models
> show #!1 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> matchstruct #8/A to #1:1000-1999
Unknown command: matchstruct #8/A to #1:1000-1999
> matchmaker #8/A to #1:1000-1999
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 cluster4_3.pdb_cluster4_3_sym_copy.pdb, chain A (#1) with
culster4_3_renumber, chain A (#8), sequence alignment score = 2078.6
RMSD between 400 pruned atom pairs is 0.240 angstroms; (across all 400 pairs:
0.240)
> show #!9 models
> show #!8 models
> hide #!1 models
> show #!1 models
> hide #!9 models
> show #!3 models
> hide #!3 models
> hide #!1 models
> show #!9 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> select add #8
11038 atoms, 11357 bonds, 17 pseudobonds, 1378 residues, 3 models selected
> select subtract #8
3 models selected
> save /Users/cruzp2/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/eNOS_Hba/Gordon_Conference/cluster4_3_renumber_2Hb.cxs
> color dark goldenrod target s
> select /AH
3276 atoms, 3372 bonds, 420 residues, 3 models selected
> select clear
> select add #8
11038 atoms, 11357 bonds, 17 pseudobonds, 1378 residues, 3 models selected
> show sel surfaces
> select clear
> select add #9
11038 atoms, 11357 bonds, 17 pseudobonds, 1378 residues, 3 models selected
> show sel surfaces
> select subtract #9
6 models selected
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!9 models
> show #!9 models
> hide #!8 models
> hide #!9 surfaces
> close #9.3-8
> close #9.2
> select #9/AH,BH,CH,DH
4456 atoms, 4584 bonds, 571 residues, 1 model selected
> show sel surfaces
> show #!8 models
> select clear
> help help:user
> save /Users/cruzp2/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/eNOS_Hba/Gordon_Conference/cluster4_3_renumber_2Hb.glb
> save /Users/cruzp2/cluster4_3_renumber_2Hb_texture.glb models #8-9
> textureColors true
> open 5f8m
Summary of feedback from opening 5f8m fetched from pdb
---
notes | Fetching compressed mmCIF 5f8m from
http://files.rcsb.org/download/5f8m.cif
Fetching CCD MG from http://ligand-expo.rcsb.org/reports/M/MG/MG.cif
Fetching CCD SO4 from http://ligand-expo.rcsb.org/reports/S/SO4/SO4.cif
Fetching CCD POP from http://ligand-expo.rcsb.org/reports/P/POP/POP.cif
Fetching CCD GOL from http://ligand-expo.rcsb.org/reports/G/GOL/GOL.cif
5f8m title:
Enterovirus 71 Polymerase Elongation Complex (C3S4/5 Form) [more info...]
Chain information for 5f8m #10
---
Chain | Description | UniProt
A | Genome polyprotein | E5RPG2_9ENTO
B | RNA (35-MER) |
C | RNA (5'-R(*UP*GP*UP*UP*CP*GP*AP*CP*GP*AP*GP*AP*GP*AP*GP*AP*CP*CP*U)-3') |
Non-standard residues in 5f8m #10
---
GOL — glycerol (glycerin; propane-1,2,3-triol)
MG — magnesium ion
POP — pyrophosphate 2-
SO4 — sulfate ion
ZN — zinc ion
> show #!10 target m
> hide #!8 models
> hide #!9 models
> close #10
> show #!8 models
> show #!9 models
> open 4r8i
Summary of feedback from opening 4r8i fetched from pdb
---
notes | Fetching compressed mmCIF 4r8i from
http://files.rcsb.org/download/4r8i.cif
Fetching CCD 0G from http://ligand-expo.rcsb.org/reports/0/0G/0G.cif
Fetching CCD 0C from http://ligand-expo.rcsb.org/reports/0/0C/0C.cif
Fetching CCD 0A from http://ligand-expo.rcsb.org/reports/0/0A/0A.cif
Fetching CCD 0U from http://ligand-expo.rcsb.org/reports/0/0U/0U.cif
Fetching CCD 0U1 from http://ligand-expo.rcsb.org/reports/0/0U1/0U1.cif
Fetching CCD SR from http://ligand-expo.rcsb.org/reports/S/SR/SR.cif
Fetching CCD K from http://ligand-expo.rcsb.org/reports/K/K/K.cif
4r8i title:
High Resolution Structure of a Mirror-Image RNA Oligonucleotide Aptamer in
Complex with the Chemokine CCL2 [more info...]
