Ticket #2597: make_win_debug.log

File make_win_debug.log, 104.7 KB (added by Tristan Croll, 6 years ago)

Added by email2trac

Line 
10.00% done: Initializing core
2Toolshed: __init__ False False None
3Toolshed: cache dir: C:\Users\tic20\AppData\Local\UCSF\ChimeraX\Cache\0.91\toolshed
4Toolshed: site dir: C:\Users\tic20\AppData\Local\UCSF\ChimeraX\0.91\site-packages
5Toolshed: loading bundles
6Toolshed: build available bundle ChimeraX_ISOLDE 1.0b3.dev7
7Toolshed: build available bundle ChimeraX_ISOLDE 1.0b3.dev7
8Toolshed: build available bundle ChimeraX_Clipper 0.9.11
9Toolshed: build available bundle ChimeraX_Clipper 0.9.11
10Toolshed: build available bundle ChimeraX_Maestro 1.5
11Toolshed: build available bundle ChimeraX_Maestro 1.4
12Toolshed: build available bundle ChimeraX_ISOLDE 1.0b3.dev6
13Toolshed: build available bundle ChimeraX_Clipper 0.9.10
14Toolshed: build available bundle ChimeraX_ISOLDE 1.0b3.dev6
15Toolshed: build available bundle ChimeraX_Clipper 0.9.10
16Toolshed: build available bundle ChimeraX_ISOLDE 1.0b3.dev6
17Toolshed: build available bundle ChimeraX_Clipper 0.9.10
18Toolshed: build available bundle ChimeraX_ISOLDE 1.0b3.dev5
19Toolshed: build available bundle ChimeraX_Clipper 0.9.9
20Toolshed: build available bundle ChimeraX_ISOLDE 1.0b3.dev5
21Toolshed: build available bundle ChimeraX_Clipper 0.9.9
22Toolshed: build available bundle ChimeraX_ISOLDE 1.0b3.dev5
23Toolshed: build available bundle ChimeraX_Clipper 0.9.9
24Toolshed: build available bundle ChimeraX_Maestro 1.3
25Toolshed: build available bundle ChimeraX_Maestro 1.2
26Toolshed: build available bundle ChimeraX_Maestro 1.1
27Toolshed: build available bundle ChimeraX_ISOLDE 1.0b3.dev4
28Toolshed: build available bundle ChimeraX_Clipper 0.9.8
29Toolshed: build available bundle ChimeraX_ISOLDE 1.0b3.dev4
30Toolshed: build available bundle ChimeraX_Clipper 0.9.8
31Toolshed: build available bundle ChimeraX_ISOLDE 1.0b3.dev4
32Toolshed: build available bundle ChimeraX_Clipper 0.9.8
33Toolshed: build available bundle ChimeraX_Maestro 1.0
34Toolshed: build available bundle ChimeraX_ISOLDE 1.0b3.dev3
35Toolshed: build available bundle ChimeraX_Clipper 0.9.7
36Toolshed: build available bundle ChimeraX_ISOLDE 1.0b3.dev3
37Toolshed: build available bundle ChimeraX_Clipper 0.9.7
38Toolshed: build available bundle ChimeraX_ISOLDE 1.0b3.dev3
39Toolshed: build available bundle ChimeraX_Clipper 0.9.7
40Toolshed: build available bundle ChimeraX_ISOLDE 1.0b3.dev2
41Toolshed: build available bundle ChimeraX_ISOLDE 1.0b3.dev2
42Toolshed: build available bundle ChimeraX_ISOLDE 1.0b3.dev2
43Toolshed: build available bundle ChimeraX_ISOLDE 1.0b3.dev1
44Toolshed: build available bundle ChimeraX_Clipper 0.9.6
45Toolshed: build available bundle ChimeraX_ISOLDE 1.0b3.dev1
46Toolshed: build available bundle ChimeraX_Clipper 0.9.6
47Toolshed: build available bundle ChimeraX_ISOLDE 1.0b3.dev1
48Toolshed: build available bundle ChimeraX_Clipper 0.9.6
49Toolshed: build available bundle ChimeraX_ISOLDE 1.0b3.dev0
50Toolshed: build available bundle ChimeraX_Clipper 0.9.5
51Toolshed: build available bundle ChimeraX_ISOLDE 1.0b3.dev0
52Toolshed: build available bundle ChimeraX_Clipper 0.9.5
53Toolshed: build available bundle ChimeraX_ISOLDE 1.0b3.dev0
54Toolshed: build available bundle ChimeraX_Clipper 0.9.5
55Toolshed: build available bundle ChimeraX_ISOLDE 1.0b3
56Toolshed: build available bundle ChimeraX_Clipper 0.9.4
57Toolshed: build available bundle ChimeraX_ISOLDE 1.0b3
58Toolshed: build available bundle ChimeraX_Clipper 0.9.4
59Toolshed: build available bundle ChimeraX_ISOLDE 1.0b3
60Toolshed: build available bundle ChimeraX_Clipper 0.9.4
61Toolshed: build available bundle ChimeraX_Clipper 0.9.3
62Toolshed: build available bundle ChimeraX_Clipper 0.9.3
63Toolshed: build available bundle ChimeraX_Clipper 0.9.2
64Toolshed: build available bundle ChimeraX_Clipper 0.9.2
65Toolshed: build available bundle ChimeraX_Clipper 0.9.1
66Toolshed: build available bundle ChimeraX_Clipper 0.9.1
67Toolshed: build available bundle ChimeraX_Clipper 0.9.1
68Toolshed: build available bundle ChimeraX_Clipper 0.9
69Toolshed: build available bundle ChimeraX_Clipper 0.9
70Toolshed: build available bundle ChimeraX_Clipper 0.9
71Toolshed: build available bundle MolecularDynamicsViewer 1.1
72Toolshed: build available bundle MolecularDynamicsViewer 1.0
73Toolshed: build available bundle ChimeraX_Clipper 0.4.0
74Toolshed: build available bundle ChimeraX_Clipper 0.3.1
75Toolshed: build available bundle ChimeraX_ISOLDE 1.0b2
76Toolshed: build available bundle ChimeraX_ISOLDE 1.0b2
77Toolshed: build available bundle ChimeraX_ISOLDE 1.0b2
78Toolshed: build available bundle ChimeraX_Clipper 0.3
79Toolshed: build available bundle ChimeraX_Clipper 0.3
80Toolshed: build available bundle ChimeraX_Clipper 0.3
81Toolshed: build available bundle ChimeraX_Clipper 0.2.1
82Toolshed: build available bundle ChimeraX_Clipper 0.2.1
83Toolshed: build available bundle ChimeraX_ISOLDE 1.0b1
84Toolshed: build available bundle ChimeraX_Clipper 0.2.0
85Toolshed: build available bundle ChimeraX_ISOLDE 1.0b1
86Toolshed: build available bundle ChimeraX_Clipper 0.2.0
87Toolshed: build available bundle ChimeraX_Tempy 0.6.0
88Toolshed: build available bundle ChimeraX_Tempy 0.5.0
89Toolshed: build available bundle ChimeraX_Tempy 0.4.0
90Toolshed: build available bundle ChimeraX_Tempy 0.3.0
91Toolshed: build available bundle ChimeraX_SignalViewer 1.0
92Toolshed: build available bundle ChimeraX_Tempy 0.2.0
93Toolshed: build available bundle ChimeraX_Tempy 0.1.0
94Toolshed: build available bundle ChimeraX_Tempy 0.0.5
95Toolshed: build available bundle ChimeraX_Tempy 0.0.4
96Toolshed: build available bundle ChimeraX_Tempy 0.0.3
97Toolshed: build available bundle ChimeraX_Tempy 0.0.2
98Toolshed: build available bundle ChimeraX_Tempy 0.0.1
99Toolshed: build available bundle ChimeraX_Stringdb 0.1
100Toolshed: build available bundle ChimeraX_Cytoscape 0.1
101Toolshed: build available bundle ChimeraX_BlastProtein 0.1
102Toolshed: reload False False
103Toolshed: _bundle_cache False
104Toolshed: InstalledBundleCache.load: rebuild_cache False
105Toolshed: InstalledBundleCache._read_cache: C:\Users\tic20\AppData\Local\UCSF\ChimeraX\Cache\0.91\toolshed\bundle_info.cache
106Toolshed: _is_cache_newer
107Toolshed: InstalledBundleCache._read_cache: 107 bundles
108Toolshed: InstalledBundleCache.load: using cached data
109Toolshed: register bundle ChimeraX-Core 0.91
110Toolshed: register bundle ChimeraX-Vive 1.0
111Toolshed: delay_registration vr
112Toolshed: delay_registration device vr
113Toolshed: register bundle ChimeraX-CellPack 1.0
114Toolshed: register_file_type cellpack
115Toolshed: register bundle ChimeraX-Preset-Mgr 1.0
116Toolshed: delay_registration preset
117Toolshed: register bundle ChimeraX-Meeting 1.0
118Toolshed: delay_registration meeting
119Toolshed: register bundle ChimeraX-WavefrontOBJ 1.0
120Toolshed: register_file_type Wavefront OBJ
121Toolshed: register bundle ChimeraX-RotamerLibs-Dynameomics 1.0
122Toolshed: register bundle ChimeraX-Morph 1.0
123Toolshed: delay_registration morph
124Toolshed: register bundle ChimeraX-RestServer 0.1
125Toolshed: delay_registration remotecontrol rest
126Toolshed: register bundle ChimeraX-Storm 1.0
127Toolshed: register_file_type STORM
128Toolshed: register bundle ChimeraX-Texture 1.0
129Toolshed: delay_registration texture
130Toolshed: register bundle ChimeraX-Movie 1.0
131Toolshed: delay_registration movie
132Toolshed: register bundle ChimeraX-RealSense 1.0
133Toolshed: delay_registration device realsense
134Toolshed: register bundle ChimeraX-RotamerLibs-Dunbrack 1.0
135Toolshed: register bundle ChimeraX-ExperimentalCommands 1.0
136Toolshed: delay_registration ribbon
137Toolshed: delay_registration ribbon hide
138Toolshed: delay_registration ~ribbon
139Toolshed: delay_registration getcrd
140Toolshed: delay_registration debug dumpspec
141Toolshed: register bundle ChimeraX-SpaceNavigator 1.0
142Toolshed: delay_registration device snav
143Toolshed: register bundle ChimeraX-gltf 1.0
144Toolshed: register_file_type glTF
145Toolshed: register bundle ChimeraX-Atomic 1.0
146Toolshed: register bundle ChimeraX-VTK 1.0
147Toolshed: register_file_type VTK PolyData
148Toolshed: register bundle ChimeraX-WebServices 1.0
149Toolshed: register bundle ChimeraX-RotamerLibs-Richardson 1.0
150Toolshed: register bundle ChimeraX-STL 1.0
151Toolshed: register_file_type StereoLithography
152Toolshed: register bundle ChimeraX-MouseModes 1.0
153Toolshed: delay_registration ui mousemode
154Toolshed: delay_registration mousemode
155Toolshed: register bundle ChimeraX-Segment 1.0
156Toolshed: register bundle ChimeraX-MLP 1.0
157Toolshed: delay_registration mlp
158Toolshed: register bundle ChimeraX-Rotamer-Lib-Mgr 1.0
159Toolshed: register bundle ChimeraX-Test 1.0
160Toolshed: delay_registration debug test
161Toolshed: delay_registration debug exectest
162Toolshed: delay_registration debug expectfail
163Toolshed: register bundle ChimeraX-Crystal 1.0
164Toolshed: register bundle ChimeraX-Dicom 1.0
165Toolshed: register bundle ChimeraX-Scheme-Mgr 1.0
166Toolshed: register bundle ChimeraX-List-Info 0.1
167Toolshed: delay_registration info
168Toolshed: register bundle ChimeraX-SmoothLines 1.0
169Toolshed: delay_registration smoothlines
170Toolshed: register bundle ChimeraX-RemoteControl 1.0
171Toolshed: delay_registration remotecontrol xmlrpc
172Toolshed: register bundle ChimeraX-Struts 1.0
173Toolshed: delay_registration struts
174Toolshed: register bundle ChimeraX-ColorGlobe 1.0
175Toolshed: register_file_type Directional FSC
176Toolshed: register bundle ChimeraX-MapData 1.0
177Toolshed: register bundle ChimeraX-Dssp 1.0
178Toolshed: register bundle ChimeraX-ChemGroup 1.0
179Toolshed: register bundle ChimeraX-PDB 1.0
180Toolshed: register_file_type PDB
181Toolshed: register bundle ChimeraX-MD-crds 1.0
182Toolshed: register_file_type Gromacs full-precision coordinates
183Toolshed: register_file_type Gromacs compressed coordinates
184Toolshed: register_file_type DCD coordinates
185Toolshed: register bundle ChimeraX-Atom-Search 1.0
186Toolshed: register bundle ChimeraX-UI 1.0
187Toolshed: delay_registration ui
188Toolshed: register bundle ChimeraX-Clipper 0.9.11
189Toolshed: delay_registration clipper
190Toolshed: delay_registration cview
191Toolshed: register_file_type Structure factor MTZ
192Toolshed: register bundle ChimeraX-Std-Commands 1.0
193Toolshed: delay_registration alias
194Toolshed: delay_registration alias list
195Toolshed: delay_registration alias delete
196Toolshed: delay_registration ~alias
197Toolshed: delay_registration align
198Toolshed: delay_registration camera
199Toolshed: delay_registration cartoon
200Toolshed: delay_registration ~cartoon
201Toolshed: delay_registration cd
202Toolshed: delay_registration clip
203Toolshed: delay_registration ~clip
204Toolshed: delay_registration close
205Toolshed: delay_registration cofr
206Toolshed: delay_registration ~cofr
207Toolshed: delay_registration color
208Toolshed: delay_registration colour
209Toolshed: delay_registration color delete
210Toolshed: delay_registration color list
211Toolshed: delay_registration color name
212Toolshed: delay_registration color show
213Toolshed: delay_registration colordef
214Toolshed: delay_registration ~colordef
215Toolshed: delay_registration colourdef
216Toolshed: delay_registration ~colourdef
217Toolshed: delay_registration coordset
218Toolshed: delay_registration crossfade
219Toolshed: delay_registration delete
220Toolshed: delay_registration dssp
221Toolshed: delay_registration exit
222Toolshed: delay_registration quit
223Toolshed: delay_registration graphics
224Toolshed: delay_registration hide
225Toolshed: delay_registration ~show
226Toolshed: delay_registration ~display
227Toolshed: delay_registration lighting
228Toolshed: delay_registration lighting model
229Toolshed: delay_registration material
230Toolshed: delay_registration measure buriedarea
231Toolshed: delay_registration measure center
232Toolshed: delay_registration measure convexity
233Toolshed: delay_registration measure inertia
234Toolshed: delay_registration measure length
235Toolshed: delay_registration measure symmetry
236Toolshed: delay_registration move
237Toolshed: delay_registration palette
238Toolshed: delay_registration pdbimages
239Toolshed: delay_registration perframe
240Toolshed: delay_registration ~perframe
241Toolshed: delay_registration pwd
242Toolshed: delay_registration rainbow
243Toolshed: delay_registration rename
244Toolshed: delay_registration roll
245Toolshed: delay_registration runscript
246Toolshed: delay_registration select
247Toolshed: delay_registration ~select
248Toolshed: delay_registration set
249Toolshed: delay_registration ~set
250Toolshed: delay_registration setattr
251Toolshed: delay_registration show
252Toolshed: delay_registration display
253Toolshed: delay_registration size
254Toolshed: delay_registration split
255Toolshed: delay_registration stop
256Toolshed: delay_registration style
257Toolshed: delay_registration sym
258Toolshed: delay_registration tile
259Toolshed: delay_registration time
260Toolshed: delay_registration transparency
261Toolshed: delay_registration turn
262Toolshed: delay_registration undo
263Toolshed: delay_registration redo
264Toolshed: delay_registration usage
265Toolshed: delay_registration version
266Toolshed: delay_registration view
267Toolshed: delay_registration wait
268Toolshed: delay_registration windowsize
269Toolshed: delay_registration select zone
270Toolshed: delay_registration zoom
271Toolshed: register bundle ChimeraX-Read-Pbonds 1.0
272Toolshed: register_file_type Pseudobonds
273Toolshed: register bundle ChimeraX-Dist-Monitor 1.0
274Toolshed: delay_registration distance
275Toolshed: delay_registration ~distance
