![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 2 years ago
Last modified 2 years ago
#9898 assigned defect
ArtiaX: not all parameters written out
| Reported by: | Owned by: | Utz Ermel | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Third Party | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-13.5.2-arm64-arm-64bit
ChimeraX Version: 1.7.dev202308312248 (2023-08-31 22:48:44 UTC)
Description
Unfortunately, ArtiaX does not write out all parameters/columns in 3D-particle star files after "cleaning" in 3D. It also happens in the Windows-10 version of chimerax/ArtiaX.
For instance, we are "loosing" the _rlnMicrographName column, which is important to keep track of where the data comes from for subtomogram averaging. (Also it adds the _rlnOriginX,Y and Z columns (all set to 0), which we do not want - this we could get rid of using awk commands later.) Could you please fix this issue? I have attached the respective file for comparison. A 1000 thanks!
Best regards, Magdalena
Log:
UCSF ChimeraX version: 1.7.dev202308312248 (2023-08-31)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/schacherl/Documents/arbeit/Kooperationen/Hillen/Deconv_warp/MGS004_T3_ts_012.mrc_12.82Apx.mrc
Opened MGS004_T3_ts_012.mrc_12.82Apx.mrc as #1, grid size 682,960,500, pixel
12.8,12.8,12.8, shown at step 1, values float32
> artiax start
Using preset: ArtiaX / Artiax Default
Preset expands to these ChimeraX commands:
set bgColor black
lighting depthCue false
camera ortho
Opened MGS004_T3_ts_012.mrc_12.82Apx.mrc as #2.1.1, grid size 682,960,500,
pixel 12.8,12.8,12.8, shown at level 0.0695, step 1, values float32
> artiax tomo #2.1.1 sliceDirection 0,0,1
> artiax view xy
> close #1
> artiax tomo #2.1.1 slice 131
> open
> /Users/schacherl/Documents/arbeit/Kooperationen/Hillen/Deconv_warp/MGS004_T3_ts_012.mrc.tomostar_all.star
> format star
Summary of feedback from opening
/Users/schacherl/Documents/arbeit/Kooperationen/Hillen/Deconv_warp/MGS004_T3_ts_012.mrc.tomostar_all.star
---
notes | 15
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']
Opened Particle list MGS004_T3_ts_012.mrc.tomostar_all.star with 151
particles.
set axis size 180.0
180.0
['.arrow', '0', '0', '0', '180.0', '0', '0', '12.0', '48.0']
> artiax particles #2.2.1 originScaleFactor 12.0
> artiax view xy
> artiax particles #2.2.1 transScaleFactor 12.0
> artiax view xy
set axis size 45.0
45.0
['.arrow', '0', '0', '0', '45.0', '0', '0', '3.0', '12.0']
> artiax particles #2.2.1 originScaleFactor 3.0
> artiax view xy
> artiax particles #2.2.1 transScaleFactor 3.0
> artiax view xy
set axis size 120.0
120.0
['.arrow', '0', '0', '0', '120.0', '0', '0', '8.0', '32.0']
> artiax particles #2.2.1 originScaleFactor 8.0
> artiax view xy
> artiax particles #2.2.1 transScaleFactor 8.0
> artiax view xy
> artiax tomo #2.1.1 pixelSize 12.822
> artiax view xy
> artiax tomo #2.1.1 pixelSize 12.822
> artiax view xy
set axis size 60.0
