Opened 2 years ago

Last modified 2 years ago

#9898 assigned defect

ArtiaX: not all parameters written out

Reported by: magdalena.schacherl@… 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

> artiax tomo #2.1.1 slice 260

> artiax tomo #2.1.1 slice 259

> artiax tomo #2.1.1 slice 258

> artiax tomo #2.1.1 slice 201

> artiax tomo #2.1.1 slice 202

> artiax tomo #2.1.1 slice 203

> artiax tomo #2.1.1 slice 204

> artiax tomo #2.1.1 slice 205

> artiax tomo #2.1.1 slice 206

> artiax tomo #2.1.1 slice 207

> artiax tomo #2.1.1 slice 208

> artiax tomo #2.1.1 slice 209

> artiax tomo #2.1.1 slice 210

> artiax tomo #2.1.1 slice 211

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> artiax tomo #2.1.1 slice 215

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> artiax tomo #2.1.1 slice 218

> artiax tomo #2.1.1 slice 219

> artiax tomo #2.1.1 slice 220

> artiax tomo #2.1.1 slice 221

> artiax tomo #2.1.1 slice 222

> artiax tomo #2.1.1 slice 223

> artiax tomo #2.1.1 slice 224

> artiax tomo #2.1.1 slice 225

> artiax tomo #2.1.1 slice 226

> artiax tomo #2.1.1 slice 227

> artiax tomo #2.1.1 slice 228

> artiax tomo #2.1.1 slice 229

> artiax tomo #2.1.1 slice 230

> artiax tomo #2.1.1 slice 231

> artiax tomo #2.1.1 slice 232

> artiax tomo #2.1.1 slice 233

> artiax tomo #2.1.1 slice 234

> artiax tomo #2.1.1 slice 235

> artiax tomo #2.1.1 slice 236

> artiax tomo #2.1.1 slice 237

> artiax tomo #2.1.1 slice 238

> artiax tomo #2.1.1 slice 239

> artiax tomo #2.1.1 slice 240

> artiax tomo #2.1.1 slice 241

> artiax tomo #2.1.1 slice 242

> artiax tomo #2.1.1 slice 243

> artiax tomo #2.1.1 slice 244

> artiax tomo #2.1.1 slice 245

> artiax tomo #2.1.1 slice 246

> artiax tomo #2.1.1 slice 247

> artiax tomo #2.1.1 slice 248

> artiax tomo #2.1.1 slice 249

> artiax tomo #2.1.1 slice 250

> artiax tomo #2.1.1 slice 251

> artiax tomo #2.1.1 slice 252

> artiax tomo #2.1.1 slice 253

> artiax tomo #2.1.1 slice 252

> artiax tomo #2.1.1 slice 251

> artiax tomo #2.1.1 slice 250

> artiax tomo #2.1.1 slice 249

> artiax tomo #2.1.1 slice 250

> artiax tomo #2.1.1 slice 251

> artiax tomo #2.1.1 slice 250

> artiax tomo #2.1.1 slice 249

> artiax tomo #2.1.1 slice 248

> artiax tomo #2.1.1 slice 247

> artiax tomo #2.1.1 slice 246

> artiax tomo #2.1.1 slice 245

> artiax tomo #2.1.1 slice 244

> artiax tomo #2.1.1 slice 243

> artiax tomo #2.1.1 slice 242

> artiax tomo #2.1.1 slice 243

> artiax tomo #2.1.1 slice 244

> artiax tomo #2.1.1 slice 245

> artiax tomo #2.1.1 slice 246

> artiax tomo #2.1.1 slice 247

> artiax tomo #2.1.1 slice 248

> artiax tomo #2.1.1 slice 249

> artiax tomo #2.1.1 slice 250

> artiax tomo #2.1.1 slice 251

> artiax tomo #2.1.1 slice 252

> artiax tomo #2.1.1 slice 253

> artiax tomo #2.1.1 slice 254

> artiax tomo #2.1.1 slice 255

> artiax tomo #2.1.1 slice 256

> artiax tomo #2.1.1 slice 257

> artiax tomo #2.1.1 slice 258

> artiax tomo #2.1.1 slice 259

> artiax tomo #2.1.1 slice 260

> artiax tomo #2.1.1 slice 261

> artiax tomo #2.1.1 slice 262

> artiax tomo #2.1.1 slice 263

