-
Notifications
You must be signed in to change notification settings - Fork 4
/
Copy pathbundle_info.xml
executable file
·498 lines (414 loc) · 25.8 KB
/
bundle_info.xml
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
<!--
ChimeraX bundle names must start with "ChimeraX-"
to avoid clashes with package names in pypi.python.org.
When uploaded to the ChimeraX toolshed, the bundle
will be displayed without the ChimeraX- prefix.
-->
<BundleInfo name="ChimeraX-ArtiaX"
version="0.6.0" package="chimerax.artiax"
minSessionVersion="1" maxSessionVersion="1">
<!-- Additional information about bundle source -->
<Author>Utz Ermel, Serena M. Arghittu, and Achilleas Frangakis</Author>
<URL>https://www.bmls.de/Electron_Microscopy/aboutus.html</URL>
<!-- Synopsis is a one-line description
Description is a full multi-line description -->
<Synopsis>ArtiaX: Cryo-ET Plugin for ChimeraX</Synopsis>
<Description>
ArtiaX is an open-source extension for visualization and processing of cryo electron tomography data. It allows
rendering of macromolecular complexes within their context in electron tomograms, picking particles for subtomogram
averaging, and assessing results of image classification or template matching procedures.
</Description>
<!-- Categories is a list where this bundle should appear -->
<Categories>
<Category name="General"/>
</Categories>
<!-- Dependencies on other ChimeraX/Python packages -->
<Dependencies>
<Dependency name="ChimeraX-Atomic" version=">=1.1"/>
<Dependency name="ChimeraX-BILD" version="~=1.0"/>
<Dependency name="ChimeraX-Core" version=">=1.7"/>
<Dependency name="ChimeraX-Geometry" version=">=1.1"/>
<Dependency name="ChimeraX-Graphics" version="~=1.1"/>
<Dependency name="ChimeraX-IMOD" version="~=1.0"/>
<Dependency name="ChimeraX-Log" version=">=1.1.4"/>
<Dependency name="ChimeraX-Map" version="~=1.1"/>
<Dependency name="ChimeraX-MapData" version="~=2.0"/>
<Dependency name="ChimeraX-Markers" version="~=1.0"/>
<Dependency name="ChimeraX-ModelPanel" version=">=1.2.1"/>
<Dependency name="ChimeraX-MouseModes" version="~=1.1"/>
<Dependency name="ChimeraX-OpenCommand" version=">=1.7"/>
<Dependency name="ChimeraX-SaveCommand" version=">=1.5"/>
<Dependency name="ChimeraX-UI" version=">=1.0"/>
<Dependency name="superqt"/>
<Dependency name="starfile"/>
<Dependency name="geomdl"/>
<Dependency name="pydantic"/>
</Dependencies>
<!-- Non-Python files that are part of package -->
<DataFiles>
<DataFile>docs/user/ArtiaX-docs-icon.svg</DataFile>
<DataFile>docs/user/*.html</DataFile>
<DataFile>docs/user/tools/*.html</DataFile>
<DataFile>docs/user/commands/*.html</DataFile>
<DataFile>docs/user/general/*.html</DataFile>
<DataFile>icons/*.png</DataFile>
</DataFiles>
<!-- Register .em format as one of the supported input file formats -->
<Providers manager="data formats">
<Provider name="Artiatomi Motivelist"
suffixes=".em"
category="particle list"
nicknames="motl,motivelist"
reference_url="https://github.com/uermel/Artiatomi/wiki/Motivelist"
synopsis="Artiatomi particle lists"/>
<Provider name="Generic Particle List"
suffixes=".tsv"
category="particle list"
nicknames="generic_particles"
reference_url="help:user/tools/generic_particle_list.html"
synopsis="TSV particle lists"/>
<Provider name="Dynamo Table"
suffixes=".tbl"
category="particle list"
nicknames="dynamo,tbl"
reference_url="https://wiki.dynamo.biozentrum.unibas.ch/w/index.php/Table"
synopsis="Dynamo particle table"/>
<Provider name="RELION STAR file"
suffixes=".star"
category="particle list"
nicknames="star,relion"
reference_url="https://relion.readthedocs.io/en/release-3.1/Reference/Conventions.html"
synopsis="RELION star files"/>
<Provider name="RELION5 STAR file"
suffixes=".star"
category="particle list"
nicknames="star,relion5"
reference_url="https://relion.readthedocs.io/en/latest/Reference/STA/Datatypes/particle_set.html#sec-sta-particle-set"
synopsis="RELION5 star files"/>
<Provider name="cryoET Data Portal"
suffixes=".ndjson"
category="particle list"
nicknames="cdp,data_portal"
reference_url=""
synopsis="CryoET data portal particle files."/>
<Provider name="Coords file"
suffixes=".coords"
category="particle list"