276Toolshed: register bundle ChimeraX-Help 0.9a1
277Toolshed: delay_registration help
278Toolshed: register_file_type HTML
279Toolshed: register bundle ChimeraX-MapEraser 1.0
280Toolshed: delay_registration volume erase
281Toolshed: register bundle ChimeraX-Map 1.0
282Toolshed: delay_registration volume
283Toolshed: delay_registration vop
284Toolshed: delay_registration molmap
285Toolshed: delay_registration measure mapstats
286Toolshed: register bundle ChimeraX-ModelPanel 1.0
287Toolshed: register bundle ChimeraX-Alignments 1.0
288Toolshed: delay_registration sequence
289Toolshed: register_file_type FASTA
290Toolshed: register_file_type MSF
291Toolshed: register_file_type PIR
292Toolshed: register_file_type ALN
293Toolshed: register_file_type HSSP
294Toolshed: register_file_type Pfam
295Toolshed: register_file_type RSF
296Toolshed: register_file_type Stockholm
297Toolshed: register bundle ChimeraX-Bug-Reporter 1.0
298Toolshed: register bundle ChimeraX-TapeMeasure 1.0
299Toolshed: register bundle ChimeraX-SwapRes 1.0
300Toolshed: delay_registration swapaa
301Toolshed: register bundle ChimeraX-PickBlobs 1.0
302Toolshed: delay_registration measure blob
303Toolshed: register bundle ChimeraX-MMTF 1.0
304Toolshed: register_file_type MMTF
305Toolshed: register bundle ChimeraX-FileHistory 1.0
306Toolshed: register bundle ChimeraX-ShowAttr 1.0
307Toolshed: register bundle ChimeraX-Label 1.0
308Toolshed: delay_registration 2dlabels
309Toolshed: delay_registration label
310Toolshed: delay_registration ~label
311Toolshed: register bundle ChimeraX-Tug 1.0
312Toolshed: register bundle ChimeraX-Zone 1.0
313Toolshed: delay_registration zone
314Toolshed: register bundle ChimeraX-Log 1.0
315Toolshed: delay_registration echo
316Toolshed: delay_registration log
317Toolshed: register bundle ChimeraX-Segger 1.0
318Toolshed: register bundle ChimeraX-Mol2 1.0
319Toolshed: register_file_type Sybyl Mol2
320Toolshed: register bundle ChimeraX-ISOLDE 1.0b3.dev7
321Toolshed: delay_registration isolde
322Toolshed: delay_registration rama
323Toolshed: delay_registration rota
324Toolshed: delay_registration ~rama
325Toolshed: delay_registration ~rota
326Toolshed: register bundle ChimeraX-Markers 1.0
327Toolshed: delay_registration marker
328Toolshed: register_file_type Marker model
329Toolshed: register bundle ChimeraX-BondRot 1.0
330Toolshed: delay_registration torsion
331Toolshed: register bundle ChimeraX-ButtonPanel 1.0
332Toolshed: delay_registration buttonpanel
333Toolshed: register bundle ChimeraX-mmCIF 1.1
334Toolshed: register_file_type mmCIF
335Toolshed: register bundle ChimeraX-Clashes 1.0
336Toolshed: delay_registration clashes
337Toolshed: delay_registration contacts
338Toolshed: delay_registration ~clashes
339Toolshed: delay_registration ~contacts
340Toolshed: register bundle ChimeraX-BasicActions 0.1
341Toolshed: delay_registration name
342Toolshed: delay_registration name frozen
343Toolshed: delay_registration name delete
344Toolshed: delay_registration name list
345Toolshed: register bundle ChimeraX-FunctionKey 1.0
346Toolshed: delay_registration ui functionkey
347Toolshed: delay_registration functionkey
348Toolshed: register bundle ChimeraX-ModelSeries 1.0
349Toolshed: delay_registration mseries
350Toolshed: register bundle ChimeraX-Contacts 1.0
351Toolshed: delay_registration interfaces
352Toolshed: register bundle ChimeraX-Shortcuts 1.0
353Toolshed: delay_registration ks
354Toolshed: register bundle ChimeraX-Connect-Structure 1.0
355Toolshed: register bundle ChimeraX-VolumeMenu 1.0
356Toolshed: register bundle ChimeraX-Dist-UI 1.0
357Toolshed: register bundle ChimeraX-SwapAA 1.0
358Toolshed: delay_registration swapaa mousemode
359Toolshed: register bundle ChimeraX-Shell 1.0
360Toolshed: register bundle ChimeraX-Hbonds 1.0
361Toolshed: delay_registration hbonds
362Toolshed: delay_registration ~hbonds
363Toolshed: register bundle ChimeraX-Registration 0.1
364Toolshed: delay_registration registration status
365Toolshed: register bundle ChimeraX-ResidueFit 1.0
366Toolshed: delay_registration resfit
367Toolshed: register bundle ChimeraX-Cage-Builder 1.0
368Toolshed: delay_registration cage
369Toolshed: register bundle ChimeraX-CommandLine 1.0
370Toolshed: register bundle ChimeraX-SideView 1.0
371Toolshed: register bundle ChimeraX-Mask 1.0
372Toolshed: delay_registration volume mask
373Toolshed: delay_registration volume onesmask
374Toolshed: register bundle ChimeraX-AlignmentMatrices 1.0
375Toolshed: register bundle ChimeraX-MapSeries 1.0
376Toolshed: delay_registration vseries
377Toolshed: delay_registration measure motion
378Toolshed: register bundle ChimeraX-IHM 1.0
379Toolshed: register_file_type IHM
380Toolshed: register bundle ChimeraX-AddH 1.0
381Toolshed: delay_registration addh
382Toolshed: register bundle ChimeraX-Modeller 1.0
383Toolshed: delay_registration modeller comparative
384Toolshed: delay_registration modeller scores
385Toolshed: register bundle ChimeraX-Bumps 1.0
386Toolshed: delay_registration bumps
387Toolshed: delay_registration cbumps
388Toolshed: register bundle ChimeraX-AlignmentHdrs 1.0
389Toolshed: register bundle ChimeraX-Toolbar 0.1
390Toolshed: register bundle ChimeraX-MapFit 1.0
391Toolshed: delay_registration fitmap
392Toolshed: register bundle ChimeraX-uniprot 1.0
393Toolshed: register_file_type UniProt
394Toolshed: register bundle ChimeraX-Crosslinks 1.0
395Toolshed: delay_registration crosslinks
396Toolshed: register bundle ChimeraX-BlastProtein 0.1
397Toolshed: delay_registration blastprotein
398Toolshed: delay_registration blastpdb
399Toolshed: register bundle ChimeraX-MapFilter 1.0
400Toolshed: register bundle ChimeraX-Surface 1.0
401Toolshed: delay_registration color electrostatic
402Toolshed: delay_registration color sample
403Toolshed: delay_registration color gradient
404Toolshed: delay_registration color radial
405Toolshed: delay_registration color cylindrical
406Toolshed: delay_registration color height
407Toolshed: delay_registration surface
408Toolshed: delay_registration ~surface
409Toolshed: delay_registration volume splitbyzone
410Toolshed: delay_registration sop
411Toolshed: delay_registration measure sasa
412Toolshed: delay_registration measure volume
413Toolshed: delay_registration measure area
414Toolshed: register_file_type Collada
415Toolshed: register bundle ChimeraX-AlignmentAlgorithms 1.0
416Toolshed: register bundle ChimeraX-ViewDockX 0.1
417Toolshed: delay_registration viewdockx
418Toolshed: delay_registration viewdockx down
419Toolshed: delay_registration viewdockx up
420Toolshed: register_file_type mol2
421Toolshed: register_file_type pdbqt
422Toolshed: register bundle ChimeraX-MatchMaker 1.0
423Toolshed: delay_registration matchmaker
424Toolshed: delay_registration mmaker
425Toolshed: register bundle ChimeraX-BILD 0.1
426Toolshed: register_file_type BILD
427Toolshed: register bundle ChimeraX-Nucleotides 0.1
428Toolshed: delay_registration nucleotides
429Toolshed: delay_registration ~nucleotides
430Toolshed: register bundle ChimeraX-SeqView 1.0
431Toolshed: finished loading bundles
43250.00% done: Initializing bundles
433Toolshed: initialize_bundles False
434Toolshed: initialize manager presets for bundle 'ChimeraX-Preset-Mgr'
435Toolshed: initialize manager rotamers for bundle 'ChimeraX-Rotamer-Lib-Mgr'
436Toolshed: skip non-GUI manager url_schemes for bundle 'ChimeraX-Scheme-Mgr'
437Toolshed: initialize manager alignments for bundle 'ChimeraX-Alignments'
438Toolshed: skip non-GUI manager toolbar for bundle 'ChimeraX-Toolbar'
439Toolshed: custom initialization for bundle 'ChimeraX-Vive'
440Toolshed: custom initialization for bundle 'ChimeraX-RestServer'
441Toolshed: custom initialization for bundle 'ChimeraX-Atomic'
442Toolshed: custom initialization for bundle 'ChimeraX-MouseModes'
443Toolshed: custom initialization for bundle 'ChimeraX-Dicom'
444Toolshed: custom initialization for bundle 'ChimeraX-ChemGroup'
445Toolshed: custom initialization for bundle 'ChimeraX-Dist-Monitor'
446Toolshed: custom initialization for bundle 'ChimeraX-Help'
447Toolshed: custom initialization for bundle 'ChimeraX-MapEraser'
448Toolshed: custom initialization for bundle 'ChimeraX-Map'
449Toolshed: custom initialization for bundle 'ChimeraX-Bug-Reporter'
450Toolshed: custom initialization for bundle 'ChimeraX-TapeMeasure'
451Toolshed: custom initialization for bundle 'ChimeraX-PickBlobs'
452Toolshed: custom initialization for bundle 'ChimeraX-Label'
453Toolshed: custom initialization for bundle 'ChimeraX-Tug'
454Toolshed: custom initialization for bundle 'ChimeraX-Zone'
455Toolshed: custom initialization for bundle 'ChimeraX-Log'
456Toolshed: custom initialization for bundle 'ChimeraX-Segger'
457Toolshed: custom initialization for bundle 'ChimeraX-ISOLDE'
458Toolshed: custom initialization for bundle 'ChimeraX-Markers'
459Toolshed: custom initialization for bundle 'ChimeraX-BondRot'
460Toolshed: custom initialization for bundle 'ChimeraX-BasicActions'
461Toolshed: custom initialization for bundle 'ChimeraX-FunctionKey'
462Toolshed: custom initialization for bundle 'ChimeraX-VolumeMenu'
463Toolshed: custom initialization for bundle 'ChimeraX-Dist-UI'
464Toolshed: custom initialization for bundle 'ChimeraX-SwapAA'
465Toolshed: custom initialization for bundle 'ChimeraX-Registration'
466Toolshed: custom initialization for bundle 'ChimeraX-CommandLine'
467Toolshed: custom initialization for bundle 'ChimeraX-MapSeries'
468Toolshed: custom initialization for bundle 'ChimeraX-Surface'
469Toolshed: custom initialization for bundle 'ChimeraX-ViewDockX'
470Toolshed: find_bundle ChimeraX-Core True None
471Toolshed: find_bundle ChimeraX-Atomic True None
472Toolshed: find_bundle ChimeraX-Core True None
473Toolshed: find_bundle ChimeraX-Atomic True None
474Toolshed: find_bundle ChimeraX-Core True None
475Toolshed: find_bundle ChimeraX-Atomic True None
476Toolshed: find_bundle ChimeraX-Core True None
477Toolshed: find_bundle ChimeraX-Atomic True None
478Toolshed: find_bundle ChimeraX-Core True None
479Toolshed: find_bundle ChimeraX-Atomic True None
480Toolshed: find_bundle ChimeraX-Core True None
481Toolshed: find_bundle ChimeraX-Atomic True None
482Toolshed: find_bundle ChimeraX-Core True None
483Toolshed: find_bundle ChimeraX-Atomic True None
484Toolshed: find_bundle ChimeraX-Core True None
485Toolshed: find_bundle ChimeraX-Atomic True None
486Toolshed: find_bundle ChimeraX-Core True None
487Toolshed: find_bundle ChimeraX-Atomic True None
488Toolshed: find_bundle ChimeraX-Core True None
489Toolshed: find_bundle ChimeraX-Atomic True None
490Toolshed: find_bundle ChimeraX-Core True None
491Toolshed: find_bundle ChimeraX-Atomic True None
492
493----------------------------------------------------------------------
494Ran 0 tests in 0.000s
495
496OK
497Toolshed: install_bundle .\dist\ChimeraX_Clipper-0.9.12-cp37-cp37m-win_amd64.whl
498Toolshed: find_bundle ChimeraX_Clipper True None
499Toolshed: deregister_command clipper
500Toolshed: deregister_command cview
501Toolshed: _run_pip command: ['install', '--upgrade', '--extra-index-url', 'https://cxtoolshed.rbvi.ucsf.edu/pypi/', '--upgrade-strategy', 'only-if-needed', '--user', '.\\dist\\ChimeraX_Clipper-0.9.12-cp37-cp37m-win_amd64.whl']
502Toolshed: _run_pip result: Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/pypi/
503
504Processing c:\users\tic20\my-gits\chimerax-clipper\dist\chimerax_clipper-0.9.12-cp37-cp37m-win_amd64.whl
505
506Requirement already satisfied, skipping upgrade: ChimeraX-Atomic>=1.0 in c:\program files\chimerax-daily\chimerax\bin\lib\site-packages (from ChimeraX-Clipper==0.9.12) (1.0)
507
508Requirement already satisfied, skipping upgrade: ChimeraX-Core==0.91 in c:\program files\chimerax-daily\chimerax\bin\lib\site-packages (from ChimeraX-Clipper==0.9.12) (0.91)
509
510Installing collected packages: ChimeraX-Clipper
511
512Successfully installed ChimeraX-Clipper-0.9.12
513
514
515Toolshed: set_install_timestamp
516Toolshed: reload True False
517Toolshed: _bundle_cache False
518Toolshed: InstalledBundleCache.load: rebuild_cache True
519Toolshed: InstalledBundleCache.load: rebuilding cache
520Toolshed: InstalledBundleCache.load: package ChimeraX-ISOLDE 1.0b3.dev7
521Toolshed: InstalledBundleCache.load: bundle ChimeraX-ISOLDE (installed) [version: 1.0b3.dev7] [api package: chimerax.isolde] [category: General] [tool: ISOLDE [categories: General] [synopsis: Interactive Molecular Dynamics Flexible Fitting (iMDFF)]] [command: isolde [categories: General] [synopsis: Command-line control of ISOLDE simulations]] [command: rama [categories: General] [synopsis: Live Ramachandran validation of models]] [command: rota [categories: General] [synopsis: Live rotamer validation of models]] [command: ~rama [categories: General] [synopsis: Turn off live Ramachandran validation of models]] [command: ~rota [categories: General] [synopsis: Turn off live rotamer validation of models]]
522Toolshed: InstalledBundleCache.load: package ChimeraX-Clipper 0.9.11
523Toolshed: InstalledBundleCache.load: bundle ChimeraX-Clipper (installed) [version: 0.9.11] [api package: chimerax.clipper] [category: General] [command: clipper [categories: General] [synopsis: Command-line control of Clipper plugin for symmetry and map visualisation]] [command: cview [categories: General] [synopsis: Re-center view on a selection, and set view mode to centerOfView with pivot indicator]] [data format: Structure factor MTZ [category: Reflection data] [suffixes: .mtz] [synopsis: Crystallographic reflection file]]
524Toolshed: InstalledBundleCache.load: package wheel 0.33.6
525Toolshed: InstalledBundleCache._make_bundle_info: no ChimeraX bundle in wheel 0.33.6
526Toolshed: InstalledBundleCache.load: package webcolors 1.9.1
527Toolshed: InstalledBundleCache._make_bundle_info: no ChimeraX bundle in webcolors 1.9.1