> artiax tomo #2.1.1 slice 264

> artiax tomo #2.1.1 slice 265

> artiax tomo #2.1.1 slice 266

> artiax tomo #2.1.1 slice 267

> artiax tomo #2.1.1 slice 268

> artiax tomo #2.1.1 slice 269

> artiax tomo #2.1.1 slice 270

> artiax tomo #2.1.1 slice 271

> artiax tomo #2.1.1 slice 272

> artiax tomo #2.1.1 slice 271

> artiax tomo #2.1.1 slice 270

> artiax tomo #2.1.1 slice 269

> artiax tomo #2.1.1 slice 268

> artiax tomo #2.1.1 slice 267

> artiax tomo #2.1.1 slice 266

> artiax tomo #2.1.1 slice 265

> artiax tomo #2.1.1 slice 264

> artiax tomo #2.1.1 slice 263

> artiax tomo #2.1.1 slice 262

> artiax tomo #2.1.1 slice 261

> artiax tomo #2.1.1 slice 260

> artiax tomo #2.1.1 slice 259

> artiax tomo #2.1.1 slice 258

> artiax tomo #2.1.1 slice 257

> artiax tomo #2.1.1 slice 256

> artiax tomo #2.1.1 slice 255

> artiax tomo #2.1.1 slice 254

> artiax tomo #2.1.1 slice 253

> artiax tomo #2.1.1 slice 252

> artiax tomo #2.1.1 slice 251

> artiax tomo #2.1.1 slice 250

> artiax tomo #2.1.1 slice 249

> artiax tomo #2.1.1 slice 248

> artiax tomo #2.1.1 slice 247

> artiax tomo #2.1.1 slice 246

> artiax tomo #2.1.1 slice 245

> artiax tomo #2.1.1 slice 244

> artiax tomo #2.1.1 slice 243

> artiax tomo #2.1.1 slice 242

> artiax tomo #2.1.1 slice 241

> artiax tomo #2.1.1 slice 240

> artiax tomo #2.1.1 slice 239

> artiax tomo #2.1.1 slice 238

> artiax tomo #2.1.1 slice 237

> artiax tomo #2.1.1 slice 236

> artiax tomo #2.1.1 slice 235

> artiax tomo #2.1.1 slice 234

> artiax tomo #2.1.1 slice 233

> artiax tomo #2.1.1 slice 232

> artiax tomo #2.1.1 slice 231

> artiax tomo #2.1.1 slice 230

> artiax tomo #2.1.1 slice 229

> artiax tomo #2.1.1 slice 228

> artiax tomo #2.1.1 slice 227

> artiax tomo #2.1.1 slice 226

> 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

> artiax tomo #2.1.1 slice 217

> 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

> artiax tomo #2.1.2 slice 148

> artiax tomo #2.1.2 slice 149

> artiax tomo #2.1.2 slice 150

> artiax tomo #2.1.2 slice 151

> artiax tomo #2.1.2 slice 152

> artiax tomo #2.1.2 slice 153

> artiax tomo #2.1.2 slice 154

> artiax tomo #2.1.2 slice 155

> artiax tomo #2.1.2 slice 156

> artiax tomo #2.1.2 slice 157

> artiax tomo #2.1.2 slice 158

> artiax tomo #2.1.2 slice 159

> artiax tomo #2.1.2 slice 160

> artiax tomo #2.1.2 slice 161

> artiax tomo #2.1.2 slice 162

> artiax tomo #2.1.2 slice 163

> artiax tomo #2.1.2 slice 164

> artiax tomo #2.1.2 slice 165

> artiax tomo #2.1.2 slice 166

> artiax tomo #2.1.2 slice 167

> artiax tomo #2.1.2 slice 168

> artiax tomo #2.1.2 slice 169

> artiax tomo #2.1.2 slice 170

> artiax tomo #2.1.2 slice 171

> artiax tomo #2.1.2 slice 172

> artiax tomo #2.1.2 slice 173

> artiax tomo #2.1.2 slice 174

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> artiax tomo #2.1.2 slice 176

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> artiax tomo #2.1.2 slice 180

> artiax tomo #2.1.2 slice 181

> artiax tomo #2.1.2 slice 182

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> artiax tomo #2.1.2 slice 184