60.0
['.arrow', '0', '0', '0', '60.0', '0', '0', '4.0', '16.0']
> artiax particles #2.2.1 originScaleFactor 4.0
> artiax view xy
> open
> /Users/schacherl/Documents/arbeit/Kooperationen/Hillen/CytRibo80s_all_clean_4.3Apx.mrc
Opened CytRibo80s_all_clean_4.3Apx.mrc as #1, grid size 128,128,128, pixel
4.27, shown at level 1.45, step 1, values float32
> artiax attach #1 toParticleList #2.2.1
Opened CytRibo80s_all_clean_4.3Apx.mrc as #2.2.1.1.1, grid size 128,128,128,
pixel 4.27, shown at level 1.45, step 1, values float32
> volume #2.2.1.1.1 capFaces false
> artiax show #2.2.1 surfaces
set axis size 65.1
65.1
['.arrow', '0', '0', '0', '65.1', '0', '0', '4.34', '17.36']
> artiax particles #2.2.1 originScaleFactor 4.34
> artiax view xy
> artiax particles #2.2.1 transScaleFactor 4.34
> artiax view xy
> artiax particles #2.2.1 surfaceLevel 1.13863
> artiax tomo #2.1.1 slice 162
> artiax tomo #2.1.1 slice 134
> artiax tomo #2.1.1 slice 271
> artiax tomo #2.1.1 slice 223
> artiax hide surfaces
> artiax show surfaces
> artiax hide axes
> artiax hide markers
> artiax tomo #2.1.1 slice 255
> artiax tomo #2.1.1 slice 242
> artiax tomo #2.1.1 slice 156
[Repeated 1 time(s)]
> artiax tomo #2.1.1 slice 258
[Repeated 2 time(s)]
> artiax tomo #2.1.1 slice 259
> artiax tomo #2.1.1 slice 260
> artiax tomo #2.1.1 slice 261
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> artiax tomo #2.1.1 slice 201
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> artiax tomo #2.1.1 slice 247
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> artiax tomo #2.1.1 slice 235
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> artiax tomo #2.1.1 slice 232
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> artiax tomo #2.1.1 slice 228
> artiax tomo #2.1.1 slice 227
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> artiax tomo #2.1.1 slice 225
> artiax tomo #2.1.1 slice 224
> artiax tomo #2.1.1 slice 223
> artiax tomo #2.1.1 slice 222
> artiax tomo #2.1.1 slice 221
> artiax tomo #2.1.1 slice 220
> artiax tomo #2.1.1 slice 219
> artiax tomo #2.1.1 slice 218
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> artiax tomo #2.1.1 slice 216
> artiax tomo #2.1.1 slice 215
> artiax tomo #2.1.1 slice 214
> artiax tomo #2.1.1 slice 213
Opened MGS006_T1_ts_003.mrc_12.82Apx.mrc as #2.1.2, grid size 682,960,500,
pixel 12.8,12.8,12.8, shown at level 0.0739, step 1, values float32
> artiax tomo #2.1.2 sliceDirection 0,0,1
> artiax view xy
> hide #!2.1.1 models
> hide #!2.2.1 models
> open
> /Users/schacherl/Documents/arbeit/Kooperationen/Hillen/Deconv_warp/MGS006_T1_ts_003.mrc.tomostar_all.star
> format star
Summary of feedback from opening
/Users/schacherl/Documents/arbeit/Kooperationen/Hillen/Deconv_warp/MGS006_T1_ts_003.mrc.tomostar_all.star
---
notes | 15
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']
Opened Particle list MGS006_T1_ts_003.mrc.tomostar_all.star with 118
particles.