528Toolshed: InstalledBundleCache.load: package wcwidth 0.1.7
529Toolshed: InstalledBundleCache._make_bundle_info: no ChimeraX bundle in wcwidth 0.1.7
530Toolshed: InstalledBundleCache.load: package urllib3 1.25.7
531Toolshed: InstalledBundleCache._make_bundle_info: no ChimeraX bundle in urllib3 1.25.7
532Toolshed: InstalledBundleCache.load: package traitlets 4.3.3
533Toolshed: InstalledBundleCache._make_bundle_info: no ChimeraX bundle in traitlets 4.3.3
534Toolshed: InstalledBundleCache.load: package tornado 6.0.3
535Toolshed: InstalledBundleCache._make_bundle_info: no ChimeraX bundle in tornado 6.0.3
536Toolshed: InstalledBundleCache.load: package tinyarray 1.2.1
537Toolshed: InstalledBundleCache._make_bundle_info: no ChimeraX bundle in tinyarray 1.2.1
538Toolshed: InstalledBundleCache.load: package tifffile 2019.7.26
539Toolshed: InstalledBundleCache._make_bundle_info: no ChimeraX bundle in tifffile 2019.7.26
540Toolshed: InstalledBundleCache.load: package tables 3.5.2
541Toolshed: InstalledBundleCache._make_bundle_info: no ChimeraX bundle in tables 3.5.2
542Toolshed: InstalledBundleCache.load: package suds-jurko 0.6
543Toolshed: InstalledBundleCache._make_bundle_info: no ChimeraX bundle in suds-jurko 0.6
544Toolshed: InstalledBundleCache.load: package sphinxcontrib-serializinghtml 1.1.3
545Toolshed: InstalledBundleCache._make_bundle_info: no classifiers in sphinxcontrib-serializinghtml 1.1.3
546Toolshed: InstalledBundleCache.load: package sphinxcontrib-qthelp 1.0.2
547Toolshed: InstalledBundleCache._make_bundle_info: no classifiers in sphinxcontrib-qthelp 1.0.2
548Toolshed: InstalledBundleCache.load: package sphinxcontrib-jsmath 1.0.1
549Toolshed: InstalledBundleCache._make_bundle_info: no ChimeraX bundle in sphinxcontrib-jsmath 1.0.1
550Toolshed: InstalledBundleCache.load: package sphinxcontrib-htmlhelp 1.0.2
551Toolshed: InstalledBundleCache._make_bundle_info: no classifiers in sphinxcontrib-htmlhelp 1.0.2
552Toolshed: InstalledBundleCache.load: package sphinxcontrib-devhelp 1.0.1
553Toolshed: InstalledBundleCache._make_bundle_info: no classifiers in sphinxcontrib-devhelp 1.0.1
554Toolshed: InstalledBundleCache.load: package sphinxcontrib-blockdiag 1.5.5
555Toolshed: InstalledBundleCache._make_bundle_info: no ChimeraX bundle in sphinxcontrib-blockdiag 1.5.5
556Toolshed: InstalledBundleCache.load: package sphinxcontrib-applehelp 1.0.1
557Toolshed: InstalledBundleCache._make_bundle_info: no classifiers in sphinxcontrib-applehelp 1.0.1
558Toolshed: InstalledBundleCache.load: package Sphinx 2.2.0
559Toolshed: InstalledBundleCache._make_bundle_info: no ChimeraX bundle in Sphinx 2.2.0
560Toolshed: InstalledBundleCache.load: package sortedcontainers 2.1.0
561Toolshed: InstalledBundleCache._make_bundle_info: no ChimeraX bundle in sortedcontainers 2.1.0
562Toolshed: InstalledBundleCache.load: package snowballstemmer 2.0.0
563Toolshed: InstalledBundleCache._make_bundle_info: no ChimeraX bundle in snowballstemmer 2.0.0
564Toolshed: InstalledBundleCache.load: package six 1.12.0
565Toolshed: InstalledBundleCache._make_bundle_info: no ChimeraX bundle in six 1.12.0
566Toolshed: InstalledBundleCache.load: package setuptools 41.2.0
567Toolshed: InstalledBundleCache._make_bundle_info: no ChimeraX bundle in setuptools 41.2.0
568Toolshed: InstalledBundleCache.load: package scipy 1.3.1
569Toolshed: InstalledBundleCache._make_bundle_info: no ChimeraX bundle in scipy 1.3.1
570Toolshed: InstalledBundleCache.load: package requests 2.22.0
571Toolshed: InstalledBundleCache._make_bundle_info: no ChimeraX bundle in requests 2.22.0
572Toolshed: InstalledBundleCache.load: package qtconsole 4.5.5
573Toolshed: InstalledBundleCache._make_bundle_info: no ChimeraX bundle in qtconsole 4.5.5
574Toolshed: InstalledBundleCache.load: package pyzmq 18.1.1
575Toolshed: InstalledBundleCache._make_bundle_info: no ChimeraX bundle in pyzmq 18.1.1
576Toolshed: InstalledBundleCache.load: package pywin32 227
577Toolshed: InstalledBundleCache._make_bundle_info: no ChimeraX bundle in pywin32 227
578Toolshed: InstalledBundleCache.load: package pytz 2019.3
579Toolshed: InstalledBundleCache._make_bundle_info: no ChimeraX bundle in pytz 2019.3
580Toolshed: InstalledBundleCache.load: package python-dateutil 2.8.0
581Toolshed: InstalledBundleCache._make_bundle_info: no ChimeraX bundle in python-dateutil 2.8.0
582Toolshed: InstalledBundleCache.load: package PyQtWebEngine-commercial 5.12.1
583Toolshed: InstalledBundleCache._make_bundle_info: no classifiers in PyQtWebEngine-commercial 5.12.1
584Toolshed: InstalledBundleCache.load: package PyQt5-sip 4.19.18
585Toolshed: InstalledBundleCache._make_bundle_info: no classifiers in PyQt5-sip 4.19.18
586Toolshed: InstalledBundleCache.load: package PyQt5-commercial 5.12.3
587Toolshed: InstalledBundleCache._make_bundle_info: no classifiers in PyQt5-commercial 5.12.3
588Toolshed: InstalledBundleCache.load: package pyparsing 2.4.5
589Toolshed: InstalledBundleCache._make_bundle_info: no ChimeraX bundle in pyparsing 2.4.5
590Toolshed: InstalledBundleCache.load: package PyOpenGL 3.1.3b2
591Toolshed: InstalledBundleCache._make_bundle_info: no ChimeraX bundle in PyOpenGL 3.1.3b2
592Toolshed: InstalledBundleCache.load: package PyOpenGL-accelerate 3.1.3b2
593Toolshed: InstalledBundleCache._make_bundle_info: no ChimeraX bundle in PyOpenGL-accelerate 3.1.3b2
594Toolshed: InstalledBundleCache.load: package Pygments 2.4.2
595Toolshed: InstalledBundleCache._make_bundle_info: no ChimeraX bundle in Pygments 2.4.2
596Toolshed: InstalledBundleCache.load: package pydicom 1.3.0
597Toolshed: InstalledBundleCache._make_bundle_info: no ChimeraX bundle in pydicom 1.3.0
598Toolshed: InstalledBundleCache.load: package pycollada 0.6
599Toolshed: InstalledBundleCache._make_bundle_info: no classifiers in pycollada 0.6
600Toolshed: InstalledBundleCache.load: package psutil 5.6.3
601Toolshed: InstalledBundleCache._make_bundle_info: no ChimeraX bundle in psutil 5.6.3
602Toolshed: InstalledBundleCache.load: package prompt-toolkit 2.0.10
603Toolshed: InstalledBundleCache._make_bundle_info: no ChimeraX bundle in prompt-toolkit 2.0.10
604Toolshed: InstalledBundleCache.load: package pkginfo 1.5.0.1
605Toolshed: InstalledBundleCache._make_bundle_info: no ChimeraX bundle in pkginfo 1.5.0.1
606Toolshed: InstalledBundleCache.load: package pip 19.2.3
607Toolshed: InstalledBundleCache._make_bundle_info: no ChimeraX bundle in pip 19.2.3
608Toolshed: InstalledBundleCache.load: package Pillow 6.1.0
609Toolshed: InstalledBundleCache._make_bundle_info: no ChimeraX bundle in Pillow 6.1.0
610Toolshed: InstalledBundleCache.load: package pickleshare 0.7.5
611Toolshed: InstalledBundleCache._make_bundle_info: no ChimeraX bundle in pickleshare 0.7.5
612Toolshed: InstalledBundleCache.load: package parso 0.5.1
613Toolshed: InstalledBundleCache._make_bundle_info: no ChimeraX bundle in parso 0.5.1
614Toolshed: InstalledBundleCache.load: package packaging 19.2
615Toolshed: InstalledBundleCache._make_bundle_info: no ChimeraX bundle in packaging 19.2
616Toolshed: InstalledBundleCache.load: package openvr 1.7.1501
617Toolshed: InstalledBundleCache._make_bundle_info: no ChimeraX bundle in openvr 1.7.1501
618Toolshed: InstalledBundleCache.load: package numpydoc 0.9.1
619Toolshed: InstalledBundleCache._make_bundle_info: no ChimeraX bundle in numpydoc 0.9.1
620Toolshed: InstalledBundleCache.load: package numpy 1.17.1+mkl
621Toolshed: InstalledBundleCache._make_bundle_info: no ChimeraX bundle in numpy 1.17.1+mkl
622Toolshed: InstalledBundleCache.load: package numexpr 2.7.0
623Toolshed: InstalledBundleCache._make_bundle_info: no classifiers in numexpr 2.7.0
624Toolshed: InstalledBundleCache.load: package networkx 2.3
625Toolshed: InstalledBundleCache._make_bundle_info: no ChimeraX bundle in networkx 2.3
626Toolshed: InstalledBundleCache.load: package msgpack 0.6.1
627Toolshed: InstalledBundleCache._make_bundle_info: no ChimeraX bundle in msgpack 0.6.1
628Toolshed: InstalledBundleCache.load: package mock 3.0.5
629Toolshed: InstalledBundleCache._make_bundle_info: no ChimeraX bundle in mock 3.0.5
630Toolshed: InstalledBundleCache.load: package matplotlib 3.1.1
631Toolshed: InstalledBundleCache._make_bundle_info: no ChimeraX bundle in matplotlib 3.1.1
632Toolshed: InstalledBundleCache.load: package MarkupSafe 1.1.1
633Toolshed: InstalledBundleCache._make_bundle_info: no ChimeraX bundle in MarkupSafe 1.1.1
634Toolshed: InstalledBundleCache.load: package lxml 4.4.1
635Toolshed: InstalledBundleCache._make_bundle_info: no ChimeraX bundle in lxml 4.4.1
636Toolshed: InstalledBundleCache.load: package line-profiler 2.1.2
637Toolshed: InstalledBundleCache._make_bundle_info: no ChimeraX bundle in line-profiler 2.1.2
638Toolshed: InstalledBundleCache.load: package kiwisolver 1.1.0
639Toolshed: InstalledBundleCache._make_bundle_info: no ChimeraX bundle in kiwisolver 1.1.0
640Toolshed: InstalledBundleCache.load: package jupyter-core 4.6.1
641Toolshed: InstalledBundleCache._make_bundle_info: no ChimeraX bundle in jupyter-core 4.6.1
642Toolshed: InstalledBundleCache.load: package jupyter-client 5.3.4
643Toolshed: InstalledBundleCache._make_bundle_info: no ChimeraX bundle in jupyter-client 5.3.4
644Toolshed: InstalledBundleCache.load: package Jinja2 2.10.1
645Toolshed: InstalledBundleCache._make_bundle_info: no ChimeraX bundle in Jinja2 2.10.1
646Toolshed: InstalledBundleCache.load: package jedi 0.15.1
647Toolshed: InstalledBundleCache._make_bundle_info: no ChimeraX bundle in jedi 0.15.1
648Toolshed: InstalledBundleCache.load: package ipython 7.8.0
649Toolshed: InstalledBundleCache._make_bundle_info: no ChimeraX bundle in ipython 7.8.0
650Toolshed: InstalledBundleCache.load: package ipython-genutils 0.2.0
651Toolshed: InstalledBundleCache._make_bundle_info: no ChimeraX bundle in ipython-genutils 0.2.0
652Toolshed: InstalledBundleCache.load: package ipykernel 5.1.2
653Toolshed: InstalledBundleCache._make_bundle_info: no ChimeraX bundle in ipykernel 5.1.2
654Toolshed: InstalledBundleCache.load: package imagesize 1.1.0
655Toolshed: InstalledBundleCache._make_bundle_info: no ChimeraX bundle in imagesize 1.1.0
656Toolshed: InstalledBundleCache.load: package imagecodecs 2019.11.18
657Toolshed: InstalledBundleCache._make_bundle_info: no ChimeraX bundle in imagecodecs 2019.11.18
658Toolshed: InstalledBundleCache.load: package imagecodecs-lite 2019.4.20
659Toolshed: InstalledBundleCache._make_bundle_info: no ChimeraX bundle in imagecodecs-lite 2019.4.20
660Toolshed: InstalledBundleCache.load: package ihm 0.13
661Toolshed: InstalledBundleCache._make_bundle_info: no ChimeraX bundle in ihm 0.13
662Toolshed: InstalledBundleCache.load: package idna 2.8
663Toolshed: InstalledBundleCache._make_bundle_info: no ChimeraX bundle in idna 2.8
664Toolshed: InstalledBundleCache.load: package html2text 2019.8.11
665Toolshed: InstalledBundleCache._make_bundle_info: no ChimeraX bundle in html2text 2019.8.11
666Toolshed: InstalledBundleCache.load: package grako 3.16.5
667Toolshed: InstalledBundleCache._make_bundle_info: no ChimeraX bundle in grako 3.16.5
668Toolshed: InstalledBundleCache.load: package funcparserlib 0.3.6
669Toolshed: InstalledBundleCache._make_bundle_info: no classifiers in funcparserlib 0.3.6
670Toolshed: InstalledBundleCache.load: package filelock 3.0.12
671Toolshed: InstalledBundleCache._make_bundle_info: no ChimeraX bundle in filelock 3.0.12
672Toolshed: InstalledBundleCache.load: package docutils 0.15.2
673Toolshed: InstalledBundleCache._make_bundle_info: no ChimeraX bundle in docutils 0.15.2
674Toolshed: InstalledBundleCache.load: package distlib 0.2.9.post0
675Toolshed: InstalledBundleCache._make_bundle_info: no ChimeraX bundle in distlib 0.2.9.post0
676Toolshed: InstalledBundleCache.load: package decorator 4.4.1
677Toolshed: InstalledBundleCache._make_bundle_info: no ChimeraX bundle in decorator 4.4.1
678Toolshed: InstalledBundleCache.load: package Cython 0.29.13
679Toolshed: InstalledBundleCache._make_bundle_info: no ChimeraX bundle in Cython 0.29.13
680Toolshed: InstalledBundleCache.load: package cycler 0.10.0
681Toolshed: InstalledBundleCache._make_bundle_info: no ChimeraX bundle in cycler 0.10.0
682Toolshed: InstalledBundleCache.load: package comtypes 1.1.7
683Toolshed: InstalledBundleCache._make_bundle_info: no ChimeraX bundle in comtypes 1.1.7
684Toolshed: InstalledBundleCache.load: package colorama 0.4.1
685Toolshed: InstalledBundleCache._make_bundle_info: no ChimeraX bundle in colorama 0.4.1
686Toolshed: InstalledBundleCache.load: package ChimeraX-Zone 1.0
687Toolshed: InstalledBundleCache.load: bundle ChimeraX-Zone (installed) [version: 1.0] [api package: chimerax.zone] [category: Volume Data] [command: zone [categories: Volume data] [synopsis: Show atoms and map in a small region]]
688Toolshed: InstalledBundleCache.load: package ChimeraX-WebServices 1.0
689Toolshed: InstalledBundleCache.load: bundle ChimeraX-WebServices (installed) [version: 1.0] [api package: chimerax.webservices] [category: General]
690Toolshed: InstalledBundleCache.load: package ChimeraX-WavefrontOBJ 1.0
691Toolshed: InstalledBundleCache.load: bundle ChimeraX-WavefrontOBJ (installed) [version: 1.0] [api package: chimerax.wavefront_obj] [category: Generic 3D objects] [data format: Wavefront OBJ [category: Generic 3D objects] [suffixes: .obj] [url: https://en.wikipedia.org/wiki/Wavefront_.obj_file] [encoding: utf-8] [synopsis: Surface format used in 3D modeling]]
692Toolshed: InstalledBundleCache.load: package ChimeraX-VTK 1.0
693Toolshed: InstalledBundleCache.load: bundle ChimeraX-VTK (installed) [version: 1.0] [api package: chimerax.vtk] [category: Generic 3D objects] [data format: VTK PolyData [category: Generic 3D objects] [suffixes: .vtk] [url: http://www.vtk.org/wp-content/uploads/2015/04/file-formats.pdf] [synopsis: VTK]]
694Toolshed: InstalledBundleCache.load: package ChimeraX-VolumeMenu 1.0
