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#15320 closed defect (limitation)
ChimeraX off screen
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | UI | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.4.1-x86_64-i386-64bit
ChimeraX Version: 1.8rc202405202242 (2024-05-20 22:42:21 UTC)
Description
Had a problem where I cannot resize the ChimeraX window, and cannot grab a corner becuase it is off screen. This is an issue since the command bar is at the bottom of the window.
Log:
UCSF ChimeraX version: 1.8rc202405202242 (2024-05-20)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/corriedacosta/Library/CloudStorage/Dropbox/Documents - Dropbox/Protein Tools/ChimeraX/2 | CXS files/2 | Matchmaker | AF2 vs PDBIDs/vs7QL6.cxs"
Log from Mon May 27 16:07:17 2024UCSF ChimeraX version: 1.8rc202405202242
(2024-05-20)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/corriedacosta/Library/CloudStorage/Dropbox/Documents - Dropbox/Protein Tools/ChimeraX/2 | CXS files/2 | Matchmaker | AF2 vs PDBIDs/vs7QL6.cxs"
Log from Mon May 27 14:31:24 2024 Startup Messages
---
warnings | No presets found in custom preset folder /Users/corriedacosta/Library/CloudStorage/Dropbox/Documents - Dropbox/Protein Tools/ChimeraX/4 | Misc
No presets found in custom preset folder /Users/corriedacosta/Library/CloudStorage/Dropbox/Documents - Dropbox/Protein Tools/ChimeraX/2 | CXS files
No presets found in custom preset folder /Users/corriedacosta/Library/CloudStorage/Dropbox/Documents - Dropbox/Protein Tools/ChimeraX/5 | Tutorials
No presets found in custom preset folder /Users/corriedacosta/Library/CloudStorage/Dropbox/Documents - Dropbox/Protein Tools/ChimeraX/1 | CIF files
No presets found in custom preset folder /Users/corriedacosta/Library/CloudStorage/Dropbox/Documents - Dropbox/Protein Tools/ChimeraX/3 | Scripts
1 messages similar to the above omitted
> cd "/Users/corriedacosta/Library/CloudStorage/Dropbox/Documents -
> Dropbox/Protein Tools/ChimeraX"
Current working directory is:
/Users/corriedacosta/Library/CloudStorage/Dropbox/Documents - Dropbox/Protein
Tools/ChimeraX
UCSF ChimeraX version: 1.8rc202405202242 (2024-05-20)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/corriedacosta/Library/CloudStorage/Dropbox/Documents - Dropbox/Protein Tools/ChimeraX/1 | CIF files/7ql6.cif"
7ql6.cif title:
Torpedo muscle-type nicotinic acetylcholine receptor - carbamylcholine-bound
conformation [more info...]
Chain information for 7ql6.cif #1
---
Chain | Description | UniProt
A D | Acetylcholine receptor subunit alpha | ACHA_TETCF 1-437
B | Acetylcholine receptor subunit beta | ACHB_TETCF 1-469
C | Acetylcholine receptor subunit delta | ACHD_TETCF 1-501
E | Acetylcholine receptor subunit gamma | ACHG_TETCF 1-489
Non-standard residues in 7ql6.cif #1
---
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)
CCE — 2-[(aminocarbonyl)oxy]-N,N,N-trimethylethanaminium (carbamyl-choline)
MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose)
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> hide atoms
> show cartoons
> lighting soft
> graphics silhouettes true
> hide #1.1
> open "/Users/corriedacosta/Library/CloudStorage/Dropbox/Documents - Dropbox/Protein Tools/ChimeraX/2 | CXS files/2 | Matchmaker | AF2 vs PDBIDs/AF2 models/Torpedo7QL6_AF2_m1.pdb"
Chain information for Torpedo7QL6_AF2_m1.pdb #2
---
Chain | Description
B C | No description available
D | No description available
E | No description available
F | No description available
> open "/Users/corriedacosta/Library/CloudStorage/Dropbox/Documents - Dropbox/Protein Tools/ChimeraX/2 | CXS files/2 | Matchmaker | AF2 vs PDBIDs/AF2 models/AncDGE_AF2_m1.pdb"
Chain information for AncDGE_AF2_m1.pdb #3
---
Chain | Description
B C | No description available
D | No description available
E F | No description available
> open "/Users/corriedacosta/Library/CloudStorage/Dropbox/Documents - Dropbox/Protein Tools/ChimeraX/2 | CXS files/2 | Matchmaker | AF2 vs PDBIDs/AF2 models/AdultHS_AF2_m4.pdb"