Chain information for 4r8i #10
---
Chain | Description | UniProt
A | C-C motif chemokine 2 | CCL2_HUMAN
B | Mirror-Image RNA Oligonucleotide Aptamer NOXE36 |
Non-standard residues in 4r8i #10
---
0A — L-adenosine-5'-monophosphate
0U1 — 2'-methylselenyl-2'-deoxy-L-uridine-5'-monophosphate
K — potassium ion
NA — sodium ion
SR — strontium ion
> hide #!8 models
> hide #!9 models
> close #10
> show #!9 models
> show #!8 models
> show #!2 models
> select add #2
3270 atoms, 3361 bonds, 9 pseudobonds, 403 residues, 3 models selected
> hide #!2 models
> save /Users/cruzp2/Desktop/enos_2Hb.cxs
——— End of log from Thu Jan 26 11:18:44 2023 ———
opened ChimeraX session
> select subtract #2
Nothing selected
> hide #9.2 models
> hide #9.3 models
> hide #9.4 models
> hide #9.5 models
> hide #8.8 models
> hide #8.7 models
> hide #8.6 models
> hide #8.5 models
> hide #8.4 models
> hide #8.3 models
> hide #8.2 models
> hide #9.1 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!8 models
> select #9/A,B
6540 atoms, 6727 bonds, 16 pseudobonds, 806 residues, 2 models selected
> hide sel cartoons
> hide sel atoms
> show #!8 models
> select #8/A:210
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #8/A
3270 atoms, 3363 bonds, 9 pseudobonds, 403 residues, 3 models selected
> ui tool show "Color Actions"
> color sel goldenrod
> color sel sandy brown
> color sel goldenrod
[Repeated 1 time(s)]
> color sel dark orange
> color sel goldenrod
> color sel dark goldenrod
> color sel dark khaki
> color sel khaki
> ui tool show "Color Actions"
> color sel goldenrod
> show sel surfaces
> select #8/B
3270 atoms, 3364 bonds, 8 pseudobonds, 403 residues, 2 models selected
> color sel sandy brown
[Repeated 1 time(s)]
> show sel surfaces
> select #8/AH
1092 atoms, 1124 bonds, 140 residues, 1 model selected
> help help:user
> color sel dark turquoise
> color sel medium turquoise
> color sel light sea green
> color sel cornflower blue
> color sel medium aquamarine
> color sel teal
> color sel medium aquamarine
> color sel cadet blue
> color sel aquamarine
> color sel dark green
> color sel aquamarine
> color sel pale green
> color sel dark sea green
> color sel pale green
> show sel surfaces
> lighting full
> select #8/AH
1092 atoms, 1124 bonds, 140 residues, 1 model selected
> color sel pale green
> color sel light green
> color sel dark sea green
> color sel pale green
> color sel medium aquamarine
> color sel green yellow
> color sel lime
> color sel chartreuse
> color sel lawn green
> color sel spring green
> color sel sea green
> color sel medium sea green
> color sel light sea green
[Repeated 1 time(s)]
> color sel medium aquamarine
> color sel light green
> color sel pale green
> color sel light green
> color sel aquamarine
> color sel light sea green
> color sel light green
> lighting soft
> lighting full
> lighting simple
> color sel light green
> color sel dark khaki
> color sel dark turquoise
> color sel medium spring green
> color sel light green
> color sel pale green
> color sel light green
> hide #!9 models
> select #8/CH
1050 atoms, 1078 bonds, 139 residues, 1 model selected
> ui tool show "Color Actions"
> color sel light sea green
> color sel medium sea green
> color sel light green
> color sel dark sea green
> show sel surfaces
> color sel dark sea green
> select #8/CB
Nothing selected
> select #8/BH
1157 atoms, 1191 bonds, 146 residues, 1 model selected
> color sel medium aquamarine
> color sel light sky blue
> color sel sky blue
> color sel light sky blue
> color sel pale turquoise
> color sel teal
> color sel steel blue
> show sel surfaces
> color sel blue
> color sel royal blue
> color sel dodger blue
> color sel light sky blue
> color sel sky blue
> color sel light blue
> color sel sky blue
> color sel turquoise
> color sel medium turquoise
> lighting simple
> lighting soft
> lighting full
> color sel dark turquoise
> color sel cyan
> color sel medium aquamarine
> color sel dark turquoise
> color sel turquoise
> hide #8.6 models
> show #8.6 models
> hide #8.4 models
> hide #!8 models
> show #!9 models
> show #9.2 models
> show #9.4 models
> hide #!9 models
> open 6bb5
6bb5 title:
Human Oxy-Hemoglobin [more info...]
