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Opened 5 years ago
Closed 5 years ago
#3404 closed defect (fixed)
ChimeraX bug report submission
| Reported by: | Owned by: | Conrad Huang | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Comparison | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Darwin-18.7.0-x86_64-i386-64bit
ChimeraX Version: 1.0 (2020-06-04 23:15:07 UTC)
Description
open attached session file, then "tile #1-2"
Log:
UCSF ChimeraX version: 1.0 (2020-06-04)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "/Users/pett/Library/Containers/com.apple.mail/Data/Library/Mail
> Downloads/05AD7787-FA49-4BB1-92AC-BD54EDBA8651/tiling fails.cxs"
Log from Mon Jun 15 11:49:13 2020UCSF ChimeraX version: 1.0 (2020-06-04)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "C:\Users\meetol\Documents\opetus\Structural Bioinformatics\chimera
> tests\ca6 test.cxs" format session
Log from Thu Jun 11 14:04:44 2020 Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.0 (2020-06-04)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 3fe4 format mmcif fromDatabase pdb
3fe4 title:
Crystal Structure of Human Carbonic Anhydrase vi [more info...]
Chain information for 3fe4 #1
---
Chain | Description
A B | Carbonic anhydrase 6
Non-standard residues in 3fe4 #1
---
GOL — glycerol (glycerin; propane-1,2,3-triol)
MG — magnesium ion
3fe4 mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> delete /a
> delete :gol
> info resattr
resattr atoms
resattr atomspec
resattr center
resattr chain
resattr chain_id
resattr chi1
resattr chi2
resattr chi3
resattr chi4
resattr cpp_pointer
resattr deleted
resattr description
resattr has_custom_attrs
resattr insertion_code
resattr is_helix
resattr is_strand
resattr label_one_letter_code
resattr label_specifier
resattr mmcif_chain_id
resattr name
resattr neighbors
resattr num_atoms
resattr number
resattr omega
resattr one_letter_code
resattr phi
resattr polymer_type
resattr principal_atom
resattr psi
resattr ribbon_adjust
resattr ribbon_color
resattr ribbon_display
resattr ribbon_hide_backbone
resattr ring_color
resattr ring_display
resattr selected
resattr session
resattr ss_id
resattr ss_type
resattr standard_aa_name
resattr structure
resattr sym_chi1
resattr sym_chi2
resattr sym_chi3
resattr sym_chi4
resattr thin_rings
> help attributes
No help found for 'attributes'
> help help:user
> show surfaces
> open "C:/Users/meetol/Documents/opetus/Structural Bioinformatics/chimera
> tests/ca6-non-mammal+human ca-dom 90.fasta" format fasta
Summary of feedback from opening C:/Users/meetol/Documents/opetus/Structural
Bioinformatics/chimera tests/ca6-non-mammal+human ca-dom 90.fasta
---
notes | Alignment identifier is ca6-non-mammal+human ca-dom 90.fasta
Associated 3fe4 chain B to ca6_human_NP_001206.2 with 8 mismatches
Opened 29 sequences from ca6-non-mammal+human ca-dom 90.fasta
> info resattr
resattr atoms
resattr atomspec
resattr center
resattr chain
resattr chain_id
resattr chi1
resattr chi2
resattr chi3
resattr chi4
resattr cpp_pointer
resattr deleted
resattr description
resattr has_custom_attrs
resattr insertion_code
resattr is_helix
resattr is_strand
resattr label_one_letter_code
resattr label_specifier
resattr mmcif_chain_id
resattr name
resattr neighbors
resattr num_atoms
resattr number
resattr omega
resattr one_letter_code
resattr phi
resattr polymer_type
resattr principal_atom
resattr psi
resattr ribbon_adjust
resattr ribbon_color
resattr ribbon_display
resattr ribbon_hide_backbone
resattr ring_color
resattr ring_display
resattr selected
resattr session
resattr ss_id
resattr ss_type
resattr standard_aa_name
resattr structure
resattr sym_chi1
resattr sym_chi2
resattr sym_chi3
resattr sym_chi4
resattr thin_rings
> measure sasa #1/b & protein
Solvent accessible area for #1/b & protein = 11898
> info resattr
resattr area
resattr atoms
resattr atomspec
resattr center
resattr chain
resattr chain_id
resattr chi1
resattr chi2
resattr chi3
resattr chi4
resattr cpp_pointer
resattr deleted
resattr description
resattr has_custom_attrs
resattr insertion_code
resattr is_helix
resattr is_strand
resattr label_one_letter_code
resattr label_specifier
resattr mmcif_chain_id
resattr name
resattr neighbors
resattr num_atoms
resattr number
resattr omega
resattr one_letter_code
resattr phi
resattr polymer_type
resattr principal_atom
resattr psi
resattr ribbon_adjust
resattr ribbon_color
resattr ribbon_display
resattr ribbon_hide_backbone
resattr ring_color
resattr ring_display
resattr selected
resattr session
resattr ss_id
resattr ss_type
resattr standard_aa_name
resattr structure
resattr sym_chi1
resattr sym_chi2
resattr sym_chi3
resattr sym_chi4
resattr thin_rings
> mlp
Map values for surface "3fe4_B SES surface": minimum -28.61, mean -4.916,
maximum 24.44
> lighting soft
> lighting full
> lighting soft
> toolshed show
> cofr frontCenter
> tile
> open 5cjf
Summary of feedback from opening 5cjf fetched from pdb
---
notes | Fetching compressed mmCIF 5cjf from
http://files.rcsb.org/download/5cjf.cif
Fetching CCD ZN from http://ligand-expo.rcsb.org/reports/Z/ZN/ZN.cif
Fetching CCD 520 from http://ligand-expo.rcsb.org/reports/5/520/520.cif
Fetching CCD SO4 from http://ligand-expo.rcsb.org/reports/S/SO4/SO4.cif
Fetching CCD NAG from http://ligand-expo.rcsb.org/reports/N/NAG/NAG.cif
Fetching CCD BMA from http://ligand-expo.rcsb.org/reports/B/BMA/BMA.cif
Fetching CCD MAN from http://ligand-expo.rcsb.org/reports/M/MAN/MAN.cif
5cjf title:
The crystal structure of the human carbonic anhydrase XIV in complex with a
1,1'-biphenyl-4-sulfonamide inhibitor. [more info...]