Chain information for AdultHS_AF2_m4.pdb #4
---
Chain | Description
B C | No description available
D | No description available
E | No description available
F | No description available
> open "/Users/corriedacosta/Library/CloudStorage/Dropbox/Documents - Dropbox/Protein Tools/ChimeraX/2 | CXS files/2 | Matchmaker | AF2 vs PDBIDs/AF2 models/FetalHS_AF2_m1.pdb"
Chain information for FetalHS_AF2_m1.pdb #5
---
Chain | Description
B C | No description available
D | No description available
E | No description available
F | No description available
> open "/Users/corriedacosta/Library/CloudStorage/Dropbox/Documents - Dropbox/Protein Tools/ChimeraX/2 | CXS files/2 | Matchmaker | AF2 vs PDBIDs/AF2 models/Banc81het_AF2Mod_m9.pdb"
Chain information for Banc81het_AF2Mod_m9.pdb #6
---
Chain | Description
A B | No description available
C D | No description available
E | No description available
> hide atoms
> show cartoons
> lighting soft
> graphics silhouettes true
> view
> select /A:1-433
6596 atoms, 6777 bonds, 1 pseudobond, 818 residues, 3 models selected
> select clear
> select :CCE
20 atoms, 18 bonds, 2 residues, 1 model selected
> show sel surfaces
> color (#!1 & sel) red
> select clear
> save "/Users/corriedacosta/Library/CloudStorage/Dropbox/Documents - Dropbox/Protein Tools/ChimeraX/2 | CXS files/2 | Matchmaker | AF2 vs PDBIDs/vs7QL6.cxs"
> set bgColor black
> set bgColor transparent
> set bgColor white
> set bgColor #ffffff00
> save "/Users/corriedacosta/Library/CloudStorage/Dropbox/Documents - Dropbox/Protein Tools/ChimeraX/2 | CXS files/2 | Matchmaker | AF2 vs PDBIDs/vs7QL6.cxs"
——— End of log from Mon May 27 14:31:24 2024 ———
opened ChimeraX session
> ui tool show Matchmaker
> matchmaker #2/C#2/D#2/E#2/B#2/F to #1/A#1/B#1/C#1/D#1/E pairing ss
> showAlignment true
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 7ql6.cif, chain A (#1) with Torpedo7QL6_AF2_m1.pdb, chain C (#2),
sequence alignment score = 2163.8
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: 7ql6.cif #1/A,
Torpedo7QL6_AF2_m1.pdb #2/C
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
Matchmaker 7ql6.cif, chain B (#1) with Torpedo7QL6_AF2_m1.pdb, chain D (#2),
sequence alignment score = 2280.1
Alignment identifier is 2
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2
Hiding conservation header for alignment 2
Chains used in RMSD evaluation for alignment 2: 7ql6.cif #1/B,
Torpedo7QL6_AF2_m1.pdb #2/D
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2
Matchmaker 7ql6.cif, chain C (#1) with Torpedo7QL6_AF2_m1.pdb, chain E (#2),
sequence alignment score = 2471.4
Alignment identifier is 3
Showing conservation header ("seq_conservation" residue attribute) for
alignment 3
Hiding conservation header for alignment 3
Chains used in RMSD evaluation for alignment 3: 7ql6.cif #1/C,
Torpedo7QL6_AF2_m1.pdb #2/E
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 3
Matchmaker 7ql6.cif, chain D (#1) with Torpedo7QL6_AF2_m1.pdb, chain B (#2),
sequence alignment score = 2044.4
Alignment identifier is 4
Showing conservation header ("seq_conservation" residue attribute) for
alignment 4
Hiding conservation header for alignment 4
Chains used in RMSD evaluation for alignment 4: 7ql6.cif #1/D,
Torpedo7QL6_AF2_m1.pdb #2/B
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 4
Matchmaker 7ql6.cif, chain E (#1) with Torpedo7QL6_AF2_m1.pdb, chain F (#2),
sequence alignment score = 2388.2
Alignment identifier is 5
Showing conservation header ("seq_conservation" residue attribute) for
alignment 5
Hiding conservation header for alignment 5
Chains used in RMSD evaluation for alignment 5: 7ql6.cif #1/E,
Torpedo7QL6_AF2_m1.pdb #2/F
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 5
RMSD between 1860 pruned atom pairs is 0.886 angstroms; (across all 1990
pairs: 1.179)
> view name p1