Chain information for 6bb5 #10
---
Chain | Description | UniProt
A | Hemoglobin subunit alpha | HBA_HUMAN
B | Hemoglobin subunit beta | HBB_HUMAN
Non-standard residues in 6bb5 #10
---
HEM — protoporphyrin IX containing Fe (HEME)
OXY — oxygen molecule
6bb5 mmCIF Assemblies
---
1| author_and_software_defined_assembly
> select #10/B:132
22 atoms, 21 bonds, 1 residue, 1 model selected
> select up
283 atoms, 285 bonds, 20 residues, 1 model selected
> select up
2210 atoms, 2239 bonds, 145 residues, 1 model selected
> open rcsb_bio:6bb5
Summary of feedback from opening 6bb5 fetched from rcsb_bio
---
note | Fetching compressed 6bb5 bioassembly 1 from
https://files.rcsb.org/download/6bb5-assembly1.cif
6bb5 bioassembly 1 title:
Human Oxy-Hemoglobin [more info...]
Chain information for 6bb5 bioassembly 1 #11
---
Chain | Description
A A-2 | Hemoglobin subunit alpha
B B-2 | Hemoglobin subunit beta
Non-standard residues in 6bb5 bioassembly 1 #11
---
HEM — protoporphyrin IX containing Fe (HEME)
OXY — oxygen molecule
Opened 1 biological assemblies for 6bb5
> close #10
> select #11/A:4
14 atoms, 14 bonds, 1 residue, 1 model selected
> select up
208 atoms, 210 bonds, 14 residues, 1 model selected
> select up
2098 atoms, 2126 bonds, 139 residues, 1 model selected
> color sel aquamarine
> select #11//chain_id='A-2':77
14 atoms, 14 bonds, 1 residue, 1 model selected
> select up
67 atoms, 67 bonds, 5 residues, 1 model selected
> select up
2098 atoms, 2126 bonds, 139 residues, 1 model selected
> color sel dark sea green
> select #11/B:53
10 atoms, 9 bonds, 1 residue, 1 model selected
> select up
90 atoms, 90 bonds, 7 residues, 1 model selected
> select up
2210 atoms, 2239 bonds, 145 residues, 1 model selected
> color sel orchid
> select clear
> select add #11
9134 atoms, 9038 bonds, 16 pseudobonds, 794 residues, 2 models selected
> show sel surfaces
> hide #11.2 models
> show #11.2 models
> hide #11.3 models
> show #11.3 models
> hide #!11 models
> show #!11 models
> hide #11.1 models
> show #11.1 models
> hide #11.2 models
> show #11.2 models
> hide #11.3 models
> show #11.3 models
> close #11
> show #!8 models
> select #8/CH:78
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
192 atoms, 194 bonds, 27 residues, 2 models selected
> select up
1050 atoms, 1078 bonds, 139 residues, 2 models selected
> show sel surfaces
> select #8/BH
1157 atoms, 1191 bonds, 146 residues, 1 model selected
> color sel dark turquoise
> color sel cyan
> color sel turquoise
[Repeated 2 time(s)]
> select #8/DH
1157 atoms, 1191 bonds, 146 residues, 1 model selected
> color sel dark turquoise
[Repeated 1 time(s)]
> show sel surfaces
> color sel deep sky blue
> color sel dark turquoise
> color sel medium turquoise
> color sel teal
> color sel steel blue
> color sel cadet blue
> color sel steel blue
[Repeated 2 time(s)]
> color sel slate gray
> color sel royal blue
> color sel aquamarine
> color sel sky blue
[Repeated 1 time(s)]
> color sel light sky blue
[Repeated 1 time(s)]
> color sel light blue
> color sel pale turquoise
> color sel light steel blue
> color sel powder blue
> color sel light sky blue
> color sel light blue
> color sel light sky blue
> select #8/BH
1157 atoms, 1191 bonds, 146 residues, 1 model selected
> color sel turquoise
[Repeated 2 time(s)]
> select clear
> save "/Users/cruzp2/OneDrive - National Institutes of
> Health/eNOS_Hba/Gordon_Conference/Gordon_conference_session.cxs"
> select ::name="HEM"
1008 atoms, 1088 bonds, 72 pseudobonds, 24 residues, 14 models selected
> color sel byelement
> select ::name="HAR"
104 atoms, 80 bonds, 16 pseudobonds, 8 residues, 10 models selected
> color sel byelement
> select ::name="H4B"
136 atoms, 144 bonds, 8 residues, 5 models selected
> color sel byelement
[Repeated 1 time(s)]
> show #!9 models
> select #9/AH
1092 atoms, 1124 bonds, 140 residues, 1 model selected
> color sel light green
> select #9/BH
1157 atoms, 1191 bonds, 146 residues, 1 model selected
> color sel sky blue
> color sel light blue
> show sel surfaces
> select #9/CH
1050 atoms, 1078 bonds, 139 residues, 1 model selected
> color sel dark olive green
> color sel dark slate gray
> color sel dark sea green
> select #9/DH:61
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #9/DH
1157 atoms, 1191 bonds, 146 residues, 1 model selected
> color sel light sky blue
> show sel surfaces
> select ::name="HEM"
1008 atoms, 1088 bonds, 72 pseudobonds, 24 residues, 14 models selected