nicknames="coords,model2point"
reference_url="https://bio3d.colorado.edu/imod/doc/man/model2point.html"
synopsis="IMOD model2point output"/>
<Provider name="Copick Picks file"
suffixes=".json"
category="particle list"
nicknames="copick"
reference_url="https://github.com/uermel/copick"
synopsis="Copick picks files"/>
<Provider name="PEET mod/csv"
suffixes=".mod"
category="particle list"
nicknames="peet"
reference_url="https://bio3d.colorado.edu/PEET/PEETmanual.html"
synopsis="PEET model/csv"/>
<Provider name="ArtiaX geometric model"
suffixes=".axm"
category="geometric model"
nicknames="geomodel"
reference_url="https://numpy.org/doc/stable/reference/generated/numpy.lib.format.html#module-numpy.lib.format"
synopsis="ArtiaX geometric model"/>
</Providers>
<Providers manager="open command">
<Provider name="Artiatomi Motivelist" want_path="true" is_default="false"/>
<Provider name="Generic Particle List" want_path="true"/>
<Provider name="Dynamo Table" want_path="true"/>
<Provider name="RELION STAR file" want_path="true"/>
<Provider name="RELION5 STAR file" want_path="true"/>
<Provider name="cryoET Data Portal" want_path="true"/>
<Provider name="Coords file" want_path="true"/>
<Provider name="Copick Picks file" want_path="true" is_default="false"/>
<Provider name="PEET mod/csv" want_path="true"/>
<Provider name="ArtiaX geometric model" want_path="true"/>
</Providers>
<Providers manager="save command">
<Provider name="Artiatomi Motivelist" />
<Provider name="Generic Particle List" />
<Provider name="Dynamo Table" />
<Provider name="RELION STAR file" />
<Provider name="RELION5 STAR file" />
<Provider name="cryoET Data Portal"/>
<Provider name="Coords file"/>
<Provider name="Copick Picks file"/>
<Provider name="PEET mod/csv"/>
<Provider name="ArtiaX geometric model"/>
</Providers>
<Providers manager="presets">
<Provider category="ArtiaX" name="artiax default" />
<Provider category="ArtiaX" name="artiax record" />
</Providers>
<Providers manager="toolbar">
<!-- ArtiaX tab -->
<!-- ArtiaX tab, General -->
<Provider tab="ArtiaX" section="General"
name="Launch" icon="start.png" description="Start ArtiaX"/>
<Provider tab="ArtiaX" section="General"
name="Help" icon="help.png" description="Open documentation"/>
<!-- ArtiaX tab, Markers -->
<Provider tab="ArtiaX" section="Markers"
name="Show Markers" display_name="Show" icon="show_markers.png" description="Show particles as spheres."/>
<Provider tab="ArtiaX" section="Markers"
name="Hide Markers" display_name="Hide" icon="hide_markers.png" description="Hide spheres."/>
<Provider tab="ArtiaX" section="Markers" name="layout-markers" compact="true"/>
<!-- ArtiaX tab, Axes -->
<Provider tab="ArtiaX" section="Axes"
name="Show Axes" display_name="Show" icon="show_axes.png" description="Show principle axes of particles."/>
<Provider tab="ArtiaX" section="Axes"
name="Hide Axes" display_name="Hide" icon="hide_axes.png" description="Hide axes."/>
<Provider tab="ArtiaX" section="Axes" name="layout-axes" compact="true"/>
<!-- ArtiaX tab, Surfaces -->
<Provider tab="ArtiaX" section="Surfaces"
name="Show Surfaces" display_name="Show" icon="show_surfaces.png" description="Show particle surfaces."/>
<Provider tab="ArtiaX" section="Surfaces"
name="Hide Surfaces" display_name="Hide" icon="hide_surfaces.png" description="Hide surfaces."/>
<Provider tab="ArtiaX" section="Surfaces" name="layout-surfaces" compact="true"/>
<!-- ArtiaX tab, View -->
<Provider tab="ArtiaX" section="View"
name="XY" icon="view_xy.png" description="Set viewing direction to XY planes."/>
<Provider tab="ArtiaX" section="View"
name="XZ" icon="view_xz.png" description="Set viewing direction to XZ planes."/>
<Provider tab="ArtiaX" section="View"
name="YZ" icon="view_yz.png" description="Set viewing direction to YZ planes."/>
<Provider tab="ArtiaX" section="View"
name="Clip" icon="clip.png" description="Turn slab-clipping on or off for all tomograms."/>
<Provider tab="ArtiaX" section="View"
name="Invert Contrast" icon="invert_contrast.png" description="Invert contrast of visible tomograms."/>
<!-- ArtiaX tab, Standard Mouse Modes -->
<Provider tab="ArtiaX" section="Movement" mouse_mode="select"