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> view name p1
[Repeated 1 time(s)]
> save "/Users/corriedacosta/Library/CloudStorage/Dropbox/Documents - Dropbox/Protein Tools/ChimeraX/2 | CXS files/2 | Matchmaker | AF2 vs PDBIDs/vs7QL6.cxs"
> ui tool show Matchmaker
> matchmaker #3/B#3/D#3/F#3/C#3/E to #1/A#1/B#1/C#1/D#1/E pairing ss
> showAlignment true
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 7ql6.cif, chain A (#1) with AncDGE_AF2_m1.pdb, chain B (#3),
sequence alignment score = 1879.7
Alignment identifier is 6
Showing conservation header ("seq_conservation" residue attribute) for
alignment 6
Hiding conservation header for alignment 6
Chains used in RMSD evaluation for alignment 6: 7ql6.cif #1/A,
AncDGE_AF2_m1.pdb #3/B
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 6
Matchmaker 7ql6.cif, chain B (#1) with AncDGE_AF2_m1.pdb, chain D (#3),
sequence alignment score = 1520
Alignment identifier is 7
Showing conservation header ("seq_conservation" residue attribute) for
alignment 7
Hiding conservation header for alignment 7
Chains used in RMSD evaluation for alignment 7: 7ql6.cif #1/B,
AncDGE_AF2_m1.pdb #3/D
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 7
Matchmaker 7ql6.cif, chain C (#1) with AncDGE_AF2_m1.pdb, chain F (#3),
sequence alignment score = 1751.2
Alignment identifier is 8
Showing conservation header ("seq_conservation" residue attribute) for
alignment 8
Hiding conservation header for alignment 8
Chains used in RMSD evaluation for alignment 8: 7ql6.cif #1/C,
AncDGE_AF2_m1.pdb #3/F
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 8
Matchmaker 7ql6.cif, chain D (#1) with AncDGE_AF2_m1.pdb, chain C (#3),
sequence alignment score = 1777.1
Alignment identifier is 9
Showing conservation header ("seq_conservation" residue attribute) for
alignment 9
Hiding conservation header for alignment 9
Chains used in RMSD evaluation for alignment 9: 7ql6.cif #1/D,
AncDGE_AF2_m1.pdb #3/C
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 9
Matchmaker 7ql6.cif, chain E (#1) with AncDGE_AF2_m1.pdb, chain E (#3),
sequence alignment score = 1763.7
Alignment identifier is 10
Showing conservation header ("seq_conservation" residue attribute) for
alignment 10
Hiding conservation header for alignment 10
Chains used in RMSD evaluation for alignment 10: 7ql6.cif #1/E,
AncDGE_AF2_m1.pdb #3/E
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 10
RMSD between 1835 pruned atom pairs is 0.969 angstroms; (across all 1978
pairs: 1.334)
> matchmaker #3/B#3/D#3/F#3/C#3/E to #1/A#1/B#1/C#1/D#1/E pairing ss
> showAlignment true
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 7ql6.cif, chain A (#1) with AncDGE_AF2_m1.pdb, chain B (#3),
sequence alignment score = 1879.7
Alignment identifier is 11
Showing conservation header ("seq_conservation" residue attribute) for
alignment 11
Hiding conservation header for alignment 11
Chains used in RMSD evaluation for alignment 11: 7ql6.cif #1/A,
AncDGE_AF2_m1.pdb #3/B
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 11
Matchmaker 7ql6.cif, chain B (#1) with AncDGE_AF2_m1.pdb, chain D (#3),
sequence alignment score = 1520
Alignment identifier is 12
Showing conservation header ("seq_conservation" residue attribute) for
alignment 12
Hiding conservation header for alignment 12
Chains used in RMSD evaluation for alignment 12: 7ql6.cif #1/B,
AncDGE_AF2_m1.pdb #3/D
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 12
Matchmaker 7ql6.cif, chain C (#1) with AncDGE_AF2_m1.pdb, chain F (#3),
sequence alignment score = 1751.2
Alignment identifier is 13
Showing conservation header ("seq_conservation" residue attribute) for
alignment 13
Hiding conservation header for alignment 13
Chains used in RMSD evaluation for alignment 13: 7ql6.cif #1/C,
AncDGE_AF2_m1.pdb #3/F
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 13
Matchmaker 7ql6.cif, chain D (#1) with AncDGE_AF2_m1.pdb, chain C (#3),
sequence alignment score = 1777.1