set axis size 65.1
65.1
['.arrow', '0', '0', '0', '65.1', '0', '0', '4.34', '17.36']
> artiax particles #2.2.2 originScaleFactor 4.34
> artiax view xy
> artiax particles #2.2.2 transScaleFactor 4.34
> artiax view xy
> open
> /Users/schacherl/Documents/arbeit/Kooperationen/Hillen/CytRibo80s_all_clean_4.3Apx.mrc
Opened CytRibo80s_all_clean_4.3Apx.mrc as #1, grid size 128,128,128, pixel
4.27, shown at level 1.45, step 1, values float32
> artiax attach #1 toParticleList #2.2.2
Opened CytRibo80s_all_clean_4.3Apx.mrc as #2.2.2.1.1, grid size 128,128,128,
pixel 4.27, shown at level 1.45, step 1, values float32
> volume #2.2.2.1.1 capFaces false
> artiax show #2.2.2 surfaces
> artiax particles #2.2.2 color 88,100,40,100
> artiax hide axes
> artiax hide markers
> artiax particles #2.2.2 surfaceLevel 1.05415
> artiax tomo #2.1.2 slice 146
> artiax tomo #2.1.2 slice 147
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> hide #!2.2.2 models
> artiax tomo #2.1.2 slice 312
> artiax tomo #2.1.2 slice 313
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> artiax tomo #2.1.2 slice 254
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> artiax tomo #2.1.2 slice 201
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> artiax tomo #2.1.2 slice 203
> artiax tomo #2.1.2 slice 204
> artiax tomo #2.1.2 slice 205
> show #!2.2.2 models
> select #2.1.2
3 models selected
> select clear
> artiax tomo #2.1.2 slice 258
> ui mousemode right translate
> artiax tomo #2.1.2 slice 207
> artiax tomo #2.1.2 slice 252
> select clear
> open
> /Users/schacherl/Documents/arbeit/Projekte/Nanobody_Library/Phage_display/H1_Mpro.fasta
> format fasta
Summary of feedback from opening
/Users/schacherl/Documents/arbeit/Projekte/Nanobody_Library/Phage_display/H1_Mpro.fasta
---
note | Alignment identifier is H1_Mpro.fasta
Opened 1 sequences from H1_Mpro.fasta
> alphafold predict H1_Mpro.fasta minimize true
Missing or invalid "sequences" argument: Sequences argument "H1_Mpro.fasta" is
not a chain specifier, alignment id, UniProt id, or sequence characters
> alphafold predict
> MAQVQLQESGGGLVQAGGSLRLSCAASGYISLSRYMGWYRQAPGKERELVASITRGTITNYADSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCAVSNYRTWFGLYGHTYWGQGTQVTVSSVESGGLNDIFEAQKIEWHEGSHHHHHH
> minimize true
Please cite ColabFold: Making protein folding accessible to all. Nature
Methods (2022) if you use these predictions.
Running AlphaFold prediction
[Repeated 1 time(s)]
> alphafold predict
> MAQVQLQESGGGLVQAGGSLRLSCAASGYISLSRYMGWYRQAPGKERELVASITRGTITNYADSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCAVSNYRTWFGLYGHTYWGQGTQVTVSSVESGGLNDIFEAQKIEWHEGSHHHHHH
> minimize true
Running AlphaFold prediction
[Repeated 1 time(s)]AlphaFold prediction finished
Results in /Users/schacherl/Downloads/ChimeraX/AlphaFold/prediction_1
> open
> /Users/schacherl/Downloads/ChimeraX/AlphaFold/prediction_1/best_model.pdb
Chain information for best_model.pdb #1
---
Chain | Description
A | No description available
Associated best_model.pdb chain A to anti-Mpro_ylib_H1 with 0 mismatches
> show #1 target m
[Repeated 1 time(s)]
> select add #1
2309 atoms, 2339 bonds, 151 residues, 1 model selected
> show #1 target m
> view #1 clip false
> save
> /Users/schacherl/Documents/arbeit/Projekte/Nanobody_Library/Phage_display/Alphafold2_aMpro_H1_model.pdb
> models #1
> select clear
> select #1/A:61
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #1/A:61-65
70 atoms, 70 bonds, 5 residues, 1 model selected
> select #1/A:27
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/A:27-39