name="Select" display_name="Select" icon="select.png" description="Select models."/>
<Provider tab="ArtiaX" section="Movement" mouse_mode="rotate"
name="Rotate" display_name="Rotate" icon="rotate.png" description="Rotate models."/>
<Provider tab="ArtiaX" section="Movement" mouse_mode="translate"
name="Translate" display_name="Translate" icon="translate.png" description="Translate models."/>
<Provider tab="ArtiaX" section="Movement" mouse_mode="pivot"
name="Pivot" display_name="Center On" icon="crosshairs.png" description="Set center of rotation on particle."/>
<!-- ArtiaX tab, Place Markers mirrored -->
<Provider tab="ArtiaX" section="Place Particles" mouse_mode="mark maximum"
name="mark maximum" display_name="Maximum" icon="maximum.png" description="Mark maximum."/>
<Provider tab="ArtiaX" section="Place Particles" mouse_mode="mark plane"
name="mark plane" display_name="Plane" icon="plane.png" description="Mark volume plane."/>
<Provider tab="ArtiaX" section="Place Particles" mouse_mode="mark surface"
name="mark surface" display_name="Surface" icon="surface.png" description="Mark surface."/>
<Provider tab="ArtiaX" section="Place Particles" mouse_mode="mark center"
name="mark center" display_name="Center" icon="center.png" description="Mark center."/>
<Provider tab="ArtiaX" section="Place Particles" mouse_mode="mark point"
name="mark point" display_name="Point" icon="point.png" description="Mark point."/>
<!-- ArtiaX tab, Manipulate Particles-->
<Provider tab="ArtiaX" section="Move Particles" mouse_mode="translate selected particles"
name="Translate Selected Particles" display_name="Translate Selected" icon="translate_selected.png"
description="Shift selected particles (hold SHIFT to rotate)."/>
<Provider tab="ArtiaX" section="Move Particles" mouse_mode="rotate selected particles"
name="Rotate Selected Particles" display_name="Rotate Selected" icon="rotate_selected.png"
description="Rotate selected particles (hold SHIFT to translate)."/>
<Provider tab="ArtiaX" section="Move Particles" mouse_mode="translate picked particle"
name="Translate Picked Particle" display_name="Translate Picked" icon="translate_picked.png"
description="Shift picked particle (hold SHIFT to rotate)."/>
<Provider tab="ArtiaX" section="Move Particles" mouse_mode="rotate picked particle"
name="Rotate Picked Particle" display_name="Rotate Picked" icon="rotate_picked.png"
description="Rotate picked particle (hold SHIFT to translate)."/>
<!-- ArtiaX tab, Delete Particles-->
<Provider tab="ArtiaX" section="Delete Particles"
name="Delete Selected Particles" display_name="Delete Selected" icon="delete_selected.png"
description="Delete picked particle."/>
<Provider tab="ArtiaX" section="Delete Particles" mouse_mode="delete picked particle"
name="Delete Picked Particle" display_name="Delete Picked" icon="delete.png"
description="Delete picked particle."/>
<!-- ArtiaX tab, Selection-->
<Provider tab="ArtiaX" section="Selection"
name="Invert Selection" display_name="Invert Selection" icon="invert_selection.png"
description="Invert particle selection."/>
<Provider tab="ArtiaX" section="Selection"
name="Select Inside Surface" display_name="Select Inside" icon="select_inside.png"
description="Selects all shown particles inside the selected surface."/>
<!-- ArtiaX tab, Reorient Particles-->
<Provider tab="ArtiaX" section="Flip Particles"
name="Flip X" display_name="X" icon="flip_x.png"
description="Rotates the selected particles 180 degrees around their x-axis."/>
<Provider tab="ArtiaX" section="Flip Particles"
name="Flip Y" display_name="Y" icon="flip_y.png"
description="Rotates the selected particles 180 degrees around their y-axis."/>
<Provider tab="ArtiaX" section="Flip Particles"
name="Flip Z" display_name="Z" icon="flip_z.png"
description="Rotates the selected particles 180 degrees around their z-axis."/>
<!-- ArtiaX models tab -->
<!-- ArtiaX Model tab, Markers -->
<Provider tab="ArtiaX Models" section="Markers"
name="Show Markers Models Tab" display_name="Show" icon="show_markers.png" description="Show particles as spheres."/>
<Provider tab="ArtiaX Models" section="Markers"
name="Hide Markers Models Tab" display_name="Hide" icon="hide_markers.png" description="Hide spheres."/>