695Toolshed: InstalledBundleCache.load: bundle ChimeraX-VolumeMenu (installed) [version: 1.0] [api package: chimerax.volume_menu] [category: Volume data] [tool: Show Volume Menu [categories: Volume Data] [synopsis: Add a top level volume menu]]
696Toolshed: InstalledBundleCache.load: package ChimeraX-Vive 1.0
697Toolshed: InstalledBundleCache.load: bundle ChimeraX-Vive (installed) [version: 1.0] [api package: chimerax.vive] [category: General] [command: vr [categories: General] [synopsis: Render to virtual reality headsets]] [command: device vr [categories: General] [synopsis: Render to virtual reality headsets]]
698Toolshed: InstalledBundleCache.load: package ChimeraX-ViewDockX 0.1
699Toolshed: InstalledBundleCache.load: bundle ChimeraX-ViewDockX (installed) [version: 0.1] [api package: chimerax.viewdockx] [category: General] [tool: ViewDockX [categories: General] [synopsis: display docking results]] [command: viewdockx [categories: General] [synopsis: Display docking results]] [command: viewdockx down [categories: General] [synopsis: Simulate down-arrow key in ViewDockX]] [command: viewdockx up [categories: General] [synopsis: Simulate up-arrow key in ViewDockX]] [data format: mol2 [category: Molecular structure] [suffixes: .mol2] [encoding: utf-8] [synopsis: mol2 format]] [data format: pdbqt [category: Molecular structure] [suffixes: .pdbqt] [encoding: utf-8] [synopsis: pdbqt format]]
700Toolshed: InstalledBundleCache.load: package ChimeraX-uniprot 1.0
701Toolshed: InstalledBundleCache.load: bundle ChimeraX-uniprot (installed) [version: 1.0] [api package: chimerax.seqlign.uniprot] [category: Sequence] [data format: UniProt [category: Sequence] [url: https://www.uniprot.org] [synopsis: UniProt sequence data]]
702Toolshed: InstalledBundleCache.load: package ChimeraX-UI 1.0
703Toolshed: InstalledBundleCache.load: bundle ChimeraX-UI (installed) [version: 1.0] [api package: chimerax.ui] [category: User Interface] [command: ui [categories: User interface] [synopsis: control user interface behavior]]
704Toolshed: InstalledBundleCache.load: package ChimeraX-Tug 1.0
705Toolshed: InstalledBundleCache.load: bundle ChimeraX-Tug (installed) [version: 1.0] [api package: chimerax.tug] [category: Molecular structure]
706Toolshed: InstalledBundleCache.load: package ChimeraX-Toolbar 0.1
707Toolshed: InstalledBundleCache.load: bundle ChimeraX-Toolbar (installed) [version: 0.1] [api package: chimerax.toolbar] [category: General] [tool: Toolbar [categories: General] [synopsis: a Windows ribbon-style toolbar]]
708Toolshed: InstalledBundleCache.load: package ChimeraX-Texture 1.0
709Toolshed: InstalledBundleCache.load: bundle ChimeraX-Texture (installed) [version: 1.0] [api package: chimerax.texture] [category: Generic 3D objects] [command: texture [categories: General] [synopsis: Color surfaces using images]]
710Toolshed: InstalledBundleCache.load: package ChimeraX-Test 1.0
711Toolshed: InstalledBundleCache.load: bundle ChimeraX-Test (installed) [version: 1.0] [api package: chimerax.test] [category: General] [command: debug test [categories: General] [synopsis: Run through test sequence of commands to check for errors]] [command: debug exectest [categories: General] [synopsis: Test running executable from bundle]] [command: debug expectfail [categories: General] [synopsis: Expect command to fail]]
712Toolshed: InstalledBundleCache.load: package ChimeraX-TapeMeasure 1.0
713Toolshed: InstalledBundleCache.load: bundle ChimeraX-TapeMeasure (installed) [version: 1.0] [api package: chimerax.atomic.tape_measure] [category: General]
714Toolshed: InstalledBundleCache.load: package ChimeraX-SwapRes 1.0
715Toolshed: InstalledBundleCache.load: bundle ChimeraX-SwapRes (installed) [version: 1.0] [api package: chimerax.atomic.rotamers.command] [category: Structure Editing] [tool: Rotamers [categories: General] [synopsis: swap residue side chain]] [command: swapaa [categories: Structure Editing] [synopsis: swap residue side chain]]
716Toolshed: InstalledBundleCache.load: package ChimeraX-SwapAA 1.0
717Toolshed: InstalledBundleCache.load: bundle ChimeraX-SwapAA (installed) [version: 1.0] [api package: chimerax.atomic.swapaa] [category: Structure Editing] [command: swapaa mousemode [categories: Replace an amino acid] [synopsis: Replaces amino acid with a specified standard amino acid]]
718Toolshed: InstalledBundleCache.load: package ChimeraX-Surface 1.0
719Toolshed: InstalledBundleCache.load: bundle ChimeraX-Surface (installed) [version: 1.0] [api package: chimerax.surface] [category: Generic 3D objects] [command: color electrostatic [categories: Surfaces] [synopsis: color surface by electrostatic potential map]] [command: color sample [categories: Surfaces] [synopsis: color surface by map value]] [command: color gradient [categories: Surfaces] [synopsis: color surface by map gradient norm]] [command: color radial [categories: Surfaces] [synopsis: color surface by distance from a point]] [command: color cylindrical [categories: Surfaces] [synopsis: color surface by distance from an axis]] [command: color height [categories: Surfaces] [synopsis: color surface by distance from a plane]] [command: surface [categories: Surfaces] [synopsis: create/modify surfaces]] [command: ~surface [categories: Surfaces] [synopsis: delete surface]] [command: volume splitbyzone [categories: Volume Data] [synopsis: split volume by color zone]] [command: sop [categories: Surfaces] [synopsis: surface operation]] [command: measure sasa [categories: Surfaces] [synopsis: measure solvent-accessible surface area]] [command: measure volume [categories: Surfaces] [synopsis: measure enclosed surface volume]] [command: measure area [categories: Surfaces] [synopsis: measure surface area]] [data format: Collada [category: Generic 3D objects] [suffixes: .dae] [url: https://www.khronos.org/collada] [synopsis: 3D scene format]]
720Toolshed: InstalledBundleCache.load: package ChimeraX-Struts 1.0
721Toolshed: InstalledBundleCache.load: bundle ChimeraX-Struts (installed) [version: 1.0] [api package: chimerax.struts] [category: Molecular structure] [command: struts [categories: Molecular structure] [synopsis: provide struts for 3D printing]]
722Toolshed: InstalledBundleCache.load: package ChimeraX-Storm 1.0
723Toolshed: InstalledBundleCache.load: bundle ChimeraX-Storm (installed) [version: 1.0] [api package: chimerax.storm] [category: Generic 3D object] [data format: STORM [category: Generic 3D objects] [suffixes: .storm] [synopsis: Point list for STORM microscopy]]
724Toolshed: InstalledBundleCache.load: package ChimeraX-STL 1.0
725Toolshed: InstalledBundleCache.load: bundle ChimeraX-STL (installed) [version: 1.0] [api package: chimerax.stl] [category: Generic 3D objects] [data format: StereoLithography [category: Generic 3D objects] [suffixes: .stl] [url: http://en.wikipedia.org/wiki/STL_(file_format)#Binary_STL] [synopsis: Simple triangle format used by 3D printers]]
726Toolshed: InstalledBundleCache.load: package ChimeraX-Std-Commands 1.0
727Toolshed: InstalledBundleCache.load: bundle ChimeraX-Std-Commands (installed) [version: 1.0] [api package: chimerax.std_commands] [category: Structure Analysis] [command: alias [categories: General Controls] [synopsis: create shorthand version of command]] [command: alias list [categories: General Controls] [synopsis: list command aliases]] [command: alias delete [categories: General Controls] [synopsis: remove command alias]] [command: ~alias [categories: General Controls] [synopsis: remove command alias]] [command: align [categories: Structure Comparison] [synopsis: superimpose specific parts of structures]] [command: camera [categories: Viewing Controls] [synopsis: change "camera" parametrs of main viewing window]] [command: cartoon [categories: Depiction] [synopsis: show stylized representation of structure]] [command: ~cartoon [categories: Depiction] [synopsis: stop show stylized representation of structure]] [command: cd [categories: General Controls] [synopsis: change ChimeraX's current working directory]] [command: clip [categories: Viewing Controls] [synopsis: control clipping of models]] [command: ~clip [categories: Viewing Controls] [synopsis: stop clipping of models]] [command: close [categories: General Controls] [synopsis: close models]] [command: cofr [categories: General Controls] [synopsis: set center of rotation]] [command: ~cofr [categories: General Controls] [synopsis: revert to default center of rotation]] [command: color [categories: Depiction] [synopsis: change model colors]] [command: colour [categories: Depiction] [synopsis: change model colors]] [command: color delete [categories: General Controls] [synopsis: delete custom color names]] [command: color list [categories: General Controls] [synopsis: list custom color names]] [command: color name [categories: General Controls] [synopsis: define custom color names]] [command: color show [categories: General Controls] [synopsis: show definition of custom color names]] [command: colordef [categories: General Controls] [synopsis: define custom color names]] [command: ~colordef [categories: General Controls] [synopsis: remove custom color names]] [command: colourdef [categories: General Controls] [synopsis: define custom color names]] [command: ~colourdef [categories: General Controls] [synopsis: remove custom color names]] [command: coordset [categories: General Controls] [synopsis: show specific coordinate set (a.k.a. frame or conformer)]] [command: crossfade [categories: Movie Making] [synopsis: fade from one view to another]] [command: delete [categories: Structure Editing] [synopsis: delete parts of a structure]] [command: dssp [categories: Structure Editing] [synopsis: compute/assign secondary structure]] [command: exit [categories: General Controls] [synopsis: quit ChimeraX]] [command: quit [categories: General Controls] [synopsis: quit ChimeraX]] [command: graphics [categories: General Controls] [synopsis: control 3D graphics parameters]] [command: hide [categories: Viewing Controls] [synopsis: stop displaying (parts of) a model]] [command: ~show [categories: Viewing Controls] [synopsis: stop displaying (parts of) a model]] [command: ~display [categories: Viewing Controls] [synopsis: stop displaying (parts of) a model]] [command: lighting [categories: Viewing Controls] [synopsis: change lighting]] [command: lighting model [categories: Viewing Controls] [synopsis: change per-model lighting]] [command: material [categories: Depiction] [synopsis: change visual surface properties of 3D objects]] [command: measure buriedarea [categories: Surface/Binding Analysis] [synopsis: measure surface area buried by contacting structures]] [command: measure center [categories: Volume] [synopsis: measure center of mass of maps or atoms]] [command: measure convexity [categories: Surface/Binding Analysis] [synopsis: color surface based on local convexity]] [command: measure inertia [categories: General Controls] [synopsis: measure moments of inertia]] [command: measure length [categories: Volume] [synopsis: measure path length of connected markers]] [command: measure symmetry [categories: Volume] [synopsis: compute map symmetry]] [command: move [categories: General Controls] [synopsis: move (parts of) a model relative to others]] [command: palette [categories: General Controls] [synopsis: list available color palettes]] [command: pdbimages [categories: Input/Output] [synopsis: batch processing of mmCIF files into images]] [command: perframe [categories: General Controls] [synopsis: execute commands every frame]] [command: ~perframe [categories: General Controls] [synopsis: stop execution of commands every frame]] [command: pwd [categories: Utilities] [synopsis: report current working directory]] [command: rainbow [categories: Depiction] [synopsis: "rainbow" color (parts of) structures]] [command: rename [categories: General Controls] [synopsis: change name or ID of model]] [command: roll [categories: General Controls] [synopsis: continuously turn model(s) about an axis]] [command: runscript [categories: General Controls] [synopsis: run a Python script with arguments]] [command: select [categories: General Controls] [synopsis: select models or parts thereof]] [command: ~select [categories: General Controls] [synopsis: unselect models or parts thereof]] [command: set [categories: General Controls] [synopsis: set various global parameters]] [command: ~set [categories: General Controls] [synopsis: revert various global parameters to their default value]] [command: setattr [categories: General Controls] [synopsis: set Python attribute values for structure elements]] [command: show [categories: Viewing Controls] [synopsis: display (parts of) a model]] [command: display [categories: Viewing Controls] [synopsis: display (parts of) a model]] [command: size [categories: Depiction] [synopsis: change display size of structural elements]] [command: split [categories: General Controls] [synopsis: split a model into multiple models]] [command: stop [categories: General Controls] [synopsis: stop an ongoing motion]] [command: style [categories: Depiction] [synopsis: change style of depiction for strcutural elements]] [command: sym [categories: Higher-Order Structure] [synopsis: generate symmetry mates]] [command: tile [categories: General Controls] [synopsis: tile models onto grid]] [command: time [categories: Utilities] [synopsis: time execution and redisplay of commands]] [command: transparency [categories: Depiction] [synopsis: change transparency of (parts of) models]] [command: turn [categories: General Controls] [synopsis: rotate a model about an axis]] [command: undo [categories: General Controls] [synopsis: undo a command]] [command: redo [categories: General Controls] [synopsis: redo an undone command]] [command: usage [categories: Utilities] [synopsis: show the required syntax for a command]] [command: version [categories: Utilities] [synopsis: report ChimeraX version number]] [command: view [categories: Viewing Controls] [synopsis: change/save/restore 3D view]] [command: wait [categories: Movie Making] [synopsis: wait a given amount of frames before executing the next command]] [command: windowsize [categories: General Controls] [synopsis: set the size of the 3D window]] [command: select zone [categories: General Controls] [synopsis: select (parts of) models within a 3D zone]] [command: zoom [categories: Viewing Controls] [synopsis: zoom in/out]]