Chain information for 5cjf #2
---
Chain | Description
A | Carbonic anhydrase 14
Non-standard residues in 5cjf #2
---
520 — 4'-(4-aminobenzoyl)biphenyl-4-sulfonamide
BMA — β-D-mannose
GOL — glycerol (glycerin; propane-1,2,3-triol)
MAN — α-D-mannose
NAG — N-acetyl-D-glucosamine
SO4 — sulfate ion
ZN — zinc ion
> ui tool show "Side View"
> ~tile
Unknown command: ~tile
> !tile
Unknown command: !tile
> tile off
Expected a models specifier or a keyword
> help tile
> undo tile
Expected fewer arguments
> undo
> ui mousemode right "translate selected models"
> help help:user/tools/sideview.html
> move #2 y -20
Missing or invalid "axis" argument: Axis argument requires 2 atoms, got 2460
atoms
> move y -20 #2
Expected an integer >= 1 or a keyword
> help move
> move y -20 models #2
> move y -20 models #2
> move y -20 models #2
> move y -20 models #2
> ui mousemode right zoom
> ui mousemode right translate
> tile
> tile columns 2
> set independent
Expected a keyword
> help set
> save "C:/Users/meetol/Documents/opetus/Structural Bioinformatics/chimera
> tests/ca6 test.cxs"
opened ChimeraX session
> select up
Nothing selected
> select up
Nothing selected
> info resattr
resattr area
resattr atoms
resattr atomspec
resattr center
resattr chain
resattr chain_id
resattr chi1
resattr chi2
resattr chi3
resattr chi4
resattr cpp_pointer
resattr deleted
resattr description
resattr has_custom_attrs
resattr insertion_code
resattr is_helix
resattr is_strand
resattr label_one_letter_code
resattr label_specifier
resattr mmcif_chain_id
resattr name
resattr neighbors
resattr num_atoms
resattr number
resattr omega
resattr one_letter_code
resattr phi
resattr polymer_type
resattr principal_atom
resattr psi
resattr ribbon_adjust
resattr ribbon_color
resattr ribbon_display
resattr ribbon_hide_backbone
resattr ring_color
resattr ring_display
resattr selected
resattr session
resattr ss_id
resattr ss_type
resattr standard_aa_name
resattr structure
resattr sym_chi1
resattr sym_chi2
resattr sym_chi3
resattr sym_chi4
resattr thin_rings
> color byattribute area
4621 atoms, 969 residues, 1 surfaces, atom area range -2.84e-14 to 75.8
> ui mousemode right zoom
> lighting soft
> show cartoons
> hide cartoons
> show cartoons
> help mmaker
> matchmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3fe4, chain B (#1) with 5cjf, chain A (#2), sequence alignment
score = 635.5
RMSD between 187 pruned atom pairs is 0.915 angstroms; (across all 237 pairs:
2.791)
> hide surfaces
> focus
Unknown command: focus
> mlp
Map values for surface "3fe4_B SES surface": minimum -28.61, mean -4.916,
maximum 24.44
Map values for surface "5cjf_A SES surface": minimum -26.33, mean -5.584,
maximum 22.67
> ui mousemode right translate
> hide surfaces
> lighting soft
> preset "initial styles" "original look"
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> lighting simple
> lighting soft
> lighting full
> lighting soft
> lighting simple
> help color
> color electrostatic
Missing or invalid "surfaces" argument: empty atom specifier
> show surfaces
> color electrostatic
Missing or invalid "surfaces" argument: empty atom specifier
> color electrostatic #2
Missing required "map" argument
> hide #2
> info atomattr
atomattr alt_loc
atomattr alt_locs
atomattr aniso_u
atomattr aniso_u6
atomattr area
atomattr atomspec
atomattr bfactor
atomattr bonds
atomattr color
atomattr coord
atomattr coord_index
atomattr cpp_pointer
atomattr default_radius
atomattr deleted
atomattr display
atomattr display_radius
atomattr draw_mode
atomattr element
atomattr has_custom_attrs
atomattr hide
atomattr idatm_type
atomattr is_ribose
atomattr is_side_chain
atomattr is_side_connector
atomattr is_side_only
atomattr name
atomattr neighbors
atomattr num_alt_locs
atomattr num_bonds
atomattr num_explicit_bonds
atomattr occupancy
atomattr pb_coord
atomattr pb_scene_coord
atomattr radius
atomattr residue
atomattr ribbon_coord
atomattr scene_coord
atomattr selected
atomattr serial_number
atomattr session
atomattr structure
atomattr structure_category
atomattr visible
> color byattribute r:area
4621 atoms, 969 residues, 2 surfaces, atom area range -1.42e-13 to 194
> help list
> info residues #1 attribute area
residue id #1/B:33 area 94.34386434995173 index 13
residue id #1/B:34 area 74.18366370112018 index 14
residue id #1/B:35 area 77.88443577973806 index 15
residue id #1/B:36 area 61.17079768925262 index 16
residue id #1/B:37 area 141.6763844460634 index 17
residue id #1/B:38 area 142.88181753807652 index 18
residue id #1/B:39 area 91.48760618537254 index 19
residue id #1/B:40 area 113.41865470092557 index 20