Alignment identifier is 14
Showing conservation header ("seq_conservation" residue attribute) for
alignment 14
Hiding conservation header for alignment 14
Chains used in RMSD evaluation for alignment 14: 7ql6.cif #1/D,
AncDGE_AF2_m1.pdb #3/C
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 14
Matchmaker 7ql6.cif, chain E (#1) with AncDGE_AF2_m1.pdb, chain E (#3),
sequence alignment score = 1763.7
Alignment identifier is 15
Showing conservation header ("seq_conservation" residue attribute) for
alignment 15
Hiding conservation header for alignment 15
Chains used in RMSD evaluation for alignment 15: 7ql6.cif #1/E,
AncDGE_AF2_m1.pdb #3/E
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 15
RMSD between 1835 pruned atom pairs is 0.969 angstroms; (across all 1978
pairs: 1.334)
> view name p1
> save "/Users/corriedacosta/Library/CloudStorage/Dropbox/Documents - Dropbox/Protein Tools/ChimeraX/2 | CXS files/2 | Matchmaker | AF2 vs PDBIDs/vs7QL6.cxs"
[Repeated 1 time(s)]
> select ~sel & ##selected
Nothing selected
> view name p2
> view p1
> view p2
> save "/Users/corriedacosta/Library/CloudStorage/Dropbox/Documents - Dropbox/Protein Tools/ChimeraX/2 | CXS files/2 | Matchmaker | AF2 vs PDBIDs/vs7QL6.cxs"
——— End of log from Mon May 27 16:07:17 2024 ———
opened ChimeraX session
> ui tool show Matchmaker
> matchmaker #4/C#4/D#4/E#4/B#4/F to #1/A#1/B#1/C#1/D#1/E pairing ss
> showAlignment true
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 7ql6.cif, chain A (#1) with AdultHS_AF2_m4.pdb, chain C (#4),
sequence alignment score = 1879.7
Alignment identifier is 16
Showing conservation header ("seq_conservation" residue attribute) for
alignment 16
Hiding conservation header for alignment 16
Chains used in RMSD evaluation for alignment 16: 7ql6.cif #1/A,
AdultHS_AF2_m4.pdb #4/C
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 16
Matchmaker 7ql6.cif, chain B (#1) with AdultHS_AF2_m4.pdb, chain D (#4),
sequence alignment score = 1520
Alignment identifier is 17
Showing conservation header ("seq_conservation" residue attribute) for
alignment 17
Hiding conservation header for alignment 17
Chains used in RMSD evaluation for alignment 17: 7ql6.cif #1/B,
AdultHS_AF2_m4.pdb #4/D
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 17
Matchmaker 7ql6.cif, chain C (#1) with AdultHS_AF2_m4.pdb, chain E (#4),
sequence alignment score = 1734
Alignment identifier is 18
Showing conservation header ("seq_conservation" residue attribute) for
alignment 18
Hiding conservation header for alignment 18
Chains used in RMSD evaluation for alignment 18: 7ql6.cif #1/C,
AdultHS_AF2_m4.pdb #4/E
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 18
Matchmaker 7ql6.cif, chain D (#1) with AdultHS_AF2_m4.pdb, chain B (#4),
sequence alignment score = 1777.1
Alignment identifier is 19
Showing conservation header ("seq_conservation" residue attribute) for
alignment 19
Hiding conservation header for alignment 19
Chains used in RMSD evaluation for alignment 19: 7ql6.cif #1/D,
AdultHS_AF2_m4.pdb #4/B
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 19
Matchmaker 7ql6.cif, chain E (#1) with AdultHS_AF2_m4.pdb, chain F (#4),
sequence alignment score = 1545.5
Alignment identifier is 20
Showing conservation header ("seq_conservation" residue attribute) for
alignment 20
Hiding conservation header for alignment 20
Chains used in RMSD evaluation for alignment 20: 7ql6.cif #1/E,
AdultHS_AF2_m4.pdb #4/F
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 20
RMSD between 1773 pruned atom pairs is 1.001 angstroms; (across all 1986
pairs: 1.569)
OpenGL version: 4.1 ATI-5.5.17
OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro16,1
Processor Name: 8-Core Intel Core i9
Processor Speed: 2.4 GHz
Number of Processors: 1
Total Number of Cores: 8
L2 Cache (per Core): 256 KB
L3 Cache: 16 MB
Hyper-Threading Technology: Enabled
Memory: 64 GB
System Firmware Version: 2022.100.22.0.0 (iBridge: 21.16.4222.0.0,0)