<Provider tab="ArtiaX Models" section="Markers" name="layout-markers models" compact="true"/>
<!-- ArtiaX Model tab, Axes -->
<Provider tab="ArtiaX Models" section="Axes"
name="Show Axes Models Tab" display_name="Show" icon="show_axes.png" description="Show principle axes of particles."/>
<Provider tab="ArtiaX Models" section="Axes"
name="Hide Axes Models Tab" display_name="Hide" icon="hide_axes.png" description="Hide axes."/>
<Provider tab="ArtiaX Models" section="Axes" name="layout-axes models" compact="true"/>
<!-- ArtiaX Model tab, Surfaces -->
<Provider tab="ArtiaX Models" section="Surfaces"
name="Show Surfaces Models Tab" display_name="Show" icon="show_surfaces.png" description="Show particle surfaces."/>
<Provider tab="ArtiaX Models" section="Surfaces"
name="Hide Surfaces Models Tab" display_name="Hide" icon="hide_surfaces.png" description="Hide surfaces."/>
<Provider tab="ArtiaX Models" section="Surfaces" name="layout-surfaces models" compact="true"/>
<!-- ArtiaX Model tab, View -->
<Provider tab="ArtiaX Models" section="View"
name="XY Models Tab" display_name="XY" icon="view_xy.png" description="Set viewing direction to XY planes."/>
<Provider tab="ArtiaX Models" section="View"
name="XZ Models Tab" display_name="XZ" icon="view_xz.png" description="Set viewing direction to XZ planes."/>
<Provider tab="ArtiaX Models" section="View"
name="YZ Models Tab" display_name="YZ" icon="view_yz.png" description="Set viewing direction to YZ planes."/>
<!-- ArtiaX Model tab, Standard Mouse Modes -->
<Provider tab="ArtiaX Models" section="Movement" mouse_mode="select"
name="Select Models Tab" display_name="Select" icon="select.png" description="Select models."/>
<Provider tab="ArtiaX Models" section="Movement" mouse_mode="rotate"
name="Rotate Models Tab" display_name="Rotate" icon="rotate.png" description="Rotate models."/>
<Provider tab="ArtiaX Models" section="Movement" mouse_mode="translate"
name="Translate Models Tab" display_name="Translate" icon="translate.png" description="Translate models."/>
<Provider tab="ArtiaX Models" section="Movement" mouse_mode="pivot"
name="Pivot Models Tab" display_name="Center On" icon="crosshairs.png" description="Set center of rotation on particle."/>
<!-- ArtiaX Model tab, Fit Geometric Model-->
<Provider tab="ArtiaX Models" section="Fit Geometric Model"
name="Sphere" icon="show_markers.png" description="Fit a sphere to the currently selected particles."/>
<Provider tab="ArtiaX Models" section="Fit Geometric Model"
name="Line" icon="fit_line.png" description="Create a geometric model line between the selected particles."/>
<Provider tab="ArtiaX Models" section="Fit Geometric Model"
name="Surface" icon="fit_surface.png" description="Create a geometric model plane between the selected particles."/>
<Provider tab="ArtiaX Models" section="Fit Geometric Model"
name="Boundary" icon="boundary.png" description="Creates a hull around the selected particles."/>
<Provider tab="ArtiaX Models" section="Fit Geometric Model"
name="Triangles From Links" icon="triangles_from_links.png" description="Creates a triangle surface between all particles marked by links."/>
<!-- ArtiaX Model tab, Links-->
<Provider tab="ArtiaX Models" section="Links"
name="Triangulate" icon="triangulate.png" description="Triangulate all selected particles using links."/>
<Provider tab="ArtiaX Models" section="Links"
name="Remove Selected" icon="remove_links.png" description="Removes links from selected particles."/>
<!-- ArtiaX Model tab, Generate New Models-->
<Provider tab="ArtiaX Models" section="Generate New Models"
name="Create Mask" icon="create_mesh.png" description="Creates a mask from the selected geometric model."/>
<Provider tab="ArtiaX Models" section="Generate New Models"
name="Volume to Geomodel" icon="vol2geo.png" description="Creates a geomodel from the shown triangles
of the selected volumes."/>
<Provider tab="ArtiaX Models" section="Generate New Models"
name="Geomodel to Volume" icon="geo2vol.png" description="Creates a new volume by merging all shown geomodels."/>
<!-- ArtiaX Model tab, Delete Surface-->
<!-- Delete triangle, not used.