> color sel byelement
> select clear
> select add #9
11038 atoms, 11357 bonds, 16 pseudobonds, 1378 residues, 2 models selected
> help help:user
> transparency sel 50 target s
> transparency sel 50 target r
> transparency sel 30 target r
> transparency sel 20 target r
> transparency sel 0 target r
> transparency sel 30 target s
> hide #!9 models
> show #!9 models
> select clear
> select #9/BH
1157 atoms, 1191 bonds, 146 residues, 1 model selected
> color sel light blue
[Repeated 1 time(s)]
> color sel turquoise
> color sel light blue
> select clear
> save "/Users/cruzp2/OneDrive - National Institutes of
> Health/eNOS_Hba/Gordon_Conference/Gordon_conference_session.cxs"
> select #9/BH
1157 atoms, 1191 bonds, 146 residues, 1 model selected
> transparency sel 30 target s
> select clear
> save "/Users/cruzp2/OneDrive - National Institutes of
> Health/eNOS_Hba/Gordon_Conference/Gordon_conference_session.cxs"
> hide #!9 models
> hide #8.5 models
> select #8/BH:4-17
Nothing selected
> hide #8.3 models
> hide #8.4 models
> hide #8.6 models
> hide #8.7 models
> hide #8.8 models
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A #2/A #3/B #8/A #8/B #9/A #9/B
Alignment identifier is 1
> ui tool show "Show Sequence Viewer"
> sequence chain #8/DH
Alignment identifier is 8/DH
> sequence chain #8/BH
Alignment identifier is 8/BH
> ui tool show "Renumber Residues"
> renumber #8/BH:1002-1146 seqStart 2
145 residues renumbered
> ui tool show "Renumber Residues"
> renumber #8/BH:141-285 start 2
145 residues renumbered
> select #8/BH:4-17
106 atoms, 108 bonds, 14 residues, 1 model selected
> ui tool show "Color Actions"
> color sel red
> select #8/BH:117-126
82 atoms, 86 bonds, 10 residues, 1 model selected
> color sel green
> select #8/BH:87-97
89 atoms, 90 bonds, 11 residues, 1 model selected
> select #8/DH:87-97
89 atoms, 90 bonds, 11 residues, 1 model selected
> color sel blue
> select #8/A:107
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #8/A:108
Nothing selected
> select #8/A:106
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:107
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #8/B:108
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui tool show "Renumber Residues"
> save "/Users/cruzp2/OneDrive - National Institutes of
> Health/eNOS_Hba/Gordon_Conference/Gordon_conference_session.cxs"
——— End of log from Tue Jan 31 14:24:37 2023 ———
opened ChimeraX session
> select #8/B:108
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/B:480
Nothing selected
> select #8/B:460
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #8/B:108-466
2874 atoms, 2957 bonds, 359 residues, 1 model selected
> ui tool show "Renumber Residues"
> renumber #8/B:108-466 start 122
359 residues renumbered
> select clear
> save /Users/cruzp2/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/eNOS_Hba/Gordon_Conference/Gordon_conference_session.cxs
> select #8/B:117-126
40 atoms, 39 bonds, 5 residues, 1 model selected
> select #8/BH:117-126
82 atoms, 86 bonds, 10 residues, 1 model selected
> color sel lime
> color sel spring green
> color sel chartreuse
> color sel medium spring green
> color sel yellow green
> color sel chartreuse
> color sel lime green
> color sel sea green
> color sel green
> select clear
> save /Users/cruzp2/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/eNOS_Hba/Gordon_Conference/Gordon_conference_session.cxs
> show #!5 models
> hide #!5 models
> show #8.5 models
> show #8.8 models
> show #8.7 models
> show #8.6 models
> show #!9 models
> hide #!9 models
> show #8.4 models
> show #8.3 models
> hide #8.8 models
> hide #8.7 models
> hide #8.6 models
> hide #8.5 models
> hide #8.4 models
> hide #8.3 models
> select #8/BH:6
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> color sel byelement
> select #8/A:67
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
[Repeated 1 time(s)]
> color sel byelement
> select #8/B:97
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select #8/A:67
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel byhetero
[Repeated 1 time(s)]
> select #8/B:97@CA
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 2 models selected
> color sel byelement
> select #8/B:98
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byelement
> select #8/BH:7
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select clear
> select #8/BH:6
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel sphere
Changed 9 atom styles