OS Loader Version: 580~1678
Software:
System Software Overview:
System Version: macOS 14.4.1 (23E224)
Kernel Version: Darwin 23.4.0
Time since boot: 19 minutes, 10 seconds
Graphics/Displays:
Intel UHD Graphics 630:
Chipset Model: Intel UHD Graphics 630
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3e9b
Revision ID: 0x0002
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Support: Metal 3
AMD Radeon Pro 5500M:
Chipset Model: AMD Radeon Pro 5500M
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 8 GB
Vendor: AMD (0x1002)
Device ID: 0x7340
Revision ID: 0x0040
ROM Revision: 113-D3220E-190
VBIOS Version: 113-D32206U1-019
Option ROM Version: 113-D32206U1-019
EFI Driver Version: 01.A1.190
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 3072 x 1920 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
DELL U2515H:
Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
UI Looks like: 2560 x 1440 @ 60.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: RYM1V4CP047L
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Adapter Type: DVI or HDMI
Adapter Firmware Version: ff.c8
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57
ChimeraX-AtomicLibrary: 14.0.5
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.4
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.4
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8rc202405202242
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.3
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
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: 1.2.2
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-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
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: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.16
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.4
ChimeraX-PDB: 2.7.5
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.0.4
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.4
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.1
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.51.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.2
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.10
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.43
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4
traitlets: 5.14.2
typing-extensions: 4.11.0
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.10
Change History (9)
comment:1 by , 17 months ago
| Component: | Unassigned → UI |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → ChimeraX off screen |
comment:2 by , 17 months ago
| Cc: | added |
|---|---|
| Status: | accepted → feedback |
comment:3 by , 17 months ago
ChimeraX was on screen. The chimney liner got pushed off screen. I had a large number of matchmaker alignments opened in the cxs file. When these all opened it pushed the command line off screen and I couldn't get it back. I had to remake the file without showing all the alignments.
Hope this helps.
Corrie
Get Outlook for Android<https://aka.ms/AAb9ysg>
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Tuesday, May 28, 2024 3:01:06 PM
To: Corrie daCosta <cdacosta@uottawa.ca>; pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>
Cc: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #15320: ChimeraX off screen
Attention : courriel externe | external email
#15320: ChimeraX off screen
---------------------------------+----------------------
Reporter: cdacosta@… | Owner: pett
Type: defect | Status: feedback
Priority: normal | Milestone:
Component: UI | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
---------------------------------+----------------------
Changes (by pett):
* cc: Tom Goddard (added)
* status: accepted => feedback
Comment:
Hi Corrie,
Thanks for reporting this problem. Did ChimeraX start offscreen,
or was it positioned there later somehow? Was it fully offscreen, or only
partially?