728Toolshed: InstalledBundleCache.load: package ChimeraX-SpaceNavigator 1.0
729Toolshed: InstalledBundleCache.load: bundle ChimeraX-SpaceNavigator (installed) [version: 1.0] [api package: chimerax.spacenavigator] [category: General] [command: device snav [categories: General] [synopsis: Control SpaceNavigator device]]
730Toolshed: InstalledBundleCache.load: package ChimeraX-SmoothLines 1.0
731Toolshed: InstalledBundleCache.load: bundle ChimeraX-SmoothLines (installed) [version: 1.0] [api package: chimerax.smooth_lines] [category: General] [command: smoothlines [categories: General] [synopsis: Smooth networks of lines]]
732Toolshed: InstalledBundleCache.load: package ChimeraX-SideView 1.0
733Toolshed: InstalledBundleCache.load: bundle ChimeraX-SideView (installed) [version: 1.0] [api package: chimerax.sideview] [category: General] [tool: Side View [categories: General] [synopsis: Show side view interface]]
734Toolshed: InstalledBundleCache.load: package ChimeraX-ShowAttr 1.0
735Toolshed: InstalledBundleCache.load: bundle ChimeraX-ShowAttr (installed) [version: 1.0] [api package: chimerax.show_attr] [category: Depiction]
736Toolshed: InstalledBundleCache.load: package ChimeraX-Shortcuts 1.0
737Toolshed: InstalledBundleCache.load: bundle ChimeraX-Shortcuts (installed) [version: 1.0] [api package: chimerax.shortcuts] [category: Toolbar] [command: ks [categories: Toolbar] [synopsis: keyboard shortcuts]]
738Toolshed: InstalledBundleCache.load: package ChimeraX-Shell 1.0
739Toolshed: InstalledBundleCache.load: bundle ChimeraX-Shell (installed) [version: 1.0] [api package: chimerax.shell] [category: General] [tool: Shell [categories: General] [synopsis: Python shell]]
740Toolshed: InstalledBundleCache.load: package ChimeraX-SeqView 1.0
741Toolshed: InstalledBundleCache.load: bundle ChimeraX-SeqView (installed) [version: 1.0] [api package: chimerax.seq-view] [category: Sequence]
742Toolshed: InstalledBundleCache.load: package ChimeraX-Segment 1.0
743Toolshed: InstalledBundleCache.load: bundle ChimeraX-Segment (installed) [version: 1.0] [api package: chimerax.segment] [category: Volume data]
744Toolshed: InstalledBundleCache.load: package ChimeraX-Segger 1.0
745Toolshed: InstalledBundleCache.load: bundle ChimeraX-Segger (installed) [version: 1.0] [api package: chimerax.segger] [category: Volume data] [tool: Segment Map [categories: Volume Data] [synopsis: Segment density maps using Segger algorithms]] [tool: Fit to Segments [categories: Volume Data] [synopsis: Fit atomic models in segmented maps]]
746Toolshed: InstalledBundleCache.load: package ChimeraX-Scheme-Mgr 1.0
747Toolshed: InstalledBundleCache.load: bundle ChimeraX-Scheme-Mgr (installed) [version: 1.0] [api package: chimerax.scheme_mgr] [category: Utilities]
748Toolshed: InstalledBundleCache.load: package ChimeraX-RotamerLibs-Richardson 1.0
749Toolshed: InstalledBundleCache.load: bundle ChimeraX-RotamerLibs-Richardson (installed) [version: 1.0] [api package: chimerax.atomic.rotamers.libs.richardson] [category: Structure Editing]
750Toolshed: InstalledBundleCache.load: package ChimeraX-RotamerLibs-Dynameomics 1.0
751Toolshed: InstalledBundleCache.load: bundle ChimeraX-RotamerLibs-Dynameomics (installed) [version: 1.0] [api package: chimerax.atomic.rotamers.libs.dynameomics] [category: Structure Editing]
752Toolshed: InstalledBundleCache.load: package ChimeraX-RotamerLibs-Dunbrack 1.0
753Toolshed: InstalledBundleCache.load: bundle ChimeraX-RotamerLibs-Dunbrack (installed) [version: 1.0] [api package: chimerax.atomic.rotamers.libs.dunbrack] [category: Structure Editing]
754Toolshed: InstalledBundleCache.load: package ChimeraX-Rotamer-Lib-Mgr 1.0
755Toolshed: InstalledBundleCache.load: bundle ChimeraX-Rotamer-Lib-Mgr (installed) [version: 1.0] [api package: chimerax.atomic.rotamers] [category: Structure Editing]
756Toolshed: InstalledBundleCache.load: package ChimeraX-RestServer 0.1
757Toolshed: InstalledBundleCache.load: bundle ChimeraX-RestServer (installed) [version: 0.1] [api package: chimerax.rest_server] [category: General] [command: remotecontrol rest [categories: General] [synopsis: Control REST server]]
758Toolshed: InstalledBundleCache.load: package ChimeraX-ResidueFit 1.0
759Toolshed: InstalledBundleCache.load: bundle ChimeraX-ResidueFit (installed) [version: 1.0] [api package: chimerax.residue_fit] [category: General] [command: resfit [categories: General] [synopsis: Display slider to show fit of each residue in density map]]
760Toolshed: InstalledBundleCache.load: package ChimeraX-RemoteControl 1.0
761Toolshed: InstalledBundleCache.load: bundle ChimeraX-RemoteControl (installed) [version: 1.0] [api package: chimerax.remote_control] [category: General] [tool: Remote Control [categories: General] [synopsis: Send commands to ChimeraX from other apps]] [command: remotecontrol xmlrpc [categories: General] [synopsis: synopsis]]
762Toolshed: InstalledBundleCache.load: package ChimeraX-Registration 0.1
763Toolshed: InstalledBundleCache.load: bundle ChimeraX-Registration (installed) [version: 0.1] [api package: chimerax.registration] [category: Utilities] [tool: Registration [categories: Utilities] [synopsis: Register ChimeraX with RBVI]] [command: registration status [categories: Utilities] [synopsis: Report registration status]]
764Toolshed: InstalledBundleCache.load: package ChimeraX-RealSense 1.0
765Toolshed: InstalledBundleCache.load: bundle ChimeraX-RealSense (installed) [version: 1.0] [api package: chimerax.realsense] [category: General] [command: device realsense [categories: General] [synopsis: Show Intel RealSense camera video]]
766Toolshed: InstalledBundleCache.load: package ChimeraX-Read-Pbonds 1.0
767Toolshed: InstalledBundleCache.load: bundle ChimeraX-Read-Pbonds (installed) [version: 1.0] [api package: chimerax.read_pbonds] [category: Generic 3D objects] [data format: Pseudobonds [category: Generic 3D objects] [suffixes: .pb] [encoding: utf-8] [synopsis: Interatomic pseudobonds]]
768Toolshed: InstalledBundleCache.load: package ChimeraX-Preset-Mgr 1.0
769Toolshed: InstalledBundleCache.load: bundle ChimeraX-Preset-Mgr (installed) [version: 1.0] [api package: chimerax.preset_mgr] [category: Depiction] [command: preset [categories: Depiction] [synopsis: apply "preset" depiction to models]]
770Toolshed: InstalledBundleCache.load: package ChimeraX-PickBlobs 1.0
771Toolshed: InstalledBundleCache.load: bundle ChimeraX-PickBlobs (installed) [version: 1.0] [api package: chimerax.pick_blobs] [category: Volume data] [tool: Measure and Color Blobs [categories: Volume Data] [synopsis: Measure and color connected parts of surfaces]] [command: measure blob [categories: Measure and Color Blobs] [synopsis: Measure and color connected parts of surfaces]]
772Toolshed: InstalledBundleCache.load: package ChimeraX-PDB 1.0
773Toolshed: InstalledBundleCache.load: bundle ChimeraX-PDB (installed) [version: 1.0] [api package: chimerax.atomic.pdb] [category: Molecular structure] [data format: PDB [category: Molecular structure] [suffixes: .pdb, .pdb1, .ent, .pqr] [url: http://www.wwpdb.org/documentation/file-format] [synopsis: Protein Databank Format (PDB)]]
774Toolshed: InstalledBundleCache.load: package ChimeraX-Nucleotides 0.1
775Toolshed: InstalledBundleCache.load: bundle ChimeraX-Nucleotides (installed) [version: 0.1] [api package: chimerax.atomic.nucleotides] [category: General] [command: nucleotides [categories: General] [synopsis: Manipulate nucleotide representations]] [command: ~nucleotides [categories: General] [synopsis: Undo nucleotide representations]]
776Toolshed: InstalledBundleCache.load: package ChimeraX-Movie 1.0
777Toolshed: InstalledBundleCache.load: bundle ChimeraX-Movie (installed) [version: 1.0] [api package: chimerax.movie] [category: General] [command: movie [categories: General] [synopsis: record movies]]
778Toolshed: InstalledBundleCache.load: package ChimeraX-MouseModes 1.0
779Toolshed: InstalledBundleCache.load: bundle ChimeraX-MouseModes (installed) [version: 1.0] [api package: chimerax.mouse_modes] [category: Toolbar] [command: ui mousemode [categories: User interface] [synopsis: set/list mouse modes]] [command: mousemode [categories: User interface] [synopsis: set/list mouse modes]]
780Toolshed: InstalledBundleCache.load: package ChimeraX-Morph 1.0
781Toolshed: InstalledBundleCache.load: bundle ChimeraX-Morph (installed) [version: 1.0] [api package: chimerax.morph] [category: Morph Structures] [command: morph [categories: Molecular structure] [synopsis: morph atomic structures]]
782Toolshed: InstalledBundleCache.load: package ChimeraX-Mol2 1.0
783Toolshed: InstalledBundleCache.load: bundle ChimeraX-Mol2 (installed) [version: 1.0] [api package: chimerax.atomic.mol2] [category: I/O] [data format: Sybyl Mol2 [category: Molecular structure] [suffixes: .mol2] [encoding: utf-8] [synopsis: Sybyl Mol2 format]]
784Toolshed: InstalledBundleCache.load: package ChimeraX-ModelSeries 1.0
785Toolshed: InstalledBundleCache.load: bundle ChimeraX-ModelSeries (installed) [version: 1.0] [api package: chimerax.model_series] [category: General] [command: mseries [categories: General] [synopsis: Display sequence of models one by one]]
786Toolshed: InstalledBundleCache.load: package ChimeraX-ModelPanel 1.0
787Toolshed: InstalledBundleCache.load: bundle ChimeraX-ModelPanel (installed) [version: 1.0] [api package: chimerax.model_panel] [category: General] [tool: Model Panel [categories: General] [synopsis: model panel]]
788Toolshed: InstalledBundleCache.load: package ChimeraX-Modeller 1.0
789Toolshed: InstalledBundleCache.load: bundle ChimeraX-Modeller (installed) [version: 1.0] [api package: chimerax.modeller] [category: Sequence] [tool: Modeller Comparative [categories: Sequence] [synopsis: Generate comparative models]] [command: modeller comparative [categories: Sequence] [synopsis: Generate comparative model]] [command: modeller scores [categories: Sequence] [synopsis: Fetch Modeller scores for a model]]
790Toolshed: InstalledBundleCache.load: package ChimeraX-MMTF 1.0
791Toolshed: InstalledBundleCache.load: bundle ChimeraX-MMTF (installed) [version: 1.0] [api package: chimerax.atomic.mmtf] [category: Molecular structure] [data format: MMTF [category: Molecular structure] [suffixes: .mmtf] [url: http://mmtf.rcsb.org/] [synopsis: Macromolecular Transmission Format (MMTF)]]
792Toolshed: InstalledBundleCache.load: package ChimeraX-mmCIF 1.1
793Toolshed: InstalledBundleCache.load: bundle ChimeraX-mmCIF (installed) [version: 1.1] [api package: chimerax.atomic.mmcif] [category: Molecular structure] [data format: mmCIF [category: Molecular structure] [suffixes: .cif, .mmcif] [mime_types: chemical/x-mmcif] [url: http://mmcif.wwpdb.org/] [synopsis: Macromolecular CIF]]
794Toolshed: InstalledBundleCache.load: package ChimeraX-MLP 1.0
795Toolshed: InstalledBundleCache.load: bundle ChimeraX-MLP (installed) [version: 1.0] [api package: chimerax.mlp] [category: Molecular structure] [command: mlp [categories: Molecular structure] [synopsis: Molecular lipophilicity calculation]]
796Toolshed: InstalledBundleCache.load: package ChimeraX-Meeting 1.0
797Toolshed: InstalledBundleCache.load: bundle ChimeraX-Meeting (installed) [version: 1.0] [api package: chimerax.meeting] [category: General] [command: meeting [categories: General] [synopsis: Shared interactive sessions]]
798Toolshed: InstalledBundleCache.load: package ChimeraX-MD-crds 1.0
799Toolshed: InstalledBundleCache.load: bundle ChimeraX-MD-crds (installed) [version: 1.0] [api package: chimerax.atomic.md_crds] [category: Molecular Dynamics] [data format: Gromacs full-precision coordinates [category: Molecular trajectory] [suffixes: .trr] [url: http://manual.gromacs.org/online/trr.html] [encoding: utf-8] [synopsis: Gromacs trr format]] [data format: Gromacs compressed coordinates [category: Molecular trajectory] [suffixes: .xtc] [url: http://manual.gromacs.org/online/xtc.html] [encoding: utf-8] [synopsis: Gromacs xtc format]] [data format: DCD coordinates [category: Molecular trajectory] [suffixes: .dcd] [encoding: utf-8] [synopsis: DCD trajectory format]]
800Toolshed: InstalledBundleCache.load: package ChimeraX-MatchMaker 1.0
801Toolshed: InstalledBundleCache.load: bundle ChimeraX-MatchMaker (installed) [version: 1.0] [api package: chimerax.match_maker] [category: Sequence] [command: matchmaker [categories: Structure Comparison] [synopsis: Superimpose structures]] [command: mmaker [categories: Structure Comparison] [synopsis: alias of matchmaker]]
802Toolshed: InstalledBundleCache.load: package ChimeraX-Mask 1.0
803Toolshed: InstalledBundleCache.load: bundle ChimeraX-Mask (installed) [version: 1.0] [api package: chimerax.mask] [category: Volume Data] [command: volume mask [categories: Volume data] [synopsis: Mask a map to a surface]] [command: volume onesmask [categories: Volume data] [synopsis: Create a onesmask inside a surface]]
804Toolshed: InstalledBundleCache.load: package ChimeraX-Markers 1.0