> style sel stick
Changed 9 atom styles
> style sel ball
Changed 9 atom styles
> select #8/A:67
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel ball
Changed 9 atom styles
> select #8/B:97
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #8/B:97
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #8/B:96
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/B:97
11 atoms, 10 bonds, 1 residue, 1 model selected
> style sel ball
Changed 11 atom styles
> select #8/B:98
11 atoms, 10 bonds, 1 residue, 1 model selected
> style sel ball
Changed 11 atom styles
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain #8/AH
Alignment identifier is 8/AH
> select #8/AH:9-123
870 atoms, 895 bonds, 115 residues, 1 model selected
> select #8/AH:9-135
958 atoms, 984 bonds, 127 residues, 1 model selected
> select clear
> select #8/AH:33
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #8/AH:33-37
43 atoms, 45 bonds, 5 residues, 1 model selected
> select #8/AH:34
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/AH:34-46
113 atoms, 119 bonds, 13 residues, 1 model selected
> select #8/AH:34
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/AH:34-43
85 atoms, 88 bonds, 10 residues, 1 model selected
> color sel purple
> select clear
> show #8.7 models
> select #8/AH:34
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/AH:34-43
85 atoms, 88 bonds, 10 residues, 1 model selected
> name frozen HBAX1 sel
> select clear
> save /Users/cruzp2/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/eNOS_Hba/Gordon_Conference/Gordon_conference_session.cxs
> open 1hbb
Summary of feedback from opening 1hbb fetched from pdb
---
note | Fetching compressed mmCIF 1hbb from
http://files.rcsb.org/download/1hbb.cif
1hbb title:
High-resolution X-ray study of deoxyhemoglobin rothschild 37Β TRP-> arg: A
mutation that creates an intersubunit chloride-binding site [more info...]
Chain information for 1hbb #10
---
Chain | Description | UniProt
A C | HEMOGLOBIN A (DEOXY) (ALPHA CHAIN) | HBA_HUMAN
B D | HEMOGLOBIN A (DEOXY) (BETA CHAIN) | HBB_HUMAN
Non-standard residues in 1hbb #10
---
HEM — protoporphyrin IX containing Fe (HEME)
> hide #!8 models
> select #10/A
1176 atoms, 1143 bonds, 5 pseudobonds, 206 residues, 2 models selected
> show #!8 models
> hide #!10 models
> hide #8.7 models
> select #10/A:34-42
74 atoms, 76 bonds, 9 residues, 1 model selected
> show #!10 models
> hide #!8 models
> hide #!10 models
> show #!8 models
> show #!9 models
> select #8/A:34-43
Nothing selected
> select #8/AH:34-43
85 atoms, 88 bonds, 10 residues, 1 model selected
> color (#!8 & sel) yellow
> color (#!8 & sel) orange
> color (#!8 & sel) cyan
> color (#!8 & sel) dark gray
> color (#!8 & sel) gray
> color (#!8 & sel) yellow
> select clear
> show #8.3 models
> help help:user
> save /Users/cruzp2/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/eNOS_Hba/Gordon_Conference/Gordon_conference_session.cxs
> hide #9
> undo
> hide #9 target m
> show #9 target m
> alias list
> show #8.4 models
> show #8.5 models
> show #8.6 models
> show #8.7 models
> show #8.8 models
> close #10
> ui tool show AlphaFold
> alphafold match #8/A
Fetching compressed AlphaFold A0A2R9BVK1 from
https://alphafold.ebi.ac.uk/files/AF-A0A2R9BVK1-F1-model_v4.cif
1 AlphaFold model found using sequence similarity searches: A0A2R9BVK1 (chain
A)
AlphaFold chains matching culster4_3_renumber
---
Chain| UniProt Name| UniProt Id| RMSD| Length| Seen| % Id
A | A0A2R9BVK1_PANPA | A0A2R9BVK1 | 0.57 | 562 | 400 | 78
Opened 1 AlphaFold model
> close #10
> alphafold match NOS3_HUMAN
1 AlphaFold model found using UniProt identifier: P29474 (UniProt NOS3_HUMAN)
Opened 1 AlphaFold model
> ui tool show Matchmaker
> matchmaker #10/A to #8/A pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker culster4_3_renumber, chain A (#8) with AlphaFold NOS3_HUMAN, chain
A (#10), sequence alignment score = 1966.4
RMSD between 392 pruned atom pairs is 0.618 angstroms; (across all 400 pairs:
1.170)
> hide #8.6 models
Fetching PAE using AlphaFold database version 2
> alphafold pae #10 uniprotId P29474 version 2
Fetching compressed AlphaFold PAE P29474 from
https://alphafold.ebi.ac.uk/files/AF-P29474-F1-predicted_aligned_error_v2.json
> color #10:64-475 lime
> color #10:1155-1203 lime
> color #10:1-69 lime
> color #10:519-721 lime
> alphafold pae #10 colorDomains true
> show #8.6 models
> alphafold match NOS3_HUMAN
1 AlphaFold model found using UniProt identifier: P29474 (UniProt NOS3_HUMAN)