--Eric
Eric Pettersen
UCSF Computer Graphics Lab
--
Ticket URL: <https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Ftrac%2FChimeraX%2Fticket%2F15320%23comment%3A2&data=05%7C02%7Ccdacosta%40uottawa.mail.onmicrosoft.com%7C8a2e9467740843ed3ac608dc7f488559%7Cd41fdab17e154cfdb5fa7200e54deb6b%7C1%7C0%7C638525196659058127%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=zcxMvtXYSUywDCpWmKygYH%2FNZuDv6Aipj0Kpm80J6Pg%3D&reserved=0<https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/15320#comment:2>>
ChimeraX <https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimerax%2F&data=05%7C02%7Ccdacosta%40uottawa.mail.onmicrosoft.com%7C8a2e9467740843ed3ac608dc7f488559%7Cd41fdab17e154cfdb5fa7200e54deb6b%7C1%7C0%7C638525196659068880%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=d3ytR%2FHPonzxbcdEL7ATVkf%2BPP0xjgJX0O93Ah7DkYs%3D&reserved=0<https://www.rbvi.ucsf.edu/chimerax/>>
ChimeraX Issue Tracker
comment:4 by , 17 months ago
Chimney liner (lol) is command line.
Get Outlook for Android<https://aka.ms/AAb9ysg>
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Tuesday, May 28, 2024 6:30:02 PM
To: pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>; Corrie daCosta <cdacosta@uottawa.ca>
Cc: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #15320: ChimeraX off screen
Attention : courriel externe | external email
#15320: ChimeraX off screen
---------------------------------+----------------------
Reporter: cdacosta@… | Owner: pett
Type: defect | Status: feedback
Priority: normal | Milestone:
Component: UI | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
---------------------------------+----------------------
Comment (by cdacosta@…):
{{{
ChimeraX was on screen. The chimney liner got pushed off screen. I had a
large number of matchmaker alignments opened in the cxs file. When these
all opened it pushed the command line off screen and I couldn't get it
back. I had to remake the file without showing all the alignments.
Hope this helps.
Corrie
Get Outlook for Android<https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Faka.ms%2FAAb9ysg&data=05%7C02%7Ccdacosta%40uottawa.mail.onmicrosoft.com%7Cd7cad2ac2726463fa08908dc7f660240%7Cd41fdab17e154cfdb5fa7200e54deb6b%7C1%7C0%7C638525323319681820%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=oQngXoVyxgjroIk4nzn3Tm60Rra7bh6S8Z2%2FKmFqJYQ%3D&reserved=0<https://aka.ms/AAb9ysg>>
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Tuesday, May 28, 2024 3:01:06 PM
To: Corrie daCosta <cdacosta@uottawa.ca>; pett@cgl.ucsf.edu
<pett@cgl.ucsf.edu>
Cc: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #15320: ChimeraX off screen
Attention : courriel externe | external email
#15320: ChimeraX off screen
---------------------------------+----------------------
Reporter: cdacosta@… | Owner: pett
Type: defect | Status: feedback
Priority: normal | Milestone:
Component: UI | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
---------------------------------+----------------------
Changes (by pett):
* cc: Tom Goddard (added)
* status: accepted => feedback
Comment:
Hi Corrie,
Thanks for reporting this problem. Did ChimeraX start offscreen,
or was it positioned there later somehow? Was it fully offscreen, or
only
partially?