805Toolshed: InstalledBundleCache.load: bundle ChimeraX-Markers (installed) [version: 1.0] [api package: chimerax.markers] [category: Volume Data] [tool: Marker Placement [categories: Volume Data] [synopsis: Place markers on density maps]] [command: marker [categories: General] [synopsis: Place markers]] [data format: Marker model [category: Generic 3D objects] [suffixes: .cmm] [url: http://rbvi.ucsf.edu/chimerax/docs/user/markers.html#markerfiles] [synopsis: Markers and links]]
806Toolshed: InstalledBundleCache.load: package ChimeraX-MapSeries 1.0
807Toolshed: InstalledBundleCache.load: bundle ChimeraX-MapSeries (installed) [version: 1.0] [api package: chimerax.map.series] [category: Volume Data] [command: vseries [categories: Volume data] [synopsis: volume series]] [command: measure motion [categories: Volume data] [synopsis: volume series cactus prickles]]
808Toolshed: InstalledBundleCache.load: package ChimeraX-MapFit 1.0
809Toolshed: InstalledBundleCache.load: bundle ChimeraX-MapFit (installed) [version: 1.0] [api package: chimerax.map.fit] [category: Volume Data] [tool: Fit in Map [categories: Volume Data] [synopsis: Fit molecules in maps]] [command: fitmap [categories: Volume data] [synopsis: fit molecules in maps]]
810Toolshed: InstalledBundleCache.load: package ChimeraX-MapFilter 1.0
811Toolshed: InstalledBundleCache.load: bundle ChimeraX-MapFilter (installed) [version: 1.0] [api package: chimerax.map.filter] [category: Volume Data]
812Toolshed: InstalledBundleCache.load: package ChimeraX-MapEraser 1.0
813Toolshed: InstalledBundleCache.load: bundle ChimeraX-MapEraser (installed) [version: 1.0] [api package: chimerax.map_eraser] [category: Volume data] [tool: Map Eraser [categories: Volume Data] [synopsis: Erase part of a density map within a sphere]] [command: volume erase [categories: Erase image data] [synopsis: Erase part of a density map within a sphere]]
814Toolshed: InstalledBundleCache.load: package ChimeraX-MapData 1.0
815Toolshed: InstalledBundleCache.load: bundle ChimeraX-MapData (installed) [version: 1.0] [api package: chimerax.map.data] [category: Volume Data]
816Toolshed: InstalledBundleCache.load: package ChimeraX-Map 1.0
817Toolshed: InstalledBundleCache.load: bundle ChimeraX-Map (installed) [version: 1.0] [api package: chimerax.map] [category: Volume Data] [tool: Volume Viewer [categories: Volume Data] [synopsis: Show density maps info]] [tool: Map Coordinates [categories: Volume Data] [synopsis: Adjust density map coordinates]] [command: volume [categories: Volume data] [synopsis: control volume data display]] [command: vop [categories: Volume data] [synopsis: filter volume data]] [command: molmap [categories: Volume data] [synopsis: create density map for molecule]] [command: measure mapstats [categories: Volume data] [synopsis: report map statistics]]
818Toolshed: InstalledBundleCache.load: package ChimeraX-Log 1.0
819Toolshed: InstalledBundleCache.load: bundle ChimeraX-Log (installed) [version: 1.0] [api package: chimerax.log] [category: General] [tool: Log [categories: General] [synopsis: Log of information and output]] [command: echo [categories: General] [synopsis: Log a line of text]] [command: log [categories: General] [synopsis: manipulate the Log tool]]
820Toolshed: InstalledBundleCache.load: package ChimeraX-List-Info 0.1
821Toolshed: InstalledBundleCache.load: bundle ChimeraX-List-Info (installed) [version: 0.1] [api package: chimerax.list_info] [category: General] [command: info [categories: General] [synopsis: Report attributes for models and atomic data]]
822Toolshed: InstalledBundleCache.load: package ChimeraX-Label 1.0
823Toolshed: InstalledBundleCache.load: bundle ChimeraX-Label (installed) [version: 1.0] [api package: chimerax.label] [category: General] [command: 2dlabels [categories: General] [synopsis: add text labels to graphics]] [command: label [categories: General] [synopsis: add 3d labels to graphics]] [command: ~label [categories: General] [synopsis: remove 3d labels from graphics]]
824Toolshed: InstalledBundleCache.load: package ChimeraX-IHM 1.0
825Toolshed: InstalledBundleCache.load: bundle ChimeraX-IHM (installed) [version: 1.0] [api package: chimerax.ihm] [category: Higher-Order Structure] [data format: IHM [category: Higher-Order Structure] [suffixes: .ihm] [url: https://pdb-dev.wwpdb.org/about/] [synopsis: Integrative Hybrid Models data]]
826Toolshed: InstalledBundleCache.load: package ChimeraX-Help 0.9a1
827Toolshed: InstalledBundleCache.load: bundle ChimeraX-Help (installed) [version: 0.9a1] [api package: chimerax.help_viewer] [category: Documentation] [command: help [categories: Documentation] [synopsis: Display ChimeraX help]] [data format: HTML [category: Documentation] [suffixes: .html, .htm, .xhtml, .xht, .xml] [mime_types: text/html, application/xhtml+xml] [url: http://en.wikipedia.org/wiki/Html] [synopsis: HyperText Markup Language (HTML)]]
828Toolshed: InstalledBundleCache.load: package ChimeraX-Hbonds 1.0
829Toolshed: InstalledBundleCache.load: bundle ChimeraX-Hbonds (installed) [version: 1.0] [api package: chimerax.atomic.hbonds] [category: Structure Analysis] [tool: H-Bonds [categories: Structure Analysis] [synopsis: Find hydrogen bonds]] [command: hbonds [categories: Structure Analysis] [synopsis: Find hydrogen bonds]] [command: ~hbonds [categories: Structure Analysis] [synopsis: Clear hydrogen bonds]]
830Toolshed: InstalledBundleCache.load: package ChimeraX-gltf 1.0
831Toolshed: InstalledBundleCache.load: bundle ChimeraX-gltf (installed) [version: 1.0] [api package: chimerax.gltf] [category: Generic 3D objects] [data format: glTF [category: Generic 3D objects] [suffixes: .glb] [url: https://github.com/KhronosGroup/glTF] [synopsis: Surface format used in 3D modeling]]
832Toolshed: InstalledBundleCache.load: package ChimeraX-FunctionKey 1.0
833Toolshed: InstalledBundleCache.load: bundle ChimeraX-FunctionKey (installed) [version: 1.0] [api package: chimerax.function_key] [category: General] [command: ui functionkey [categories: General] [synopsis: Assign function keys to run commands]] [command: functionkey [categories: General] [synopsis: Assign function keys to run commands]]
834Toolshed: InstalledBundleCache.load: package ChimeraX-FileHistory 1.0
835Toolshed: InstalledBundleCache.load: bundle ChimeraX-FileHistory (installed) [version: 1.0] [api package: chimerax.file_history] [category: General] [tool: File History [categories: General] [synopsis: Show recently opened files]]
836Toolshed: InstalledBundleCache.load: package ChimeraX-ExperimentalCommands 1.0
837Toolshed: InstalledBundleCache.load: bundle ChimeraX-ExperimentalCommands (installed) [version: 1.0] [api package: chimerax.exp_cmd] [category: General] [command: ribbon [categories: General] [synopsis: show cartoon for selected residues]] [command: ribbon hide [categories: General] [synopsis: hide cartoon for selected residues]] [command: ~ribbon [categories: General] [synopsis: hide cartoon for selected residues]] [command: getcrd [categories: General] [synopsis: report atomic coordinates]] [command: debug dumpspec [categories: General] [synopsis: report what a specifier matches]]
838Toolshed: InstalledBundleCache.load: package ChimeraX-Dssp 1.0
839Toolshed: InstalledBundleCache.load: bundle ChimeraX-Dssp (installed) [version: 1.0] [api package: chimerax.atomic.dssp] [category: Structure Analysis]
840Toolshed: InstalledBundleCache.load: package ChimeraX-Dist-UI 1.0
841Toolshed: InstalledBundleCache.load: bundle ChimeraX-Dist-UI (installed) [version: 1.0] [api package: chimerax.dist_ui] [category: Structure Analysis] [tool: Distances [categories: Structure Analysis] [synopsis: inter-atomic distances]]
842Toolshed: InstalledBundleCache.load: package ChimeraX-Dist-Monitor 1.0
843Toolshed: InstalledBundleCache.load: bundle ChimeraX-Dist-Monitor (installed) [version: 1.0] [api package: chimerax.dist_monitor] [category: Structure Analysis] [command: distance [categories: Structure Analysis] [synopsis: determine distance]] [command: ~distance [categories: Structure Analysis] [synopsis: remove distance monitors]]
844Toolshed: InstalledBundleCache.load: package ChimeraX-Dicom 1.0
845Toolshed: InstalledBundleCache.load: bundle ChimeraX-Dicom (installed) [version: 1.0] [api package: chimerax.dicom] [category: Volume Data]
846Toolshed: InstalledBundleCache.load: package ChimeraX-Crystal 1.0
847Toolshed: InstalledBundleCache.load: bundle ChimeraX-Crystal (installed) [version: 1.0] [api package: chimerax.crystal] [category: Generic 3D objects]
848Toolshed: InstalledBundleCache.load: package ChimeraX-Crosslinks 1.0
849Toolshed: InstalledBundleCache.load: bundle ChimeraX-Crosslinks (installed) [version: 1.0] [api package: chimerax.crosslinks] [category: General] [command: crosslinks [categories: General] [synopsis: Plot or minimize crosslink lengths]]
850Toolshed: InstalledBundleCache.load: package ChimeraX-Core 0.91
851Toolshed: InstalledBundleCache.load: bundle ChimeraX-Core (installed) [version: 0.91] [api package: chimerax.core] [category: Core]
852Toolshed: InstalledBundleCache.load: package ChimeraX-Contacts 1.0
853Toolshed: InstalledBundleCache.load: bundle ChimeraX-Contacts (installed) [version: 1.0] [api package: chimerax.interfaces] [category: Molecular structure] [command: interfaces [categories: Molecular structure] [synopsis: Display chain contact maps]]
854Toolshed: InstalledBundleCache.load: package ChimeraX-Connect-Structure 1.0
855Toolshed: InstalledBundleCache.load: bundle ChimeraX-Connect-Structure (installed) [version: 1.0] [api package: chimerax.atomic.connect_structure] [category: Structure Analysis]
856Toolshed: InstalledBundleCache.load: package ChimeraX-CommandLine 1.0
857Toolshed: InstalledBundleCache.load: bundle ChimeraX-CommandLine (installed) [version: 1.0] [api package: chimerax.cmd_line] [category: General] [tool: Command Line Interface [categories: General] [synopsis: Command Line Interface]]
858Toolshed: InstalledBundleCache.load: package ChimeraX-ColorGlobe 1.0
859Toolshed: InstalledBundleCache.load: bundle ChimeraX-ColorGlobe (installed) [version: 1.0] [api package: chimerax.color_globe] [category: General] [data format: Directional FSC [category: Generic 3D objects] [suffixes: .dres] [encoding: utf-8] [synopsis: Direction dependent resolution values]]
860Toolshed: InstalledBundleCache.load: package ChimeraX-Clashes 1.0
861Toolshed: InstalledBundleCache.load: bundle ChimeraX-Clashes (installed) [version: 1.0] [api package: chimerax.atomic.clashes] [category: Structure Analysis] [command: clashes [categories: Structure Analysis] [synopsis: Find atoms with steric clashes]] [command: contacts [categories: Structure Analysis] [synopsis: Finds atoms in contact with one another]] [command: ~clashes [categories: Structure Analysis] [synopsis: Clear clash pseudobond]] [command: ~contacts [categories: Structure Analysis] [synopsis: Clear contact pseudobond]]
862Toolshed: InstalledBundleCache.load: package ChimeraX-ChemGroup 1.0
863Toolshed: InstalledBundleCache.load: bundle ChimeraX-ChemGroup (installed) [version: 1.0] [api package: chimerax.atomic.chem_group] [category: Structure Analysis]
864Toolshed: InstalledBundleCache.load: package ChimeraX-CellPack 1.0
865Toolshed: InstalledBundleCache.load: bundle ChimeraX-CellPack (installed) [version: 1.0] [api package: chimerax.cellpack] [category: Molecular structure] [data format: cellpack [category: Molecular structure] [url: http://www.cellpack.org/] [synopsis: cellpack data]]
866Toolshed: InstalledBundleCache.load: package ChimeraX-Cage-Builder 1.0
867Toolshed: InstalledBundleCache.load: bundle ChimeraX-Cage-Builder (installed) [version: 1.0] [api package: chimerax.cage_builder] [category: Higher-Order Structure] [tool: Cage Builder [categories: Higher-Order Structure] [synopsis: Build polygonal meshes]] [command: cage [categories: Higher-Order Structure] [synopsis: Place copies of model on polygons of cage]]
868Toolshed: InstalledBundleCache.load: package ChimeraX-ButtonPanel 1.0
869Toolshed: InstalledBundleCache.load: bundle ChimeraX-ButtonPanel (installed) [version: 1.0] [api package: chimerax.buttonpanel] [category: General] [command: buttonpanel [categories: General] [synopsis: Create custom user interface panels]]
870Toolshed: InstalledBundleCache.load: package ChimeraX-BundleBuilder 1.0
871Toolshed: InstalledBundleCache._make_bundle_info: no ChimeraX bundle in ChimeraX-BundleBuilder 1.0
872Toolshed: InstalledBundleCache.load: package ChimeraX-Bumps 1.0
873Toolshed: InstalledBundleCache.load: bundle ChimeraX-Bumps (installed) [version: 1.0] [api package: chimerax.bumps] [category: Volume Data] [command: bumps [categories: Volume Data] [synopsis: find protrusions in density maps]] [command: cbumps [categories: Volume Data] [synopsis: find convex surface patches]]
874Toolshed: InstalledBundleCache.load: package ChimeraX-Bug-Reporter 1.0
875Toolshed: InstalledBundleCache.load: bundle ChimeraX-Bug-Reporter (installed) [version: 1.0] [api package: chimerax.bug_reporter] [category: General]
876Toolshed: InstalledBundleCache.load: package ChimeraX-BondRot 1.0
877Toolshed: InstalledBundleCache.load: bundle ChimeraX-BondRot (installed) [version: 1.0] [api package: chimerax.atomic.bond_rot] [category: Structure Editing] [command: torsion [categories: Report or set torsion angle] [synopsis: Report torsion angle of 4 atoms, or set it (middle two atoms much be bonded for setting)]]
878Toolshed: InstalledBundleCache.load: package ChimeraX-BlastProtein 0.1
879Toolshed: InstalledBundleCache.load: bundle ChimeraX-BlastProtein (installed) [version: 0.1] [api package: chimerax.blastprotein] [category: Sequence] [tool: Blast Protein [categories: Sequence] [synopsis: Search PDB/NR using BLAST]] [command: blastprotein [categories: Sequence] [synopsis: Search PDB/NR using BLAST]] [command: blastpdb [categories: Sequence] [synopsis: Search PDB/NR using BLAST]]
880Toolshed: InstalledBundleCache.load: package ChimeraX-BILD 0.1