residue id #1/B:41 area 35.33062251097273 index 21
residue id #1/B:42 area 7.596227004807886 index 22
residue id #1/B:43 area 49.7004181560805 index 23
residue id #1/B:44 area 26.83974295129471 index 24
residue id #1/B:45 area 109.40815291764649 index 25
residue id #1/B:46 area 83.25550027373205 index 26
residue id #1/B:47 area 5.030085953918999 index 27
residue id #1/B:48 area -5.684341886080802e-14 index 28
residue id #1/B:49 area -1.1368683772161603e-13 index 29
residue id #1/B:50 area 0.22613792897499252 index 30
residue id #1/B:51 area 33.128920013872374 index 31
residue id #1/B:52 area 0.08002342136023799 index 32
residue id #1/B:53 area 82.75927397029321 index 33
residue id #1/B:54 area 129.93194931063715 index 34
residue id #1/B:55 area 134.67868455634937 index 35
residue id #1/B:56 area 89.18872541549811 index 36
residue id #1/B:57 area 22.95843224393228 index 37
residue id #1/B:58 area 127.2474144579092 index 38
residue id #1/B:59 area 89.78250101728736 index 39
residue id #1/B:60 area 34.43665461414203 index 40
residue id #1/B:61 area 101.94967821200719 index 41
residue id #1/B:62 area 87.8152922809759 index 42
residue id #1/B:63 area 26.546601972263986 index 43
residue id #1/B:64 area 71.01872794403754 index 44
residue id #1/B:65 area 28.7457055368601 index 45
residue id #1/B:66 area 7.519260755290986 index 46
residue id #1/B:67 area 87.2707085520421 index 47
residue id #1/B:68 area 35.49498908156387 index 48
residue id #1/B:69 area 89.63200593315636 index 49
residue id #1/B:70 area 20.940073467578046 index 50
residue id #1/B:71 area 3.1704188898343233 index 51
residue id #1/B:72 area 93.35777364638432 index 52
residue id #1/B:73 area 97.45840636779958 index 53
residue id #1/B:74 area 48.814414859293706 index 54
residue id #1/B:75 area 90.95332663733102 index 55
residue id #1/B:76 area 31.463996118386433 index 56
residue id #1/B:77 area 138.42268952411294 index 57
residue id #1/B:78 area 1.5410804435711896 index 58
residue id #1/B:79 area 44.35813992360559 index 59
residue id #1/B:80 area 0.140239149321431 index 60
residue id #1/B:81 area 21.301617167469857 index 61
residue id #1/B:82 area -5.684341886080802e-14 index 62
residue id #1/B:83 area 46.01974507273803 index 63
residue id #1/B:84 area 7.734989002210298 index 64
residue id #1/B:85 area 117.9261198157027 index 65
residue id #1/B:86 area 5.988794784473924 index 66
residue id #1/B:87 area -1.1368683772161603e-13 index 67
residue id #1/B:88 area 45.52179117304429 index 68
residue id #1/B:89 area 0.013501603518989214 index 69
residue id #1/B:90 area 40.67097404530877 index 70
residue id #1/B:91 area 16.739370629907796 index 71
residue id #1/B:92 area 43.90108877723539 index 72
residue id #1/B:93 area 62.759921450726736 index 73
residue id #1/B:94 area 94.51452700495848 index 74
residue id #1/B:95 area 0.03899002746932467 index 75
residue id #1/B:96 area 88.66214395159793 index 76
residue id #1/B:97 area 0.7240141258331647 index 77
residue id #1/B:98 area 40.0498417198817 index 78
residue id #1/B:99 area 12.523077196246632 index 79
residue id #1/B:100 area 69.56492618921459 index 80
residue id #1/B:101 area 120.72681970212585 index 81
residue id #1/B:102 area 44.49190579037236 index 82
residue id #1/B:103 area 31.961975598116027 index 83
residue id #1/B:104 area 45.211617660365945 index 84
residue id #1/B:105 area 7.720187585814784 index 85
residue id #1/B:106 area 12.19445577531188 index 86
residue id #1/B:107 area 1.6788457279054967 index 87
residue id #1/B:108 area 56.30578325377353 index 88
residue id #1/B:109 area 17.727058081217038 index 89
residue id #1/B:110 area 0.015422641400164139 index 90
residue id #1/B:111 area 23.9539051834859 index 91
residue id #1/B:112 area 4.628132756622378 index 92
residue id #1/B:113 area 44.38078892579017 index 93
residue id #1/B:114 area 17.027864747534608 index 94
residue id #1/B:115 area 7.881979009324468 index 95
residue id #1/B:116 area 78.03189450867043 index 96
residue id #1/B:120 area 143.45822508474464 index 100
residue id #1/B:121 area 104.99628369060763 index 101
residue id #1/B:122 area 38.487938747689554 index 102
residue id #1/B:123 area 3.6104252834795716 index 103
residue id #1/B:124 area -5.684341886080802e-14 index 104
residue id #1/B:125 area 11.231678641509092 index 105
residue id #1/B:126 area 0.03791440233243293 index 106
residue id #1/B:127 area 6.650604177441551 index 107
residue id #1/B:128 area 17.884920712233594 index 108
residue id #1/B:129 area 62.63001626602464 index 109
residue id #1/B:130 area 53.463146096354336 index 110
residue id #1/B:131 area 107.14589079889927 index 111