<Provider tab="ArtiaX Models" section="Delete Surface" mouse_mode="delete picked triangle"
name="Delete Picked Triangle" display_name="Delete Triangle" icon="delete.png"
description="Delete picked triangle from a boundary or surface model."/>
-->
<Provider tab="ArtiaX Models" section="Change Models" mouse_mode="delete tetra from boundary"
name="Delete Tetra From Boundary" display_name="Delete Tetra" icon="delete_tetra.png"
description="Delete picked tetrahedron from a boundary model."/>
<Provider tab="ArtiaX Models" section="Change Models" mouse_mode="mask connected triangles"
name="Mask Connected Triangles" display_name="Mask Triangles" icon="mask_triangle.png"
description="Hides all triangles connected to the picked triangle."/>
<!-- <Provider tab="ArtiaX Models" section="Change Models" mouse_mode="color connected triangles"-->
<!-- name="Color Connected Triangles" display_name="Color Triangles" icon="mask_triangle.png"-->
<!-- description="Color all triangles connected to the picked triangle."/>-->
<!-- <Provider tab="ArtiaX Models" section="Change Models" mouse_mode="extract connected triangles"-->
<!-- name="Extract Connected Triangles" display_name="Extract Triangles" icon="mask_triangle.png"-->
<!-- description="Extract all triangles connected to the picked triangle and save them as a new tomogram."/>-->
</Providers>
<!-- Python and ChimeraX-specific classifiers
From https://pypi.python.org/pypi?%3Aaction=list_classifiers
Some Python classifiers are always inserted by the build process.
These include the Environment and Operating System classifiers
as well as:
Framework :: ChimeraX
Intended Audience :: Science/Research
Programming Language :: Python :: 3
Topic :: Scientific/Engineering :: Visualization
Topic :: Scientific/Engineering :: Chemistry
Topic :: Scientific/Engineering :: Bio-Informatics
The "ChimeraX :: Bundle" classifier is also supplied automatically. -->
<Classifiers>
<!-- Development Status should be compatible with bundle version number -->
<PythonClassifier>Development Status :: 3 - Alpha</PythonClassifier>
<PythonClassifier>License :: Freeware</PythonClassifier>
<!-- ChimeraX classifiers describe supplied functionality -->
<ChimeraXClassifier>ChimeraX :: Tool :: ArtiaX :: General ::
Opens Tomo Plugin GUI</ChimeraXClassifier>
<!-- Commands -->
<ChimeraXClassifier>ChimeraX :: Command :: artiax start :: General ::
Start and Initialize ArtiaX plugin.</ChimeraXClassifier>
<ChimeraXClassifier>ChimeraX :: Command :: artiax view :: General ::
Set standard viewing directions.</ChimeraXClassifier>
<ChimeraXClassifier>ChimeraX :: Command :: artiax open tomo :: General ::
Open a Tomogram in ArtiaX.</ChimeraXClassifier>
<ChimeraXClassifier>ChimeraX :: Command :: artiax add tomo :: General ::
Add a volume loaded by ChimeraX to ArtiaX.</ChimeraXClassifier>
<ChimeraXClassifier>ChimeraX :: Command :: artiax attach :: General ::
Attach a model to an ArtiaX particle list.</ChimeraXClassifier>
<ChimeraXClassifier>ChimeraX :: Command :: artiax show :: General ::
Render particles of the specified lists with this style.</ChimeraXClassifier>
<ChimeraXClassifier>ChimeraX :: Command :: artiax hide :: General ::
Hide particles of the specified lists with this style.</ChimeraXClassifier>
<ChimeraXClassifier>ChimeraX :: Command :: artiax lock :: General ::
Prevent types of movement for these particle lists.</ChimeraXClassifier>
<ChimeraXClassifier>ChimeraX :: Command :: artiax unlock :: General ::
Allow types of movement for these particle lists.</ChimeraXClassifier>
<ChimeraXClassifier>ChimeraX :: Command :: artiax particles :: General ::
Set particle list properties.</ChimeraXClassifier>
<ChimeraXClassifier>ChimeraX :: Command :: artiax tomo :: General ::
Set tomogram properties.</ChimeraXClassifier>