881Toolshed: InstalledBundleCache.load: bundle ChimeraX-BILD (installed) [version: 0.1] [api package: chimerax.bild] [category: Generic 3D objects] [data format: BILD [category: Generic 3D objects] [suffixes: .bild, .bld] [url: help:user/formats/bild.html] [synopsis: UCSF Chimera BILD format]]
882Toolshed: InstalledBundleCache.load: package ChimeraX-BasicActions 0.1
883Toolshed: InstalledBundleCache.load: bundle ChimeraX-BasicActions (installed) [version: 0.1] [api package: chimerax.basic_actions] [category: General] [tool: Basic Actions [categories: General] [synopsis: show/hide atoms, ribbons and surfaces]] [command: name [categories: General] [synopsis: Define specifier name as a string]] [command: name frozen [categories: General] [synopsis: Define specifier name as atoms in current session matching a string]] [command: name delete [categories: General] [synopsis: Remove user-defined specifier name]] [command: name list [categories: General] [synopsis: List user-defined specifier names]]
884Toolshed: InstalledBundleCache.load: package ChimeraX-Atomic 1.0
885Toolshed: InstalledBundleCache.load: bundle ChimeraX-Atomic (installed) [version: 1.0] [api package: chimerax.atomic] [category: Structure Analysis, Structure Editing]
886Toolshed: InstalledBundleCache.load: package ChimeraX-Atom-Search 1.0
887Toolshed: InstalledBundleCache.load: bundle ChimeraX-Atom-Search (installed) [version: 1.0] [api package: chimerax.atomic.search] [category: Structure Analysis]
888Toolshed: InstalledBundleCache.load: package ChimeraX-Alignments 1.0
889Toolshed: InstalledBundleCache.load: bundle ChimeraX-Alignments (installed) [version: 1.0] [api package: chimerax.seqalign] [category: Sequence] [command: sequence [categories: Sequence alignment] [synopsis: control/open sequence alignments]] [data format: FASTA [category: Sequence alignment] [suffixes: .fa, .fasta, .afasta, .afa] [url: https://en.wikipedia.org/wiki/FASTA_format] [encoding: utf-8] [synopsis: FASTA format]] [data format: MSF [category: Sequence alignment] [suffixes: .msf] [encoding: utf-8] [synopsis: GCG MSF (multiple sequence file) format]] [data format: PIR [category: Sequence alignment] [suffixes: .ali, .pir] [url: http://www.bioinformatics.nl/tools/crab_pir.html] [encoding: utf-8] [synopsis: PIR (NBRF) format]] [data format: ALN [category: Sequence alignment] [suffixes: .aln, .clustal, .clustalw, .clustalx] [encoding: utf-8] [synopsis: Clustal ALN format]] [data format: HSSP [category: Sequence alignment] [suffixes: .hssp] [encoding: utf-8] [synopsis: HSSP format]] [data format: Pfam [category: Sequence alignment] [suffixes: .selex, .slx, .pfam] [encoding: utf-8] [synopsis: Selex (Pfam) format]] [data format: RSF [category: Sequence alignment] [suffixes: .rsf] [encoding: utf-8] [synopsis: GCG RSF format]] [data format: Stockholm [category: Sequence alignment] [suffixes: .sth, .sto] [url: https://en.wikipedia.org/wiki/Stockholm_format] [encoding: utf-8] [synopsis: Stockholm format]]
890Toolshed: InstalledBundleCache.load: package ChimeraX-AlignmentMatrices 1.0
891Toolshed: InstalledBundleCache.load: bundle ChimeraX-AlignmentMatrices (installed) [version: 1.0] [api package: chimerax.seqalign.sim_matrices] [category: Sequence alignment]
892Toolshed: InstalledBundleCache.load: package ChimeraX-AlignmentHdrs 1.0
893Toolshed: InstalledBundleCache.load: bundle ChimeraX-AlignmentHdrs (installed) [version: 1.0] [api package: chimerax.seqalign.headers] [category: Sequence]
894Toolshed: InstalledBundleCache.load: package ChimeraX-AlignmentAlgorithms 1.0
895Toolshed: InstalledBundleCache.load: bundle ChimeraX-AlignmentAlgorithms (installed) [version: 1.0] [api package: chimerax.seqalign.align_algs] [category: Sequence alignment]
896Toolshed: InstalledBundleCache.load: package ChimeraX-AddH 1.0
897Toolshed: InstalledBundleCache.load: bundle ChimeraX-AddH (installed) [version: 1.0] [api package: chimerax.atomic.addh] [category: Structure Editing] [command: addh [categories: Structure Editing] [synopsis: Add hydrogens]]
898Toolshed: InstalledBundleCache.load: package chardet 3.0.4
899Toolshed: InstalledBundleCache._make_bundle_info: no ChimeraX bundle in chardet 3.0.4
900Toolshed: InstalledBundleCache.load: package certifi 2019.9.11
901Toolshed: InstalledBundleCache._make_bundle_info: no ChimeraX bundle in certifi 2019.9.11
902Toolshed: InstalledBundleCache.load: package blockdiag 1.5.4
903Toolshed: InstalledBundleCache._make_bundle_info: no ChimeraX bundle in blockdiag 1.5.4
904Toolshed: InstalledBundleCache.load: package backcall 0.1.0
905Toolshed: InstalledBundleCache._make_bundle_info: no ChimeraX bundle in backcall 0.1.0
906Toolshed: InstalledBundleCache.load: package Babel 2.7.0
907Toolshed: InstalledBundleCache._make_bundle_info: no ChimeraX bundle in Babel 2.7.0
908Toolshed: InstalledBundleCache.load: package appdirs 1.4.3
909Toolshed: InstalledBundleCache._make_bundle_info: no ChimeraX bundle in appdirs 1.4.3
910Toolshed: InstalledBundleCache.load: package alabaster 0.7.12
911Toolshed: InstalledBundleCache._make_bundle_info: no ChimeraX bundle in alabaster 0.7.12
912Toolshed: InstalledBundleCache.load: write_cache
913Toolshed: InstalledBundleCache._write_cache C:\Users\tic20\AppData\Local\UCSF\ChimeraX\Cache\0.91\toolshed\bundle_info.cache
914Toolshed: deregister_command nucleotides
915Toolshed: deregister_command ~nucleotides
916Toolshed: deregister_command matchmaker
917Toolshed: deregister_command mmaker
918Toolshed: deregister_command viewdockx
919Toolshed: deregister_command viewdockx down
920Toolshed: deregister_command viewdockx up
921Toolshed: deregister_command color electrostatic
922Toolshed: deregister_command color sample
923Toolshed: deregister_command color gradient
924Toolshed: deregister_command color radial
925Toolshed: deregister_command color cylindrical
926Toolshed: deregister_command color height
927Toolshed: deregister_command surface
928Toolshed: deregister_command ~surface
929Toolshed: deregister_command volume splitbyzone
930Toolshed: deregister_command sop
931Toolshed: deregister_command measure sasa
932Toolshed: deregister_command measure volume
933Toolshed: deregister_command measure area
934Toolshed: deregister_command blastprotein
935Toolshed: deregister_command blastpdb
936Toolshed: deregister_command crosslinks
937Toolshed: deregister_command fitmap
938Toolshed: deregister_command bumps
939Toolshed: deregister_command cbumps
940Toolshed: deregister_command modeller comparative
941Toolshed: deregister_command modeller scores
942Toolshed: deregister_command addh
943Toolshed: deregister_command vseries
944Toolshed: deregister_command measure motion
945Toolshed: deregister_command volume mask
946Toolshed: deregister_command volume onesmask
947Toolshed: deregister_command cage
948Toolshed: deregister_command resfit
949Toolshed: deregister_command registration status
950Toolshed: deregister_command hbonds
951Toolshed: deregister_command ~hbonds
952Toolshed: deregister_command swapaa mousemode
953Toolshed: deregister_command ks
954Toolshed: deregister_command interfaces
955Toolshed: deregister_command mseries
956Toolshed: deregister_command ui functionkey
957Toolshed: deregister_command functionkey
958Toolshed: deregister_command name
959Toolshed: deregister_command name frozen
960Toolshed: deregister_command name delete
961Toolshed: deregister_command name list
962Toolshed: deregister_command clashes
963Toolshed: deregister_command contacts
964Toolshed: deregister_command ~clashes
965Toolshed: deregister_command ~contacts
966Toolshed: deregister_command buttonpanel
967Toolshed: deregister_command torsion
968Toolshed: deregister_command marker
969Toolshed: deregister_command isolde
970Toolshed: deregister_command rama
971Toolshed: deregister_command rota
972Toolshed: deregister_command ~rama
973Toolshed: deregister_command ~rota
974Toolshed: deregister_command echo
975Toolshed: deregister_command log
976Toolshed: deregister_command zone
977Toolshed: deregister_command 2dlabels
978Toolshed: deregister_command label
979Toolshed: deregister_command ~label
980Toolshed: deregister_command measure blob
981Toolshed: deregister_command swapaa
982Toolshed: deregister_command sequence
983Toolshed: deregister_command volume
984Toolshed: deregister_command vop
985Toolshed: deregister_command molmap
986Toolshed: deregister_command measure mapstats
987Toolshed: deregister_command volume erase
988Toolshed: deregister_command help
989Toolshed: deregister_command distance
990Toolshed: deregister_command ~distance
991Toolshed: deregister_command alias
992Toolshed: deregister_command alias list
993Toolshed: deregister_command alias delete
994Toolshed: deregister_command ~alias
995Toolshed: deregister_command align
996Toolshed: deregister_command camera
997Toolshed: deregister_command cartoon
998Toolshed: deregister_command ~cartoon
999Toolshed: deregister_command cd
1000Toolshed: deregister_command clip
1001Toolshed: deregister_command ~clip
1002Toolshed: deregister_command close
1003Toolshed: deregister_command cofr
1004Toolshed: deregister_command ~cofr
1005Toolshed: deregister_command color
1006Toolshed: deregister_command colour
1007Toolshed: deregister_command color delete
1008Toolshed: deregister_command color list
1009Toolshed: deregister_command color name
1010Toolshed: deregister_command color show
1011Toolshed: deregister_command colordef
1012Toolshed: deregister_command ~colordef
1013Toolshed: deregister_command colourdef
1014Toolshed: deregister_command ~colourdef
1015Toolshed: deregister_command coordset
1016Toolshed: deregister_command crossfade
1017Toolshed: deregister_command delete
1018Toolshed: deregister_command dssp
1019Toolshed: deregister_command exit
1020Toolshed: deregister_command quit
1021Toolshed: deregister_command graphics
1022Toolshed: deregister_command hide
1023Toolshed: deregister_command ~show
1024Toolshed: deregister_command ~display
1025Toolshed: deregister_command lighting
1026Toolshed: deregister_command lighting model
1027Toolshed: deregister_command material
1028Toolshed: deregister_command measure buriedarea
1029Toolshed: deregister_command measure center
1030Toolshed: deregister_command measure convexity
1031Toolshed: deregister_command measure inertia
1032Toolshed: deregister_command measure length
1033Toolshed: deregister_command measure symmetry
1034Toolshed: deregister_command move
1035Toolshed: deregister_command palette
1036Toolshed: deregister_command pdbimages
1037Toolshed: deregister_command perframe
1038Toolshed: deregister_command ~perframe
1039Toolshed: deregister_command pwd
1040Toolshed: deregister_command rainbow
1041Toolshed: deregister_command rename
1042Toolshed: deregister_command roll
1043Toolshed: deregister_command runscript
1044Toolshed: deregister_command select
1045Toolshed: deregister_command ~select
1046Toolshed: deregister_command set
1047Toolshed: deregister_command ~set
1048Toolshed: deregister_command setattr
1049Toolshed: deregister_command show
1050Toolshed: deregister_command display
1051Toolshed: deregister_command size
1052Toolshed: deregister_command split
1053Toolshed: deregister_command stop
1054Toolshed: deregister_command style
1055Toolshed: deregister_command sym
1056Toolshed: deregister_command tile
1057Toolshed: deregister_command time
1058Toolshed: deregister_command transparency
1059Toolshed: deregister_command turn
1060Toolshed: deregister_command undo
1061Toolshed: deregister_command redo
1062Toolshed: deregister_command usage
1063Toolshed: deregister_command version
1064Toolshed: deregister_command view
1065Toolshed: deregister_command wait
1066Toolshed: deregister_command windowsize
1067Toolshed: deregister_command select zone
1068Toolshed: deregister_command zoom
1069Toolshed: deregister_command ui
1070Toolshed: deregister_command struts
1071Toolshed: deregister_command remotecontrol xmlrpc
1072Toolshed: deregister_command smoothlines
1073Toolshed: deregister_command info
1074Toolshed: deregister_command debug test
1075Toolshed: deregister_command debug exectest
1076Toolshed: deregister_command debug expectfail
1077Toolshed: deregister_command mlp
1078Toolshed: deregister_command ui mousemode
1079Toolshed: deregister_command mousemode
1080Toolshed: deregister_command device snav
1081Toolshed: deregister_command ribbon
1082Toolshed: deregister_command ribbon hide
1083Toolshed: deregister_command ~ribbon
1084Toolshed: deregister_command getcrd
1085Toolshed: deregister_command debug dumpspec
1086Toolshed: deregister_command device realsense
1087Toolshed: deregister_command movie
1088Toolshed: deregister_command texture
1089Toolshed: deregister_command remotecontrol rest
1090Toolshed: deregister_command morph
1091Toolshed: deregister_command meeting
1092Toolshed: deregister_command preset
1093Toolshed: deregister_command vr
1094Toolshed: deregister_command device vr
1095Toolshed: register bundle ChimeraX-Core 0.91
1096Toolshed: register bundle ChimeraX-MouseModes 1.0
1097Toolshed: delay_registration ui mousemode
1098Toolshed: delay_registration mousemode
1099Toolshed: register bundle ChimeraX-MapData 1.0
1100Toolshed: register bundle ChimeraX-ExperimentalCommands 1.0
1101Toolshed: delay_registration ribbon
1102Toolshed: delay_registration ribbon hide
1103Toolshed: delay_registration ~ribbon
1104Toolshed: delay_registration getcrd
1105Toolshed: delay_registration debug dumpspec
1106Toolshed: register bundle ChimeraX-RealSense 1.0
1107Toolshed: delay_registration device realsense
1108Toolshed: register bundle ChimeraX-Movie 1.0
1109Toolshed: delay_registration movie
1110Toolshed: register bundle ChimeraX-Texture 1.0
1111Toolshed: delay_registration texture
1112Toolshed: register bundle ChimeraX-gltf 1.0
1113Toolshed: register_file_type glTF
1114Toolshed: register bundle ChimeraX-Crystal 1.0
1115Toolshed: register bundle ChimeraX-Test 1.0
1116Toolshed: delay_registration debug test