residue id #1/B:132 area 45.87660583153087 index 112
residue id #1/B:133 area 29.23432166395952 index 113
residue id #1/B:134 area 29.16961135271127 index 114
residue id #1/B:135 area 0.6545852845051172 index 115
residue id #1/B:136 area 0.15704392427828395 index 116
residue id #1/B:137 area 0.6321885588678811 index 117
residue id #1/B:138 area 5.017318151916086 index 118
residue id #1/B:139 area 0.02433500828780666 index 119
residue id #1/B:140 area 13.57550061462284 index 120
residue id #1/B:141 area 0.0017694009411997058 index 121
residue id #1/B:142 area 23.01855381912989 index 122
residue id #1/B:143 area 3.229802968511592 index 123
residue id #1/B:144 area 45.50816689974185 index 124
residue id #1/B:145 area 125.08967864018426 index 125
residue id #1/B:146 area 42.94589549583108 index 126
residue id #1/B:147 area 194.47129494839606 index 127
residue id #1/B:148 area 39.92445802799867 index 128
residue id #1/B:149 area 49.65025774125857 index 129
residue id #1/B:150 area 107.72188934389145 index 130
residue id #1/B:151 area 93.55684983776517 index 131
residue id #1/B:152 area -5.684341886080802e-14 index 132
residue id #1/B:153 area 64.27578051488139 index 133
residue id #1/B:154 area 131.24336640135206 index 134
residue id #1/B:155 area 9.026446765298317 index 135
residue id #1/B:156 area 97.31289505925629 index 136
residue id #1/B:157 area 78.62381923085229 index 137
residue id #1/B:158 area -2.842170943040401e-14 index 138
residue id #1/B:159 area 3.9307880700621496 index 139
residue id #1/B:160 area -5.684341886080802e-14 index 140
residue id #1/B:161 area 7.839748020456042 index 141
residue id #1/B:162 area 0.43165629477519474 index 142
residue id #1/B:163 area 0.5558590753523447 index 143
residue id #1/B:164 area 0.5152275293241928 index 144
residue id #1/B:165 area 3.6524107550023217 index 145
residue id #1/B:166 area 0.7522736636297225 index 146
residue id #1/B:167 area 27.098842205044278 index 147
residue id #1/B:168 area 35.71027984381274 index 148
residue id #1/B:169 area 126.11882322541328 index 149
residue id #1/B:170 area 96.63169567621209 index 150
residue id #1/B:171 area 48.91947268248987 index 151
residue id #1/B:172 area 110.07942628896593 index 152
residue id #1/B:173 area 97.87449536316255 index 153
residue id #1/B:174 area 25.73725752157229 index 154
residue id #1/B:175 area 97.19330157864779 index 155
residue id #1/B:176 area 109.67387051724103 index 156
residue id #1/B:177 area 2.2965597660192714 index 157
residue id #1/B:178 area 32.46879668711833 index 158
residue id #1/B:179 area 97.04706479741701 index 159
residue id #1/B:180 area 1.6895718570546592 index 160
residue id #1/B:181 area 11.968857527482584 index 161
residue id #1/B:182 area 78.49464302844223 index 162
residue id #1/B:183 area 50.05178510296413 index 163
residue id #1/B:184 area 1.6084767167472762 index 164
residue id #1/B:185 area 81.67391973112258 index 165
residue id #1/B:186 area 82.43237672404267 index 166
residue id #1/B:187 area -1.4210854715202004e-13 index 167
residue id #1/B:188 area 92.91787057427308 index 168
residue id #1/B:189 area 97.41115406154093 index 169
residue id #1/B:190 area 35.358364536685585 index 170
residue id #1/B:191 area 53.72594885008023 index 171
residue id #1/B:192 area 75.12947784606762 index 172
residue id #1/B:193 area 158.84089645530543 index 173
residue id #1/B:194 area 20.086736795922008 index 174
residue id #1/B:195 area 77.99129952031535 index 175
residue id #1/B:196 area 3.4796463792745556 index 176
residue id #1/B:197 area 112.96161930511707 index 177
residue id #1/B:198 area 25.59236021549235 index 178
residue id #1/B:199 area 14.426322990976445 index 179
residue id #1/B:200 area 18.971998326353585 index 180
residue id #1/B:201 area 0.02073627134598155 index 181
residue id #1/B:202 area 75.58136752986677 index 182
residue id #1/B:203 area 55.126664525181155 index 183
residue id #1/B:204 area 0.14787321020183697 index 184
residue id #1/B:205 area 8.425829477520907 index 185
residue id #1/B:206 area 3.037786520366538 index 186
residue id #1/B:207 area 109.30211629371396 index 187
residue id #1/B:208 area 38.30706468615996 index 188
residue id #1/B:209 area 31.31932924558143 index 189
residue id #1/B:210 area 115.03807648176331 index 190
residue id #1/B:211 area 72.28334416794311 index 191
residue id #1/B:212 area 4.843398766326715 index 192
residue id #1/B:213 area 18.95649091086669 index 193
residue id #1/B:214 area 9.894677251800914 index 194
residue id #1/B:215 area 6.74828033600123 index 195
residue id #1/B:216 area 92.19220922538358 index 196
residue id #1/B:217 area -2.842170943040401e-14 index 197