213 atoms, 217 bonds, 13 residues, 1 model selected
> select #1/A:110-111
24 atoms, 24 bonds, 2 residues, 1 model selected
> select #1/A:98-111
225 atoms, 230 bonds, 14 residues, 1 model selected
> select #1/A:146
17 atoms, 17 bonds, 1 residue, 1 model selected
> select #1/A:146-151
103 atoms, 108 bonds, 6 residues, 1 model selected
Opened shrink_MGS001_T1_ts_001.mrc_12.00Apx.mrc as #2.1.3, grid size
765,1076,187, pixel 24, shown at level 0.148, step 1, values float32
> artiax tomo #2.1.3 sliceDirection 0,0,1
> artiax view xy
> hide #!2.1.2 models
> hide #!2.2.2 models
> open
> /Users/schacherl/Documents/arbeit/Projekte/Spahn_unfinished/60S_HeLa/tomo/reconstructions/star_files/MGS001_T1_ts_001.mrc_12.00Apx_ref60S_12Apx.sorted.24Apx.star
> format star
Summary of feedback from opening
/Users/schacherl/Documents/arbeit/Projekte/Spahn_unfinished/60S_HeLa/tomo/reconstructions/star_files/MGS001_T1_ts_001.mrc_12.00Apx_ref60S_12Apx.sorted.24Apx.star
---
notes | 15
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']
Opened Particle list
MGS001_T1_ts_001.mrc_12.00Apx_ref60S_12Apx.sorted.24Apx.star with 5000
particles.
set axis size 360.0
360.0
['.arrow', '0', '0', '0', '360.0', '0', '0', '24.0', '96.0']
> artiax particles #2.2.3 originScaleFactor 24.0
> artiax view xy
> artiax particles #2.2.3 transScaleFactor 24.0
> artiax view xy
> artiax tomo #2.1.3 slice 4
> artiax tomo #2.1.3 slice 115
> open
> /Users/schacherl/Documents/arbeit/Projekte/Spahn_unfinished/60S_HeLa/ref60S_12Apx.mrc
Opened ref60S_12Apx.mrc as #3, grid size 34,34,34, pixel 12.2, shown at level
1.26, step 1, values float32
> artiax attach #3 toParticleList #2.2.3
Opened ref60S_12Apx.mrc as #2.2.3.1.1, grid size 34,34,34, pixel 12.2, shown
at level 1.26, step 1, values float32
> volume #2.2.3.1.1 capFaces false
> artiax show #2.2.3 surfaces
> artiax particles #2.2.3 surfaceLevel 0.18403
> artiax hide axes
> artiax hide markers
> artiax tomo #2.1.3 slice 94
> artiax tomo #2.1.3 slice 125
[Repeated 1 time(s)]
> artiax tomo #2.1.3 slice 84
> artiax tomo #2.1.3 slice 85
> artiax tomo #2.1.3 slice 86
> artiax tomo #2.1.3 slice 87
> artiax tomo #2.1.3 slice 88
> artiax tomo #2.1.3 slice 89
> artiax tomo #2.1.3 slice 90
> artiax tomo #2.1.3 slice 91
> artiax tomo #2.1.3 slice 92
> artiax tomo #2.1.3 slice 93
> artiax tomo #2.1.3 slice 94
> artiax tomo #2.1.3 slice 95
> artiax tomo #2.1.3 slice 96
> artiax tomo #2.1.3 slice 97
> artiax tomo #2.1.3 slice 98
> artiax tomo #2.1.3 slice 99
> artiax tomo #2.1.3 slice 100
> artiax tomo #2.1.3 slice 101
> artiax tomo #2.1.3 slice 102
> hide #!2.1.3 models
> show #!2.1.3 models
> hide #!2.1.3 models
> open
> /Users/schacherl/Documents/arbeit/Projekte/Spahn_unfinished/60S_HeLa/tomo/2023_60S/shrink_MGS001_T1_ts_001.mrc_12.00Apx.mrc
Opened shrink_MGS001_T1_ts_001.mrc_12.00Apx.mrc as #3, grid size 765,1076,187,
pixel 24, shown at level 0.147, step 4, values float32
> volume #3 step 1
> volume #3 step 8
> volume #3 level 0.1177
> hide #!2.2.3 models
> volume #3 style image colorMode opaque8 showOutlineBox true orthoplanes xyz
> positionPlanes 382,537,93 imageMode orthoplanes
> volume #3 region 0,0,88,764,1075,88 step 2 colorMode auto8 imageMode "full
> region"
> volume #3 region 0,0,0,764,1075,186 step 8
> volume #3 style surface region 0,0,0,764,1075,186 step 8
> volume #3 step 2
> view
> show #!2.2.3 models
> open
> /Users/schacherl/Documents/arbeit/Projekte/Spahn_unfinished/60S_HeLa/tomo/2023_60S/shrink_MGS001_T1_ts_002.mrc_12.00Apx.mrc