Opened 1 AlphaFold model
> matchmaker #11/A to #8/B pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker culster4_3_renumber, chain B (#8) with AlphaFold NOS3_HUMAN, chain
A (#11), sequence alignment score = 1995.4
RMSD between 389 pruned atom pairs is 0.624 angstroms; (across all 400 pairs:
1.170)
> alphafold pae #10 colorDomains true
Fetching PAE using AlphaFold database version 2
> alphafold pae #11 uniprotId P29474 version 2
> alphafold pae #11 colorDomains true
> save /Users/cruzp2/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/eNOS_Hba/Gordon_Conference/Gordon_conference_session_AF.cxs
> help help:user
> open /Users/cruzp2/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/eNOS_Hba/rosetta_reductase/VR/r_0409_3.pdb
Summary of feedback from opening /Users/cruzp2/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/eNOS_Hba/rosetta_reductase/VR/r_0409_3.pdb
---
warnings | Ignored bad PDB record found on line 9209
CAPRI_rank 0
Ignored bad PDB record found on line 9210
Fnat 0
Ignored bad PDB record found on line 9211
I_sc -24.5951
Ignored bad PDB record found on line 9212
Irms 14.1115
Ignored bad PDB record found on line 9213
Irms_leg 13.0251
590 messages similar to the above omitted
Chain information for r_0409_3.pdb #12
---
Chain | Description
A | No description available
B | No description available
C | No description available
> ui tool show Matchmaker
> open 1umk
1umk title:
The Structure of Human Erythrocyte NADH-cytochrome b5 Reductase [more info...]
Chain information for 1umk #13
---
Chain | Description | UniProt
A | NADH-cytochrome b5 reductase | NCB5R_HUMAN
Non-standard residues in 1umk #13
---
FAD — flavin-adenine dinucleotide
> ui tool show Matchmaker
[Repeated 1 time(s)]
> matchmaker #13 to #12/C pairing bs
Parameters
---
Chain pairing | bs
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 r_0409_3.pdb, chain C (#12) with 1umk, chain A (#13), sequence
alignment score = 1431.6
RMSD between 271 pruned atom pairs is 0.001 angstroms; (across all 271 pairs:
0.001)
> combine #12,13 name r_0409_3_FAD
Remapping chain ID 'A' in 1umk #13 to 'D'
> hide #!9 models
> hide #10 models
> ui tool show Matchmaker
> matchmaker #!14 to #8/A pairing bs
Parameters
---
Chain pairing | bs
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 culster4_3_renumber, chain A (#8) with r_0409_3_FAD, chain A (#14),
sequence alignment score = 618.2
RMSD between 104 pruned atom pairs is 0.042 angstroms; (across all 180 pairs:
21.551)
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> hide #11 models
> show #11 models
> show #10 models
> hide #!12 models
> hide #13 models
> select ::name="FAD"
106 atoms, 116 bonds, 2 residues, 2 models selected
> ui tool show "Color Actions"
> color sel byelement
> style sel & #!14 sphere
Changed 53 atom styles
> select clear
> select add #14
12167 atoms, 11579 bonds, 33 pseudobonds, 1602 residues, 2 models selected
> show sel surfaces
> hide #14.5 models
> show #14.5 models
> hide #14.5 models
> select ::name="FAD"
106 atoms, 116 bonds, 2 residues, 2 models selected
> hide #!14 models
> show #!14 models
> hide #14.2 models
> hide #14.3 models
> hide #14.4 models
> show #14.5 models
> hide #14.5 models
> show #14.5 models
> hide #14.5 models
> select #14/A,B,C
9196 atoms, 9296 bonds, 33 pseudobonds, 577 residues, 2 models selected
> hide sel cartoons
> select #14/A,B,C
9196 atoms, 9296 bonds, 33 pseudobonds, 577 residues, 2 models selected
> delete atoms (#!14 & sel)
> delete bonds (#!14 & sel)
> show #14.5 models
> hide #14.5 models
> show #14.5 models
> hide #14.5 models
> select #14/D
2971 atoms, 2283 bonds, 1025 residues, 1 model selected
> show sel surfaces
> color #14 #12894cff
> hide #14.5 models
> select ::name="FAD"
106 atoms, 116 bonds, 2 residues, 2 models selected
> color sel byelement target cspf
[Repeated 1 time(s)]
> color sel byelement
> select clear
> show #14.5 models
> save /Users/cruzp2/Desktop/Gordon_conference_session_AF_1umk.cxs
——— End of log from Wed Feb 1 14:51:18 2023 ———
opened ChimeraX session
> select ::name="FAD"::name="H4B"::name="HAR"::name="HEM"::name="HOH"
2860 atoms, 1428 bonds, 88 pseudobonds, 1548 residues, 16 models selected
> style sel & #!8,14 sphere
Changed 1118 atom styles
> select clear
[Repeated 1 time(s)]
> save /Users/cruzp2/Desktop/Gordon_conference_session_AF_1umk_working.cxs
> show #!1 models
> hide #!1 models