residue id #1/B:218 area -5.684341886080802e-14 index 198
residue id #1/B:219 area 50.76166177880985 index 199
residue id #1/B:220 area 21.308011830238655 index 200
residue id #1/B:221 area 77.29507136379071 index 201
residue id #1/B:222 area 34.40010651846123 index 202
residue id #1/B:223 area 71.76788830315255 index 203
residue id #1/B:224 area -4.263256414560601e-14 index 204
residue id #1/B:225 area 34.81356584044538 index 205
residue id #1/B:226 area 46.330620057360505 index 206
residue id #1/B:227 area 11.447314171236044 index 207
residue id #1/B:228 area 2.9033675050789327 index 208
residue id #1/B:229 area 30.888816056492033 index 209
residue id #1/B:230 area 7.282139357962308 index 210
residue id #1/B:231 area 5.9638974601042065 index 211
residue id #1/B:232 area 1.131193370967253 index 212
residue id #1/B:233 area 1.8770227124365846 index 213
residue id #1/B:234 area 33.08225756816317 index 214
residue id #1/B:235 area 52.17533694867929 index 215
residue id #1/B:236 area 65.77152153196604 index 216
residue id #1/B:237 area 2.762432147628971 index 217
residue id #1/B:238 area 115.89796396284895 index 218
residue id #1/B:239 area 4.672202099049699 index 219
residue id #1/B:240 area 13.162155392672574 index 220
residue id #1/B:241 area 149.2556466982108 index 221
residue id #1/B:242 area 79.59784090612158 index 222
residue id #1/B:243 area 5.075042366623364 index 223
residue id #1/B:244 area 11.373123079977901 index 224
residue id #1/B:245 area 152.05913452181414 index 225
residue id #1/B:246 area 85.68610775320519 index 226
residue id #1/B:247 area 3.808319330287077 index 227
residue id #1/B:248 area 24.553020904342134 index 228
residue id #1/B:249 area 62.96718603913125 index 229
residue id #1/B:250 area 24.558936686077004 index 230
residue id #1/B:251 area 1.6703225026085562 index 231
residue id #1/B:252 area 27.730946126078038 index 232
residue id #1/B:253 area 37.36049804253537 index 233
residue id #1/B:254 area 148.29004373093937 index 234
residue id #1/B:255 area 86.46973477118931 index 235
residue id #1/B:256 area 99.68240375705935 index 236
residue id #1/B:257 area 49.488514488071786 index 237
residue id #1/B:258 area 48.07439590142826 index 238
residue id #1/B:259 area 8.137462975015694 index 239
residue id #1/B:260 area 97.75233830475723 index 240
residue id #1/B:261 area 68.32433132215206 index 241
residue id #1/B:262 area 103.19074364872591 index 242
residue id #1/B:263 area 79.14474195637841 index 243
residue id #1/B:264 area 30.015542860601855 index 244
residue id #1/B:265 area 164.1907131159213 index 245
residue id #1/B:266 area 43.83520240864074 index 246
residue id #1/B:267 area 32.84440845083702 index 247
residue id #1/B:268 area 89.29060095463939 index 248
residue id #1/B:269 area 41.124714153573265 index 249
residue id #1/B:270 area 71.13006309335131 index 250
residue id #1/B:271 area 179.56655788142584 index 251
residue id #1/B:272 area 29.342234159311886 index 252
residue id #1/B:273 area 66.7178235785266 index 253
residue id #1/B:274 area 3.9738679525651577 index 254
residue id #1/B:275 area 31.43550449619525 index 255
residue id #1/B:276 area 2.462695054910313 index 256
residue id #1/B:277 area 21.254410389723304 index 257
residue id #1/B:278 area 43.89813264487772 index 258
residue id #1/B:279 area 87.68493246729994 index 259
residue id #1/B:280 area 185.29171113641758 index 260
> hide surfaces
> info resattr
resattr area
resattr atoms
resattr atomspec
resattr center
resattr chain
resattr chain_id
resattr chi1
resattr chi2
resattr chi3
resattr chi4
resattr cpp_pointer
resattr deleted
resattr description
resattr has_custom_attrs
resattr insertion_code
resattr is_helix
resattr is_strand
resattr label_one_letter_code
resattr label_specifier
resattr mmcif_chain_id
resattr name
resattr neighbors
resattr num_atoms
resattr number
resattr omega
resattr one_letter_code
resattr phi
resattr polymer_type
resattr principal_atom
resattr psi
resattr ribbon_adjust
resattr ribbon_color
resattr ribbon_display
resattr ribbon_hide_backbone
resattr ring_color
resattr ring_display
resattr selected
resattr session
resattr ss_id
resattr ss_type
resattr standard_aa_name
resattr structure
resattr sym_chi1
resattr sym_chi2
resattr sym_chi3
resattr sym_chi4
resattr thin_rings
> ui mousemode right zoom
> help ribbon
> cartoon style #1 xzection oval
Expected a keyword
> cartoon style #1 xsection oval
> hide #2
> cartoon hide #2
> cartoon style #1 xsection barbell
> cartoon style #1 xsection oval
> cartoon style #1 xsection modehelix wrap
Invalid "xsection" argument: Should be one of 'barbell', 'oval', 'piping',