Opened shrink_MGS001_T1_ts_002.mrc_12.00Apx.mrc as #4, grid size 765,1076,187,
pixel 24, shown at level 0.155, step 4, values float32
Opened shrink_MGS001_T1_ts_002.mrc_12.00Apx.mrc as #2.1.4, grid size
765,1076,187, pixel 24, shown at level 0.155, step 1, values float32
> artiax tomo #2.1.4 sliceDirection 0,0,1
> artiax view xy
> hide #!2.2.3 models
> open
> /Users/schacherl/Documents/arbeit/Projekte/Spahn_unfinished/60S_HeLa/tomo/reconstructions/star_files/MGS001_T1_ts_002.mrc_12.00Apx_ref60S_12Apx.sorted.24Apx.star
> format star
Summary of feedback from opening
/Users/schacherl/Documents/arbeit/Projekte/Spahn_unfinished/60S_HeLa/tomo/reconstructions/star_files/MGS001_T1_ts_002.mrc_12.00Apx_ref60S_12Apx.sorted.24Apx.star
---
notes | 15
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']
Opened Particle list
MGS001_T1_ts_002.mrc_12.00Apx_ref60S_12Apx.sorted.24Apx.star with 5000
particles.
set axis size 360.0
360.0
['.arrow', '0', '0', '0', '360.0', '0', '0', '24.0', '96.0']
> artiax particles #2.2.4 originScaleFactor 24.0
> artiax view xy
> artiax particles #2.2.4 transScaleFactor 24.0
> artiax view xy
> artiax attach #3 toParticleList #2.2.4
Opened shrink_MGS001_T1_ts_001.mrc_12.00Apx.mrc as #2.2.4.1.1, grid size
765,1076,187, pixel 24, shown at level 0.148, step 1, values float32
> volume #2.2.4.1.1 capFaces false
> artiax particles #2.2.4 surfaceLevel -0.79387
> open
> /Users/schacherl/Documents/arbeit/Projekte/Spahn_unfinished/60S_HeLa/ref60S_12Apx.mrc
Opened ref60S_12Apx.mrc as #3, grid size 34,34,34, pixel 12.2, shown at level
1.26, step 1, values float32
> artiax attach #3 toParticleList #2.2.4
Opened ref60S_12Apx.mrc as #2.2.4.1.1, grid size 34,34,34, pixel 12.2, shown
at level 1.26, step 1, values float32
> volume #2.2.4.1.1 capFaces false
> artiax show #2.2.4 surfaces
> artiax particles #2.2.4 surfaceLevel 0.09785
> artiax hide axes
> artiax hide markers
> hide #!2.1.4 models
> show #!2.1.3 models
> hide #!2.1.3 models
> show #!2.1.4 models
> hide #!2.1.4 models
> show #!2.1.4 models
> hide #!2.1.4 models
> show #!2.2.3 models
> hide #!4 models
> hide #!2.2.3 models
> hide #!2.2.4 models
> show #!2.1.4 models
> artiax tomo #2.1.4 slice 79
> show #!2.2.4 models
> hide #!2.1.4 models
> save
> /Users/schacherl/Documents/arbeit/Projekte/Spahn_unfinished/60S_HeLa/tomo/test.star
> partlist #2.2.4
OpenGL version: 4.1 Metal - 83.1
OpenGL renderer: Apple M1 Max
OpenGL vendor: Apple
Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,4
Model Number: Z15H00054D/A
Chip: Apple M1 Max
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 64 GB
System Firmware Version: 8422.141.2
OS Loader Version: 8422.141.2
Software:
System Software Overview:
System Version: macOS 13.5.2 (22G91)
Kernel Version: Darwin 22.6.0
Time since boot: 7 Tage, 10 Stunden und 46 Minuten
Graphics/Displays:
Apple M1 Max:
Chipset Model: Apple M1 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 24
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
LG HDR 4K:
Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2022.12.7
cftime: 1.6.2
charset-normalizer: 3.2.0
ChimeraX-AddCharge: 1.5.11
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-ArtiaX: 0.3
ChimeraX-Atomic: 1.47.2
ChimeraX-AtomicLibrary: 10.0.8
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.10.4
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.0.3
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7.dev202308312248
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.2
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: 1.1.8