> show #!1 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> close #1-7
> help help:user
> combine #8 close true model(D 1 name cluster4_4_renumber
Expected a keyword
> combine #8 close true modelID 1 name cluster4_4_renumber
Expected a keyword
> combine #8 close true modelID #1 name cluster4_4_renumber
Expected a keyword
> combine #8 close true modelID #1
Expected a keyword
> combine #8 close true modelID 1
Expected a keyword
> combine #8 modelID 1
Expected a keyword
> combine #8
> close #1
> combine #8.1-8
No structures specified
> combine #8,8.1-8
No structures specified
> rename #8 cluster_4_3_renumber id 1
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #10 models
> hide #11 models
> show #11 models
> show #10 models
> show #!1 models
> rename #2 cluster_4_3_renumber_copy id 2
> rename #9 cluster_4_3_renumber_copy id 2
> show #!2 models
> rename #14 rosetta_0409_3_FAD id 3
> rename #10 AlphaFold NOS3_HUMAN id 4
Expected a keyword
> rename #10 AlphaFold_NOS3_HUMAN id 4
> rename #11 AlphaFold_NOS3_HUMAN_copy id 5
> close #13#12
> save /Users/cruzp2/Desktop/Gordon_conference_session_AF_1umk_working.cxs
> hide #5 models
> hide #4 models
> hide #!3 models
> hide #!2 models
> hide #1.8 models
> hide #1.7 models
> hide #1.6 models
> hide #1.5 models
> hide #1.4 models
> hide #1.3 models
> select #1/BH,CH,DH
3364 atoms, 3460 bonds, 431 residues, 1 model selected
> select #1/BH,CH,DH,Z
3406 atoms, 3506 bonds, 432 residues, 1 model selected
> select #1/AH,BH,CH,DH,Z
4498 atoms, 4630 bonds, 572 residues, 1 model selected
> name HB1 #1/AH,BH,CH,DH,Z
> hide sel atoms
> hide sel cartoons
> save /Users/cruzp2/Desktop/Gordon_conference_session_AF_1umk_working.cxs
——— End of log from Thu Feb 2 10:34:00 2023 ———
opened ChimeraX session
> alias a show #1/AH target r;show #1:201;~sel
> a
Nothing selected
> save /Users/cruzp2/Desktop/Gordon_conference_session_AF_1umk_working_a.cxs
> alias b show #1/BH,CH,DH,Z target r;show #1:201,1201,3147,3148 target a;~sel
> b
Nothing selected
> save /Users/cruzp2/Desktop/Gordon_conference_session_AF_1umk_working_b.cxs
> alias c show #1/BH:6
> alias c show #1/BH:6 target
> alias c show #1/BH:6 target a
> c
> help help:user
> save /Users/cruzp2/Desktop/Gordon_conference_session_AF_1umk_working_c.cxs
> show #1.3
> hide #1.3
> show #1.3-1.8
> show #1.3
> hide #1.3
> show #1.3-8
> hide #1.3-8
> alias delete show #1.3-8
Expected fewer arguments
> alias delete show #1.3-8
Expected fewer arguments
> alias delete show "#1.3-8"
Expected fewer arguments
> alias e show #1.3-8
> alias dd show #1.3-8
> alias e show #1.3-8
> e
> save /Users/cruzp2/Desktop/Gordon_conference_session_AF_1umk_working_dd.cxs
——— End of log from Thu Feb 2 11:36:33 2023 ———
opened ChimeraX session
> meeting start andi
Meeting "andi" started at chimeraxmeeting.net port 52203
Participants can join with command "meeting andi"
Connection from ::1 port 54162 established, waiting for join message
Connection accepted from ::1 port 54162
Disconnected from ::1 port 54162
Connection from ::1 port 54184 established, waiting for join message
Connection accepted from ::1 port 54184
Connection from ::1 port 54192 established, waiting for join message
Connection accepted from ::1 port 54192
——— End of log from Fri Apr 14 09:17:41 2023 ———
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 1584, in _mouse_hover_cb
self._participant._send_message(msg)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 972, in _send_message
msg_bytes = MessageStream.message_as_bytes(msg)
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\meeting\meeting.py", line 1306, in message_as_bytes
bytes = packb(message)
File "C:\Program Files\ChimeraX\bin\lib\site-packages\msgpack\\__init__.py",
line 38, in packb
return Packer(**kwargs).pack(o)
File "msgpack\\_packer.pyx", line 294, in msgpack._cmsgpack.Packer.pack
File "msgpack\\_packer.pyx", line 300, in msgpack._cmsgpack.Packer.pack
File "msgpack\\_packer.pyx", line 297, in msgpack._cmsgpack.Packer.pack
File "msgpack\\_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack
File "msgpack\\_packer.pyx", line 264, in msgpack._cmsgpack.Packer._pack
File "msgpack\\_packer.pyx", line 291, in msgpack._cmsgpack.Packer._pack
TypeError: can not serialize 'numpy.uint8' object
Error processing trigger "mouse hover":
TypeError: can not serialize 'numpy.uint8' object
File "msgpack\\_packer.pyx", line 291, in msgpack._cmsgpack.Packer._pack
See log for complete Python traceback.