'rectangle', 'round', or 'square'
> cartoon style #1 modeHelix wrap
> cartoon style #1 modeHelix tube
> cartoon style #1 modeHelix wrap
> cartoon style #1 modeHelix default
> cartoon style #1 modeHelix wrap
> cartoon style #1 modeHelix default
> alias licorice car style protein modeh default arrows f xsect oval width 1
> thick 1
> licorice
> cartoon style
3fe4 #1
\- helix mode=default xsection=round width=1 height=1 arrow=False arrow
scale=2
\- strand mode=default xsection=round width=1 height=1 arrow=False arrow
scale=2
\- coil xsection=round width=1 height=1
\- nucleic xsection=square width=0.4 height=2
\- divisions=20
\- oval parameters: sides=12
\- barbell parameters: sides=18 scale=0.5
5cjf #2
\- helix mode=default xsection=round width=1 height=1 arrow=False arrow
scale=2
\- strand mode=default xsection=round width=1 height=1 arrow=False arrow
scale=2
\- coil xsection=round width=1 height=1
\- nucleic xsection=square width=0.4 height=2
\- divisions=20
\- oval parameters: sides=12
\- barbell parameters: sides=18 scale=0.5
> tether #1
Unknown command: tether #1
> cartoon tether #1
3fe4 #1
\- scales 1.0
\- shapes cone
\- sides 4
\- opacity 0.5
> alias reset car style protein modeh default arrows t xsect oval width 2.0
> thick 0.4
> reset
> ui tool show "Color Actions"
> color list
No custom colors.
248 builtin colors: alice blue
, aliceblue
, antique white
, antiquewhite
, aqua
, aquamarine
, azure
, beige
, bisque
, black
, blanched almond
, blanchedalmond
, blue
, blue violet
, blueviolet
, brown
, burly wood
, burlywood
, cadet blue
, cadetblue
, chartreuse
, chocolate
, coral
, cornflower blue
, cornflowerblue
, cornsilk
, crimson
, cyan
, dark blue
, dark cyan
, dark goldenrod
, dark gray
, dark green
, dark grey
, dark khaki
, dark magenta
, dark olive green
, dark orange
, dark orchid
, dark red
, dark salmon
, dark sea green
, dark seagreen
, dark slate blue
, dark slate gray
, dark slate grey
, dark turquoise
, dark violet
, darkblue
, darkcyan
, darkgoldenrod
, darkgray
, darkgreen
, darkgrey
, darkkhaki
, darkmagenta
, darkolivegreen
, darkorange
, darkorchid
, darkred
, darksalmon
, darkseagreen
, darkslateblue
, darkslategray
, darkslategrey
, darkturquoise
, darkviolet
, deep pink
, deep sky blue
, deep skyblue
, deeppink
, deepskyblue
, dim gray
, dim grey
, dimgray
, dimgrey
, dodger blue
, dodgerblue
, fire brick
, firebrick
, floral white
, floralwhite
, forest green
, forestgreen
, fuchsia
, gainsboro
, ghost white
, ghostwhite
, gold
, goldenrod
, gray
, green
, green yellow
, greenyellow
, grey
, honeydew
, hot pink
, hotpink
, indian red
, indianred
, indigo
, ivory
, khaki
, lavender
, lavender blush
, lavenderblush
, lawn green
, lawngreen
, lemon chiffon
, lemonchiffon
, light blue
, light coral
, light cyan
, light goldenrod yellow
, light gray
, light green
, light grey
, light pink
, light salmon
, light sea green
, light seagreen
, light sky blue
, light skyblue
, light slate gray
, light slate grey
, light steel blue
, light yellow
, lightblue
, lightcoral
, lightcyan
, lightgoldenrodyellow
, lightgray
, lightgreen
, lightgrey
, lightpink
, lightsalmon
, lightseagreen
, lightskyblue
, lightslategray
, lightslategrey
, lightsteelblue
, lightyellow
, lime
, lime green
, limegreen
, linen
, magenta
, maroon
, medium aquamarine
, medium blue
, medium orchid
, medium purple
, medium sea green
, medium seagreen
, medium slate blue
, medium spring green
, medium turquoise
, medium violet red
, mediumaquamarine
, mediumblue
, mediumorchid
, mediumpurple
, mediumseagreen
, mediumslateblue
, mediumspringgreen
, mediumturquoise
, mediumvioletred
, midnight blue
, midnightblue
, mint cream
, mintcream
, misty rose
, mistyrose
, moccasin
, navajo white
, navajowhite
, navy
, old lace
, oldlace
, olive
, olive drab
, olivedrab
, orange
, orange red
, orangered
, orchid
, pale goldenrod
, pale green
, pale turquoise
, pale violet red
, palegoldenrod
, palegreen
, paleturquoise
, palevioletred
, papaya whip
, papayawhip
, peach puff
, peachpuff
, peru
, pink
, plum
, powder blue
, powderblue
, purple
, rebecca purple
, rebeccapurple
, red
, rosy brown
, rosybrown
, royal blue
, royalblue
, saddle brown
, saddlebrown
, salmon
, sandy brown
, sandybrown
, sea green
, seagreen
, seashell
, sienna
, silver
, sky blue
, skyblue
, slate blue
, slate gray
, slate grey
, slateblue
, slategray
, slategrey
, snow
, spring green
, springgreen
, steel blue
, steelblue
, tan
, teal
, thistle
, tomato
, transparent
, turquoise
, violet
, wheat
, white
, white smoke
, whitesmoke
, yellow
, yellow green
, and yellowgreen
.