ChimeraX-ListInfo: 1.2
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.12
ChimeraX-ModelPanel: 1.4
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: 1.1
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.2
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0.1
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: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.9.1
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: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12.2
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.2
ChimeraX-TapeMeasure: 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: 1.31.4
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.4
contourpy: 1.1.0
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7.post1
decorator: 5.1.1
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.42.1
funcparserlib: 1.0.1
geomdl: 5.3.1
glfw: 2.6.2
grako: 3.16.5
h5py: 3.9.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.38
imagecodecs: 2023.7.10
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.1.0
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.3.1
jupyterlab-widgets: 3.0.8
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.3
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.7
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.5
numpy: 1.25.1
openvr: 1.23.701
packaging: 21.3
pandas: 2.1.0
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 10.0.0
pip: 23.2.1
pkginfo: 1.9.6
platformdirs: 3.10.0
prompt-toolkit: 3.0.39
psutil: 5.9.5
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.16.1
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.2801
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
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: 2023.3
pyzmq: 25.1.1
qtconsole: 5.4.3
QtPy: 2.4.0
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4.1
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.7
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.5
sphinxcontrib-htmlhelp: 2.0.4
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.6
sphinxcontrib-serializinghtml: 1.1.9
stack-data: 0.6.2
starfile: 0.4.12
superqt: 0.5.0
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.3
traitlets: 5.9.0
typing-extensions: 4.7.1
tzdata: 2023.3
urllib3: 2.0.4
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.8
File attachment: Selected_from_MGS003_T1_ts_003_ref55S.star
Attachments (2)
Change History (4)
by , 2 years ago
| Attachment: | Selected_from_MGS003_T1_ts_003_ref55S.star added |
|---|
comment:1 by , 2 years ago
P.S. The original file for comparison is attached. Am 04.10.23, 13:49 schrieb "ChimeraX" <ChimeraX-bugs-admin@cgl.ucsf.edu <mailto:ChimeraX-bugs-admin@cgl.ucsf.edu>>: #9898: ChimeraX bug report submission --------------------------------------------+-------------------- Reporter: magdalena.schacherl@… | Owner: (none) Type: defect | Status: new Priority: normal | Milestone: Component: Unassigned | Version: Resolution: | Keywords: Blocked By: | Blocking: Notify when closed: | --------------------------------------------+-------------------- Changes (by magdalena.schacherl@…): * Attachment "Selected_from_MGS003_T1_ts_003_ref55S.star" added. Added by email2trac
by , 2 years ago
| Attachment: | MGS003_T1_ts_003.mrc_12.00Apx_ref55S_12Apx_realxyz.star added |
|---|
Added by email2trac
comment:2 by , 2 years ago
| Component: | Unassigned → Third Party |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → ArtiaX: not all parameters written out |
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