> artiax tomo #2.1.2 slice 185

> artiax tomo #2.1.2 slice 186

> artiax tomo #2.1.2 slice 187

> artiax tomo #2.1.2 slice 188

> artiax tomo #2.1.2 slice 189

> artiax tomo #2.1.2 slice 190

> artiax tomo #2.1.2 slice 191

> artiax tomo #2.1.2 slice 192

> artiax tomo #2.1.2 slice 193

> artiax tomo #2.1.2 slice 194

> artiax tomo #2.1.2 slice 193

> artiax tomo #2.1.2 slice 192

> artiax tomo #2.1.2 slice 191

> artiax tomo #2.1.2 slice 190

> artiax tomo #2.1.2 slice 189

> artiax tomo #2.1.2 slice 190

> artiax tomo #2.1.2 slice 191

> artiax tomo #2.1.2 slice 192

> artiax tomo #2.1.2 slice 193

> artiax tomo #2.1.2 slice 194

> artiax tomo #2.1.2 slice 195

> artiax tomo #2.1.2 slice 196

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> artiax tomo #2.1.2 slice 199

> artiax tomo #2.1.2 slice 200

> artiax tomo #2.1.2 slice 201

> artiax tomo #2.1.2 slice 202

> artiax tomo #2.1.2 slice 203

> artiax tomo #2.1.2 slice 204

> artiax tomo #2.1.2 slice 205

> artiax tomo #2.1.2 slice 206

> artiax tomo #2.1.2 slice 207

> artiax tomo #2.1.2 slice 208

> artiax tomo #2.1.2 slice 209

> artiax tomo #2.1.2 slice 210

> artiax tomo #2.1.2 slice 211

> artiax tomo #2.1.2 slice 212

> artiax tomo #2.1.2 slice 213

> artiax tomo #2.1.2 slice 214

> artiax tomo #2.1.2 slice 215

> artiax tomo #2.1.2 slice 216

> artiax tomo #2.1.2 slice 217

> artiax tomo #2.1.2 slice 218

> artiax tomo #2.1.2 slice 219

> artiax tomo #2.1.2 slice 220

> artiax tomo #2.1.2 slice 221

> artiax tomo #2.1.2 slice 222

> artiax tomo #2.1.2 slice 223

> artiax tomo #2.1.2 slice 224

> artiax tomo #2.1.2 slice 225

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> artiax tomo #2.1.2 slice 233

> artiax tomo #2.1.2 slice 234

> artiax tomo #2.1.2 slice 235

> artiax tomo #2.1.2 slice 236

> artiax tomo #2.1.2 slice 237

> artiax tomo #2.1.2 slice 238

> artiax tomo #2.1.2 slice 239

> artiax tomo #2.1.2 slice 240

> artiax tomo #2.1.2 slice 241

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> artiax tomo #2.1.2 slice 247

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> artiax tomo #2.1.2 slice 245

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> artiax tomo #2.1.2 slice 246

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> artiax tomo #2.1.2 slice 255

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> artiax tomo #2.1.2 slice 263

> artiax tomo #2.1.2 slice 264

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> artiax tomo #2.1.2 slice 271

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> artiax tomo #2.1.2 slice 303

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> hide #!2.2.2 models

> artiax tomo #2.1.2 slice 312

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> artiax tomo #2.1.2 slice 194

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> artiax tomo #2.1.2 slice 199

> artiax tomo #2.1.2 slice 200

> 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

Selected_from_MGS003_T1_ts_003_ref55S.star​

Attachments (2)

Selected_from_MGS003_T1_ts_003_ref55S.star​ (32.5 KB ) - added by magdalena.schacherl@… 2 years ago.
Added by email2trac
MGS003_T1_ts_003.mrc_12.00Apx_ref55S_12Apx_realxyz.star​ (31.3 KB ) - added by magdalena.schacherl@… 2 years ago.
Added by email2trac

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Change History (4)

by magdalena.schacherl@…, 2 years ago

Attachment: Selected_from_MGS003_T1_ts_003_ref55S.star​ added

Added by email2trac

comment:1 by magdalena.schacherl@…, 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

MGS003_T1_ts_003.mrc_12.00Apx_ref55S_12Apx_realxyz.star​

by magdalena.schacherl@…, 2 years ago

Attachment: MGS003_T1_ts_003.mrc_12.00Apx_ref55S_12Apx_realxyz.star​ added

Added by email2trac

comment:2 by Eric Pettersen, 2 years ago

Component: Unassigned → Third Party
Owner: set to Utz Ermel
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → ArtiaX: not all parameters written out
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