--Eric
Eric Pettersen
UCSF Computer Graphics Lab
--
Ticket URL:
<https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Ftrac%2FChimeraX%2Fticket%2F15320%23comment%3A2&data=05%7C02%7Ccdacosta%40uottawa.mail.onmicrosoft.com%7Cd7cad2ac2726463fa08908dc7f660240%7Cd41fdab17e154cfdb5fa7200e54deb6b%7C1%7C0%7C638525323319693802%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=uF0kVtJngwd%2FmpPx5jMwi6I4dl41phB3E0lc0IMh7qw%3D&reserved=0<https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Ftrac%2FChimeraX%2Fticket%2F15320%23comment%3A2&data=05%7C02%7Ccdacosta%40uottawa.mail.onmicrosoft.com%7Cd7cad2ac2726463fa08908dc7f660240%7Cd41fdab17e154cfdb5fa7200e54deb6b%7C1%7C0%7C638525323319702089%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=W30CC3TrzbA7Gew753ShZ5kQmthxuLYAsd1Vhzn%2Fkbs%3D&reserved=0<https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/15320#comment:2>>>
ChimeraX
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ChimeraX Issue Tracker
}}}
--
Ticket URL: <https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Ftrac%2FChimeraX%2Fticket%2F15320%23comment%3A3&data=05%7C02%7Ccdacosta%40uottawa.mail.onmicrosoft.com%7Cd7cad2ac2726463fa08908dc7f660240%7Cd41fdab17e154cfdb5fa7200e54deb6b%7C1%7C0%7C638525323319716145%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=xHNThjf4DBbLZBYuBR%2BX5VFS8ZJi9xNJd0mGPilvcZQ%3D&reserved=0<https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/15320#comment:3>>
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ChimeraX Issue Tracker
comment:5 by , 17 months ago
| Resolution: | → limitation |
|---|---|
| Status: | feedback → closed |
So I imagine everything fit on the screen okay when you originally saved the session? Were you restoring the session on a computer with a smaller screen?
Regardless, if you click into the main graphics window, any keystrokes you then type will be forwarded to the command line. So if this happens to you in the future, you could blindly type "windowsize" to have the current width and height of the window in pixels reported to the log, and then another "windowsize" command with the same width and a smaller height to cause the window to shrink and hopefully show the command line.
comment:6 by , 17 months ago
Q: So I imagine everything fit on the screen okay when you originally saved the session? A: No. I saved it before I noticed the effect. When I reopened it, as the alignment windows appeared, the command line disappeared off screen and I couldn't resize my window by dragging corners. Q: Were you restoring the session on a computer with a smaller screen? A: No. Same screen. Thanks for the 'windowsize' tip. Since I am using 1.8rc I thought I would report the 'bug'. As I said, upon reflection, I think the issue stemmed from the very large number of alignment windows (upon running matchmaker) that opened, which basically pushed the bottom of my window down/off screen. Strangely, I could not adjust the window height by dragging from the top or any corners... I could only adjust window width? Thanks again for all your help, and please feel free to close the ticket/incident report. P.S. I'm learning ChimeraX as a recent convert from PyMOL, and I have to say it has come a long way since I tried the original Chimera approximately 7 years ago. I love the presets, and some of the awesome lighting and silhouetting features, as well as all the myriads of color palettes (through ColorBrewer no less!). Is there a repository of presets available through a 'ChimeraX Wiki' (i.e. like the PyMOL wiki)? The ChimeraX documentation is very extensive and generally very good (I find myself searching directly from my Google browser), but sometimes I feel as though more explicit examples of command line usage would be beneficial. Often I find myself knowing what command I want, but not how to string it together and implement it. In the end, things often turn out to be simpler than I thought, which says something about how accessible command scripting is becoming... Well done, and thanks for this important service to the structural biology community! Cheers, Corrie Corrie J.B. daCosta Professeur agrégé | Associate Professor Chimie et sciences biomoléculaires | Chemistry and Biomolecular Sciences Faculté des sciences | Faculty of Science Université d\u2019Ottawa | University of Ottawa Ottawa ON Canada K1N 6N5 STM 362 t: (613) 562-5800 x 2546 f: (613) 562-5170 http://www.dacosta.net/ <http://www.dacosta.net/> \ufeff-----Original Message----- From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu <mailto:ChimeraX-bugs-admin@cgl.ucsf.edu>> Reply-To: "ChimeraX-bugs@cgl.ucsf.edu <mailto:ChimeraX-bugs@cgl.ucsf.edu>" <ChimeraX-bugs@cgl.ucsf.edu <mailto:ChimeraX-bugs@cgl.ucsf.edu>> Date: Wednesday, May 29, 2024 at 3:51 PM To: Corrie daCosta <cdacosta@uottawa.ca <mailto:cdacosta@uottawa.ca>>, "pett@cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu>" <pett@cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu>> Cc: "goddard@cgl.ucsf.edu <mailto:goddard@cgl.ucsf.edu>" <goddard@cgl.ucsf.edu <mailto:goddard@cgl.ucsf.edu>> Subject: Re: [ChimeraX] #15320: ChimeraX off screen Attention : courriel externe | external email #15320: ChimeraX off screen ---------------------------------+-------------------- Reporter: cdacosta@\u2026 | Owner: pett Type: defect | Status: closed Priority: normal | Milestone: Component: UI | Version: Resolution: limitation | Keywords: Blocked By: | Blocking: Notify when closed: | Platform: all Project: ChimeraX | ---------------------------------+-------------------- Changes (by pett): * resolution: => limitation * status: feedback => closed Comment: So I imagine everything fit on the screen okay when you originally saved the session? Were you restoring the session on a computer with a smaller screen? Regardless, if you click into the main graphics window, any keystrokes you then type will be forwarded to the command line. So if this happens to you in the future, you could blindly type "windowsize" to have the current width and height of the window in pixels reported to the log, and then another "windowsize" command with the same width and a smaller height to cause the window to shrink and hopefully show the command line. -- Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/15320#comment:5> <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/15320#comment:5;> ChimeraX <https://www.rbvi.ucsf.edu/chimerax/> <https://www.rbvi.ucsf.edu/chimerax/;> ChimeraX Issue Tracker
comment:7 by , 17 months ago
The multiple alignment tools were probably forcing the main window to be a certain minimum height, and therefore you couldn't resize it horizontally. Probably if you dragged some of the tools out into their own separate windows you would then be able to resize the main window. I will change MatchMaker to ask for confirmation before opening many alignments at once. I'm glad that despite this you still like ChimeraX. :-). I don't know of any preset repositories, but the SEQCROW bundle adds presets useful for depicting small molecules, and the NIHPresets bundle adds some generally useful presets along with presets specifically for 3D printing. --Eric
comment:8 by , 17 months ago
Okay, I have modified MatchMaker to ask for confirmation before opening a zillion alignments (and open those alignments in floating windows if you say "yes").
comment:9 by , 17 months ago
That will be a nice addition. Thanks for the support! Corrie \ufeff-----Original Message----- From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu <mailto:ChimeraX-bugs-admin@cgl.ucsf.edu>> Reply-To: "ChimeraX-bugs@cgl.ucsf.edu <mailto:ChimeraX-bugs@cgl.ucsf.edu>" <ChimeraX-bugs@cgl.ucsf.edu <mailto:ChimeraX-bugs@cgl.ucsf.edu>> Date: Wednesday, May 29, 2024 at 5:32 PM To: Corrie daCosta <cdacosta@uottawa.ca <mailto:cdacosta@uottawa.ca>>, "pett@cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu>" <pett@cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu>> Cc: "goddard@cgl.ucsf.edu <mailto:goddard@cgl.ucsf.edu>" <goddard@cgl.ucsf.edu <mailto:goddard@cgl.ucsf.edu>> Subject: Re: [ChimeraX] #15320: ChimeraX off screen Attention : courriel externe | external email #15320: ChimeraX off screen ---------------------------------+-------------------- Reporter: cdacosta@\u2026 | Owner: pett Type: defect | Status: closed Priority: normal | Milestone: Component: UI | Version: Resolution: limitation | Keywords: Blocked By: | Blocking: Notify when closed: | Platform: all Project: ChimeraX | ---------------------------------+-------------------- Comment (by pett): Okay, I have modified MatchMaker to ask for confirmation before opening a zillion alignments (and open those alignments in floating windows if you say "yes"). -- Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/15320#comment:8> <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/15320#comment:8;> ChimeraX <https://www.rbvi.ucsf.edu/chimerax/> <https://www.rbvi.ucsf.edu/chimerax/;> ChimeraX Issue Tracker
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Hi Corrie,
--Eric