> mlp #1
Map values for surface "3fe4_B SES surface": minimum -28.61, mean -4.916,
maximum 24.44
Fetching compressed palette marooncyan from
http://www.colourlovers.com/api/palettes?keywords=marooncyan&format=json&numResults=100
Could not find palette marooncyan at COLOURlovers.com using keyword search
> mlp #1 palette cyanmaroon
Map values for surface "3fe4_B SES surface": minimum -28.61, mean -4.916,
maximum 24.44
> help turn
> help measure
> transparency 50
> help bgcolor
No help found for 'bgcolor'
> help color
> tile
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 258, in execute
cmd.run(cmd_text)
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\std_commands\tile.py", line 27, in tile
spacing = max([m.bounds().radius() for m in models]) * spacing_factor
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\std_commands\tile.py", line 27, in <listcomp>
spacing = max([m.bounds().radius() for m in models]) * spacing_factor
AttributeError: 'NoneType' object has no attribute 'radius'
AttributeError: 'NoneType' object has no attribute 'radius'
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\std_commands\tile.py", line 27, in
spacing = max([m.bounds().radius() for m in models]) * spacing_factor
See log for complete Python traceback.
> tile #1-2
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 258, in execute
cmd.run(cmd_text)
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\std_commands\tile.py", line 27, in tile
spacing = max([m.bounds().radius() for m in models]) * spacing_factor
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\std_commands\tile.py", line 27, in <listcomp>
spacing = max([m.bounds().radius() for m in models]) * spacing_factor
AttributeError: 'NoneType' object has no attribute 'radius'
AttributeError: 'NoneType' object has no attribute 'radius'
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\std_commands\tile.py", line 27, in
spacing = max([m.bounds().radius() for m in models]) * spacing_factor
See log for complete Python traceback.
> show cartoons
> help tile
> tile #1-2 columns 2
> tile #1-2
> tile #1-2 columns 2
> turn y #1
Expected a number or a keyword
> turn y models #1
> turn y -90 models #1
> help cofr
> matchmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3fe4, chain B (#1) with 5cjf, chain A (#2), sequence alignment
score = 635.5
RMSD between 187 pruned atom pairs is 0.915 angstroms; (across all 237 pairs:
2.791)
> tile
> tile #1-2 columns 2
> cofr #1
> turn y #1
Expected a number or a keyword
> turn y models #1
> turn y models #1
> turn y models #1
> turn y models #1
> turn y models #1
> turn y models #1
> turn y models #1
> turn y models #1
> turn y models #1
> turn y models #1
> turn y models #1
> turn y models #1
> turn y models #1
> turn y models #1
> turn y models #1
> cofr #2
> turn y models #2
> turn y models #2
> select #2/A:4
10 atoms, 10 bonds, 1 model selected
> select #1/B:271@CE1
1 atom, 1 model selected
> cofr #1
> turn y 1 models #1
> cofr #1
> turn y 1 models #1
> cofr #1
> turn y 1 models #1
> wait
wait requires a frame count argument unless motion is in progress
> cofr #1
> turn y 1 90 models #1
> wait
> cofr #1
> turn y 1 90 models #1
> wait
> cofr #2
> turn y 1 90 models #2
> (cofr #1; turn y 1 models #1; cofr #2; turn y 1 models #2) 90
Unknown command: (cofr #1; turn y 1 models #1; cofr #2; turn y 1 models #2) 90
> (cofr #1; turn y 1 models #1; cofr #2; turn y 1 models #2)
Unknown command: (cofr #1; turn y 1 models #1; cofr #2; turn y 1 models #2)
> cofr #1
> turn y 1 models #1
> cofr #2
> turn y 1 models #2
> cofr #1
> turn y 1 models #1
> cofr #2
> turn y 1 models #2
> cofr #1
> turn y 1 models #1
> cofr #2
> turn y 1 models #2
> cofr #1
> turn y 1 models #1
> cofr #2
> turn y 1 models #2
> cofr #1
> turn y 1 models #1