<ChimeraXClassifier>ChimeraX :: Command :: artiax fit sphere :: General ::
Fits a sphere to the currently selected particles.</ChimeraXClassifier>
<ChimeraXClassifier>ChimeraX :: Command :: artiax fit line :: General ::
Fits a line to two selected particles.</ChimeraXClassifier>
<ChimeraXClassifier>ChimeraX :: Command :: artiax fit surface :: General ::
Fits a plane through the selected particles.</ChimeraXClassifier>
<ChimeraXClassifier>ChimeraX :: Command :: artiax boundary :: General ::
Creates a hull around the selected particles.</ChimeraXClassifier>
<ChimeraXClassifier>ChimeraX :: Command :: artiax mask :: General ::
Creates a mask from the selected geometric model.</ChimeraXClassifier>
<ChimeraXClassifier>ChimeraX :: Command :: artiax fit curved line :: General ::
Fits a smooth line between the selected particles.</ChimeraXClassifier>
<ChimeraXClassifier>ChimeraX :: Command :: artiax triangulate :: General ::
Triangulates all selected particles.</ChimeraXClassifier>
<ChimeraXClassifier>ChimeraX :: Command :: artiax remove links :: General ::
Removes links from selected particles.</ChimeraXClassifier>
<ChimeraXClassifier>ChimeraX :: Command :: artiax triangles from links :: General ::
Creates a triangle surface between all particles marked by links.</ChimeraXClassifier>
<ChimeraXClassifier>ChimeraX :: Command :: artiax flip :: General ::
Rotates the selected particles 180 degrees around the given axis. Default degree is 180. </ChimeraXClassifier>
<ChimeraXClassifier>ChimeraX :: Command :: artiax select inside surface :: General ::
Selects all shown particles inside the selected surface.</ChimeraXClassifier>
<ChimeraXClassifier>ChimeraX :: Command :: artiax geomodel color :: General ::
Set geomodel color.</ChimeraXClassifier>
<ChimeraXClassifier>ChimeraX :: Command :: artiax moveCameraAlongLine :: General ::
Moves camera along a specified line.</ChimeraXClassifier>
<ChimeraXClassifier>ChimeraX :: Command :: artiax filter tomo :: General ::
Filter a tomogram using low, high, or band-pass filters.</ChimeraXClassifier>
<ChimeraXClassifier>ChimeraX :: Command :: artiax gen in surface :: General ::
Generates points inside a specified surface.</ChimeraXClassifier>
<ChimeraXClassifier>ChimeraX :: Command :: artiax gen on surface :: General ::
Generates points on a specified surface.</ChimeraXClassifier>
<ChimeraXClassifier>ChimeraX :: Command :: artiax geo2vol :: General ::
Add geomodels to volumes.</ChimeraXClassifier>
<ChimeraXClassifier>ChimeraX :: Command :: artiax vol2geo :: General ::
Create geomodels from volumes.</ChimeraXClassifier>
<ChimeraXClassifier>ChimeraX :: Command :: artiax mask triangle radius :: General ::
Mouse mode for masking connected triangles.</ChimeraXClassifier>
<ChimeraXClassifier>ChimeraX :: Command :: artiax remove overlap :: General ::
Moves particles with attached surfaces so that no surfaces overlap.</ChimeraXClassifier>
<ChimeraXClassifier>ChimeraX :: Command :: artiax info :: General ::
Print information about tomograms or particle lists.</ChimeraXClassifier>
<ChimeraXClassifier>ChimeraX :: Command :: artiax colormap :: General ::
Color particles by attribute.</ChimeraXClassifier>
<ChimeraXClassifier>ChimeraX :: Command :: artiax label :: General ::
Label particles with attribute.</ChimeraXClassifier>
<ChimeraXClassifier>ChimeraX :: Command :: artiax clip :: General ::
Turn on slab-dependent clipping planes for a tomogram.</ChimeraXClassifier>
<ChimeraXClassifier>ChimeraX :: Command :: artiax cap :: General ::
Turn on/off surface capping for particle lists.</ChimeraXClassifier>
<ChimeraXClassifier>ChimeraX :: Command :: artiax invert :: General ::
Invert the contrast of specified or all visible tomograms.</ChimeraXClassifier>
</Classifiers>
</BundleInfo>