> lighting simple
OpenGL version: 3.3.0 NVIDIA 466.47
OpenGL renderer: NVIDIA GeForce RTX 2080 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.9.11
Locale: en_US.cp1252
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: windows
Manufacturer: HP
Model: HP Z4 G4 Workstation
OS: Microsoft Windows 10 Enterprise (Build 19044)
Memory: 137,220,087,808
MaxProcessMemory: 137,438,953,344
CPU: 20 Intel(R) Core(TM) i9-10900X CPU @ 3.70GHz
OSLanguage: en-US
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
asttokens: 2.1.0
Babel: 2.11.0
backcall: 0.2.0
blockdiag: 3.0.0
build: 0.8.0
certifi: 2022.9.24
cftime: 1.6.2
charset-normalizer: 2.1.1
ChimeraX-AddCharge: 1.4
ChimeraX-AddH: 2.2.1
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.6
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.41.5
ChimeraX-AtomicLibrary: 8.0.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3
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: 2.7.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.1
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.2
ChimeraX-CommandLine: 1.2.4
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.5
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.3
ChimeraX-DockPrep: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 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: 1.1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.1
ChimeraX-MatchMaker: 2.0.9
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.8
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.6
ChimeraX-ModelPanel: 1.3.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.1
ChimeraX-MouseModes: 1.1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.9.1
ChimeraX-PDB: 2.6.8
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-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
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
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.7.2
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
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.1.3
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.24.3
ChimeraX-uniprot: 2.2.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.1.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.1
ChimeraX-WebServices: 1.1.0
ChimeraX-Zone: 1.0.1
colorama: 0.4.5
comtypes: 1.1.10
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.32
debugpy: 1.6.4
decorator: 5.1.1
docutils: 0.19
entrypoints: 0.4
executing: 1.2.0
filelock: 3.7.1
fonttools: 4.38.0
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.33
imagecodecs: 2022.7.31
imagesize: 1.4.1
importlib-metadata: 5.1.0
ipykernel: 6.15.3
ipython: 8.4.0
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.1.2
jupyter-client: 7.3.4
jupyter-core: 5.1.0
kiwisolver: 1.4.4
line-profiler: 3.5.1
lxml: 4.9.1
lz4: 4.0.2
MarkupSafe: 2.1.1
matplotlib: 3.5.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.0
networkx: 2.8.5
numexpr: 2.8.4
numpy: 1.23.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pickleshare: 0.7.5
Pillow: 9.2.0
pip: 22.2.2
pkginfo: 1.8.3
platformdirs: 2.5.4
prompt-toolkit: 3.0.33
psutil: 5.9.1
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.12.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2022.6
pywin32: 303
pyzmq: 24.0.1
qtconsole: 5.3.1
QtPy: 2.3.0
RandomWords: 0.4.0
requests: 2.28.1
scipy: 1.9.0
setuptools: 65.1.1
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 5.1.1
sphinx-autodoc-typehints: 1.19.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tifffile: 2022.7.31
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.2
traitlets: 5.3.0
urllib3: 1.26.13
wcwidth: 0.2.5
webcolors: 1.12
wheel: 0.37.1
wheel-filename: 1.4.1
WMI: 1.5.1
zipp: 3.11.0
Change History (2)
comment:1 by , 3 years ago
| Component: | Unassigned → VR |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Error while hovering mouse in VR |
comment:2 by , 3 years ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
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Fixed in ChimeraX 1.6 release candidate and daily build (available April 15).
This error when using the meeting command and hovering the mouse happened when using a custom participant color. Setting the custom color with the color button or by specifying it with the meeting command color option caused the color to be specified as uint8 values instead of simple integer and the uint8 was not handled by the meeting network synchronization code. Fixed my making the code always use integer values when transmitting colors.
Hadn't seen this bug before because meeting is usually used in VR, not with desktop display, and participant color usually isn't changed. So that makes it a rare problem.