1117Toolshed: delay_registration debug exectest
1118Toolshed: delay_registration debug expectfail
1119Toolshed: register bundle ChimeraX-List-Info 0.1
1120Toolshed: delay_registration info
1121Toolshed: register bundle ChimeraX-WavefrontOBJ 1.0
1122Toolshed: register_file_type Wavefront OBJ
1123Toolshed: register bundle ChimeraX-SpaceNavigator 1.0
1124Toolshed: delay_registration device snav
1125Toolshed: register bundle ChimeraX-RemoteControl 1.0
1126Toolshed: delay_registration remotecontrol xmlrpc
1127Toolshed: register bundle ChimeraX-Dicom 1.0
1128Toolshed: register bundle ChimeraX-Storm 1.0
1129Toolshed: register_file_type STORM
1130Toolshed: register bundle ChimeraX-Scheme-Mgr 1.0
1131Toolshed: register bundle ChimeraX-Segment 1.0
1132Toolshed: register bundle ChimeraX-MLP 1.0
1133Toolshed: delay_registration mlp
1134Toolshed: register bundle ChimeraX-SmoothLines 1.0
1135Toolshed: delay_registration smoothlines
1136Toolshed: register bundle ChimeraX-Morph 1.0
1137Toolshed: delay_registration morph
1138Toolshed: register bundle ChimeraX-RotamerLibs-Richardson 1.0
1139Toolshed: register bundle ChimeraX-STL 1.0
1140Toolshed: register_file_type StereoLithography
1141Toolshed: register bundle ChimeraX-RestServer 0.1
1142Toolshed: delay_registration remotecontrol rest
1143Toolshed: register bundle ChimeraX-Meeting 1.0
1144Toolshed: delay_registration meeting
1145Toolshed: register bundle ChimeraX-CellPack 1.0
1146Toolshed: register_file_type cellpack
1147Toolshed: register bundle ChimeraX-Atomic 1.0
1148Toolshed: register bundle ChimeraX-Rotamer-Lib-Mgr 1.0
1149Toolshed: register bundle ChimeraX-Struts 1.0
1150Toolshed: delay_registration struts
1151Toolshed: register bundle ChimeraX-WebServices 1.0
1152Toolshed: register bundle ChimeraX-RotamerLibs-Dynameomics 1.0
1153Toolshed: register bundle ChimeraX-Preset-Mgr 1.0
1154Toolshed: delay_registration preset
1155Toolshed: register bundle ChimeraX-VTK 1.0
1156Toolshed: register_file_type VTK PolyData
1157Toolshed: register bundle ChimeraX-Vive 1.0
1158Toolshed: delay_registration vr
1159Toolshed: delay_registration device vr
1160Toolshed: register bundle ChimeraX-ColorGlobe 1.0
1161Toolshed: register_file_type Directional FSC
1162Toolshed: register bundle ChimeraX-RotamerLibs-Dunbrack 1.0
1163Toolshed: register bundle ChimeraX-Dssp 1.0
1164Toolshed: register bundle ChimeraX-PDB 1.0
1165Toolshed: register_file_type PDB
1166Toolshed: register bundle ChimeraX-MD-crds 1.0
1167Toolshed: register_file_type Gromacs full-precision coordinates
1168Toolshed: register_file_type Gromacs compressed coordinates
1169Toolshed: register_file_type DCD coordinates
1170Toolshed: register bundle ChimeraX-Atom-Search 1.0
1171Toolshed: register bundle ChimeraX-Clipper 0.9.11
1172Toolshed: delay_registration clipper
1173Toolshed: delay_registration cview
1174Toolshed: register_file_type Structure factor MTZ
1175Toolshed: register bundle ChimeraX-Read-Pbonds 1.0
1176Toolshed: register_file_type Pseudobonds
1177Toolshed: register bundle ChimeraX-ChemGroup 1.0
1178Toolshed: register bundle ChimeraX-UI 1.0
1179Toolshed: delay_registration ui
1180Toolshed: register bundle ChimeraX-Std-Commands 1.0
1181Toolshed: delay_registration alias
1182Toolshed: delay_registration alias list
1183Toolshed: delay_registration alias delete
1184Toolshed: delay_registration ~alias
1185Toolshed: delay_registration align
1186Toolshed: delay_registration camera
1187Toolshed: delay_registration cartoon
1188Toolshed: delay_registration ~cartoon
1189Toolshed: delay_registration cd
1190Toolshed: delay_registration clip
1191Toolshed: delay_registration ~clip
1192Toolshed: delay_registration close
1193Toolshed: delay_registration cofr
1194Toolshed: delay_registration ~cofr
1195Toolshed: delay_registration color
1196Toolshed: delay_registration colour
1197Toolshed: delay_registration color delete
1198Toolshed: delay_registration color list
1199Toolshed: delay_registration color name
1200Toolshed: delay_registration color show
1201Toolshed: delay_registration colordef
1202Toolshed: delay_registration ~colordef
1203Toolshed: delay_registration colourdef
1204Toolshed: delay_registration ~colourdef
1205Toolshed: delay_registration coordset
1206Toolshed: delay_registration crossfade
1207Toolshed: delay_registration delete
1208Toolshed: delay_registration dssp
1209Toolshed: delay_registration exit
1210Toolshed: delay_registration quit
1211Toolshed: delay_registration graphics
1212Toolshed: delay_registration hide
1213Toolshed: delay_registration ~show
1214Toolshed: delay_registration ~display
1215Toolshed: delay_registration lighting
1216Toolshed: delay_registration lighting model
1217Toolshed: delay_registration material
1218Toolshed: delay_registration measure buriedarea
1219Toolshed: delay_registration measure center
1220Toolshed: delay_registration measure convexity
1221Toolshed: delay_registration measure inertia
1222Toolshed: delay_registration measure length
1223Toolshed: delay_registration measure symmetry
1224Toolshed: delay_registration move
1225Toolshed: delay_registration palette
1226Toolshed: delay_registration pdbimages
1227Toolshed: delay_registration perframe
1228Toolshed: delay_registration ~perframe
1229Toolshed: delay_registration pwd
1230Toolshed: delay_registration rainbow
1231Toolshed: delay_registration rename
1232Toolshed: delay_registration roll
1233Toolshed: delay_registration runscript
1234Toolshed: delay_registration select
1235Toolshed: delay_registration ~select
1236Toolshed: delay_registration set
1237Toolshed: delay_registration ~set
1238Toolshed: delay_registration setattr
1239Toolshed: delay_registration show
1240Toolshed: delay_registration display
1241Toolshed: delay_registration size
1242Toolshed: delay_registration split
1243Toolshed: delay_registration stop
1244Toolshed: delay_registration style
1245Toolshed: delay_registration sym
1246Toolshed: delay_registration tile
1247Toolshed: delay_registration time
1248Toolshed: delay_registration transparency
1249Toolshed: delay_registration turn
1250Toolshed: delay_registration undo
1251Toolshed: delay_registration redo
1252Toolshed: delay_registration usage
1253Toolshed: delay_registration version
1254Toolshed: delay_registration view
1255Toolshed: delay_registration wait
1256Toolshed: delay_registration windowsize
1257Toolshed: delay_registration select zone
1258Toolshed: delay_registration zoom
1259Toolshed: register bundle ChimeraX-Dist-Monitor 1.0
1260Toolshed: delay_registration distance
1261Toolshed: delay_registration ~distance
1262Toolshed: register bundle ChimeraX-Contacts 1.0
1263Toolshed: delay_registration interfaces
1264Toolshed: register bundle ChimeraX-Clashes 1.0
1265Toolshed: delay_registration clashes
1266Toolshed: delay_registration contacts
1267Toolshed: delay_registration ~clashes
1268Toolshed: delay_registration ~contacts
1269Toolshed: register bundle ChimeraX-ISOLDE 1.0b3.dev7
1270Toolshed: delay_registration isolde
1271Toolshed: delay_registration rama
1272Toolshed: delay_registration rota
1273Toolshed: delay_registration ~rama
1274Toolshed: delay_registration ~rota
1275Toolshed: register bundle ChimeraX-Shortcuts 1.0
1276Toolshed: delay_registration ks
1277Toolshed: register bundle ChimeraX-ButtonPanel 1.0
1278Toolshed: delay_registration buttonpanel
1279Toolshed: register bundle ChimeraX-TapeMeasure 1.0
1280Toolshed: register bundle ChimeraX-Segger 1.0
1281Toolshed: register bundle ChimeraX-mmCIF 1.1
1282Toolshed: register_file_type mmCIF
1283Toolshed: register bundle ChimeraX-MMTF 1.0
1284Toolshed: register_file_type MMTF
1285Toolshed: register bundle ChimeraX-Zone 1.0
1286Toolshed: delay_registration zone
1287Toolshed: register bundle ChimeraX-Markers 1.0
1288Toolshed: delay_registration marker
1289Toolshed: register_file_type Marker model
1290Toolshed: register bundle ChimeraX-FileHistory 1.0
1291Toolshed: register bundle ChimeraX-BondRot 1.0
1292Toolshed: delay_registration torsion
1293Toolshed: register bundle ChimeraX-ResidueFit 1.0
1294Toolshed: delay_registration resfit
1295Toolshed: register bundle ChimeraX-Connect-Structure 1.0
1296Toolshed: register bundle ChimeraX-SwapRes 1.0
1297Toolshed: delay_registration swapaa
1298Toolshed: register bundle ChimeraX-Mol2 1.0
1299Toolshed: register_file_type Sybyl Mol2
1300Toolshed: register bundle ChimeraX-BasicActions 0.1
1301Toolshed: delay_registration name
1302Toolshed: delay_registration name frozen
1303Toolshed: delay_registration name delete
1304Toolshed: delay_registration name list
1305Toolshed: register bundle ChimeraX-Bug-Reporter 1.0
1306Toolshed: register bundle ChimeraX-Dist-UI 1.0
1307Toolshed: register bundle ChimeraX-SwapAA 1.0
1308Toolshed: delay_registration swapaa mousemode
1309Toolshed: register bundle ChimeraX-ModelSeries 1.0
1310Toolshed: delay_registration mseries
1311Toolshed: register bundle ChimeraX-Log 1.0
1312Toolshed: delay_registration echo
1313Toolshed: delay_registration log
1314Toolshed: register bundle ChimeraX-Hbonds 1.0
1315Toolshed: delay_registration hbonds
1316Toolshed: delay_registration ~hbonds
1317Toolshed: register bundle ChimeraX-ShowAttr 1.0
1318Toolshed: register bundle ChimeraX-Label 1.0
1319Toolshed: delay_registration 2dlabels
1320Toolshed: delay_registration label
1321Toolshed: delay_registration ~label
1322Toolshed: register bundle ChimeraX-ModelPanel 1.0
1323Toolshed: register bundle ChimeraX-Tug 1.0
1324Toolshed: register bundle ChimeraX-FunctionKey 1.0
1325Toolshed: delay_registration ui functionkey
1326Toolshed: delay_registration functionkey
1327Toolshed: register bundle ChimeraX-MapEraser 1.0
1328Toolshed: delay_registration volume erase
1329Toolshed: register bundle ChimeraX-SideView 1.0
1330Toolshed: register bundle ChimeraX-Alignments 1.0
1331Toolshed: delay_registration sequence
1332Toolshed: register_file_type FASTA
1333Toolshed: register_file_type MSF
1334Toolshed: register_file_type PIR
1335Toolshed: register_file_type ALN
1336Toolshed: register_file_type HSSP
1337Toolshed: register_file_type Pfam
1338Toolshed: register_file_type RSF
1339Toolshed: register_file_type Stockholm
1340Toolshed: register bundle ChimeraX-CommandLine 1.0
1341Toolshed: register bundle ChimeraX-Registration 0.1
1342Toolshed: delay_registration registration status
1343Toolshed: register bundle ChimeraX-Shell 1.0
1344Toolshed: register bundle ChimeraX-Map 1.0
1345Toolshed: delay_registration volume
1346Toolshed: delay_registration vop
1347Toolshed: delay_registration molmap
1348Toolshed: delay_registration measure mapstats
1349Toolshed: register bundle ChimeraX-Help 0.9a1
1350Toolshed: delay_registration help
1351Toolshed: register_file_type HTML
1352Toolshed: register bundle ChimeraX-PickBlobs 1.0
1353Toolshed: delay_registration measure blob
1354Toolshed: register bundle ChimeraX-VolumeMenu 1.0
1355Toolshed: register bundle ChimeraX-Cage-Builder 1.0
1356Toolshed: delay_registration cage
1357Toolshed: register bundle ChimeraX-MapSeries 1.0
1358Toolshed: delay_registration vseries
1359Toolshed: delay_registration measure motion
1360Toolshed: register bundle ChimeraX-Crosslinks 1.0
1361Toolshed: delay_registration crosslinks
1362Toolshed: register bundle ChimeraX-IHM 1.0
1363Toolshed: register_file_type IHM
1364Toolshed: register bundle ChimeraX-AlignmentHdrs 1.0
1365Toolshed: register bundle ChimeraX-Mask 1.0
1366Toolshed: delay_registration volume mask
1367Toolshed: delay_registration volume onesmask
1368Toolshed: register bundle ChimeraX-Modeller 1.0
1369Toolshed: delay_registration modeller comparative
1370Toolshed: delay_registration modeller scores
1371Toolshed: register bundle ChimeraX-Surface 1.0
1372Toolshed: delay_registration color electrostatic
1373Toolshed: delay_registration color sample
1374Toolshed: delay_registration color gradient
1375Toolshed: delay_registration color radial
1376Toolshed: delay_registration color cylindrical
1377Toolshed: delay_registration color height
1378Toolshed: delay_registration surface
1379Toolshed: delay_registration ~surface
1380Toolshed: delay_registration volume splitbyzone
1381Toolshed: delay_registration sop
1382Toolshed: delay_registration measure sasa
1383Toolshed: delay_registration measure volume
1384Toolshed: delay_registration measure area
1385Toolshed: register_file_type Collada
1386Toolshed: register bundle ChimeraX-AlignmentMatrices 1.0
1387Toolshed: register bundle ChimeraX-MapFit 1.0
1388Toolshed: delay_registration fitmap
1389Toolshed: register bundle ChimeraX-Toolbar 0.1
1390Toolshed: register bundle ChimeraX-AddH 1.0
1391Toolshed: delay_registration addh
1392Toolshed: register bundle ChimeraX-MapFilter 1.0
1393Toolshed: register bundle ChimeraX-BlastProtein 0.1
1394Toolshed: delay_registration blastprotein
1395Toolshed: delay_registration blastpdb
1396Toolshed: register bundle ChimeraX-AlignmentAlgorithms 1.0
1397Toolshed: register bundle ChimeraX-uniprot 1.0
1398Toolshed: register_file_type UniProt
1399Toolshed: register bundle ChimeraX-Bumps 1.0
1400Toolshed: delay_registration bumps
1401Toolshed: delay_registration cbumps
1402Toolshed: register bundle ChimeraX-ViewDockX 0.1
1403Toolshed: delay_registration viewdockx
1404Toolshed: delay_registration viewdockx down
1405Toolshed: delay_registration viewdockx up
1406Toolshed: register_file_type mol2
1407Toolshed: register_file_type pdbqt
1408Toolshed: register bundle ChimeraX-MatchMaker 1.0
1409Toolshed: delay_registration matchmaker
1410Toolshed: delay_registration mmaker
1411Toolshed: register bundle ChimeraX-Nucleotides 0.1
1412Toolshed: delay_registration nucleotides
1413Toolshed: delay_registration ~nucleotides
1414Toolshed: register bundle ChimeraX-BILD 0.1
1415Toolshed: register_file_type BILD
1416Toolshed: register bundle ChimeraX-SeqView 1.0
1417Toolshed: find_bundle ChimeraX-Clipper True 0.9.11
1418Toolshed: find_bundle ChimeraX-Clipper True 0.9.11