> cofr #2
> turn y 1 models #2
> cofr #1
> turn y 1 models #1
> cofr #2
> turn y 1 models #2
> cofr #1
> turn y 1 models #1
> cofr #2
> turn y 1 models #2
> cofr #1
> turn y 1 models #1
> cofr #2
> turn y 1 models #2
> cofr #1
> turn y 1 models #1
> cofr #2
> turn y 1 models #2
> cofr #1
> turn y 1 models #1
> cofr #2
> turn y 1 models #2
> cofr #1
> turn y 1 models #1
> cofr #2
> turn y 1 models #2
> cofr #1
> turn y 1 models #1
> cofr #2
> turn y 1 models #2
> cofr #1
> turn y 1 models #1
> cofr #2
> turn y 1 models #2
> cofr #1
> turn y 1 models #1
> cofr #2
> turn y 1 models #2
> cofr #1
> turn y 1 models #1
> cofr #2
> turn y 1 models #2
> cofr #1
> turn y 1 models #1
> cofr #2
> turn y 1 models #2
> cofr #1
> turn y 1 models #1
> cofr #2
> turn y 1 models #2
> cofr #1
> turn y 1 models #1
> cofr #2
> turn y 1 models #2
> cofr #1
> turn y 1 models #1
> cofr #2
> turn y 1 models #2
> cofr #1
> turn y 1 models #1
> cofr #2
> turn y 1 models #2
> cofr #1
> turn y 1 models #1
> cofr #2
> turn y 1 models #2
> cofr #1
> turn y 1 models #1
> cofr #2
> turn y 1 models #2
> cofr #1
> turn y 1 models #1
> cofr #2
> turn y 1 models #2
> cofr #1
> turn y 3 models #1
> cofr #2
> turn y 3 models #2
> cofr #1
> turn y 3 models #1
> cofr #2
> turn y 3 models #2
> cofr #1
> turn y 3 models #1
> cofr #2
> turn y 3 models #2
> cofr #1
> turn y 3 models #1
> cofr #2
> turn y 3 models #2
> cofr #1
> turn y 3 models #1
> cofr #2
> turn y 3 models #2
> cofr #1
> turn y 3 models #1
> cofr #2
> turn y 3 models #2
> cofr #1
> turn y 3 models #1
> cofr #2
> turn y 3 models #2
> cofr #1
> turn y 3 models #1
> cofr #2
> turn y 3 models #2
> cofr #1
> turn y 3 models #1
> cofr #2
> turn y 3 models #2
> cofr #1
> turn y 3 models #1
> cofr #2
> turn y 3 models #2
> cofr #1
> turn y 3 models #1
> cofr #2
> turn y 3 models #2
> cofr #1
> turn y 3 models #1
> cofr #2
> turn y 3 models #2
> cofr #1
> turn y 3 models #1
> cofr #2
> turn y 3 models #2
> cofr #1
> turn y 3 models #1
> cofr #2
> turn y 3 models #2
> cofr #1
> turn y 3 models #1
> cofr #2
> turn y 3 models #2
> cofr #1
> turn y 3 models #1
> cofr #2
> turn y 3 models #2
> cofr #1
> turn y 3 models #1
> cofr #2
> turn y 3 models #2
> cofr #1
> turn y 3 models #1
> cofr #2
> turn y 3 models #2
> cofr #1
> turn y 3 models #1
> cofr #2
> turn y 3 models #2
> cofr #1
> turn y 3 models #1
> cofr #2
> turn y 3 models #2
> cofr #1
> turn y 3 models #1
> cofr #2
> turn y 3 models #2
> cofr #1
> turn y 3 models #1
> cofr #2
> turn y 3 models #2
> cofr #1
> turn y 3 models #1
> cofr #2
> turn y 3 models #2
> cofr #1
> turn y 3 models #1
> cofr #2
> turn y 3 models #2
> cofr #1
> turn y 3 models #1
> cofr #2
> turn y 3 models #2
> cofr #1
> turn y 3 models #1
> cofr #2
> turn y 3 models #2
> cofr #1
> turn y 3 models #1
> cofr #2
> turn y 3 models #2
> cofr #1
> turn y 3 models #1
> cofr #2
> turn y 3 models #2
> cofr #1
> turn y 3 models #1
> cofr #2
> turn y 3 models #2
> hide sel cartoons
> show sel cartoons
> select clear
> show cartoons
> hide cartoons
> ~tile
Unknown command: ~tile
> tile columns 1
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 258, in execute
cmd.run(cmd_text)
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\std_commands\tile.py", line 27, in tile
spacing = max([m.bounds().radius() for m in models]) * spacing_factor
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\std_commands\tile.py", line 27, in <listcomp>
spacing = max([m.bounds().radius() for m in models]) * spacing_factor
AttributeError: 'NoneType' object has no attribute 'radius'
AttributeError: 'NoneType' object has no attribute 'radius'
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\std_commands\tile.py", line 27, in
spacing = max([m.bounds().radius() for m in models]) * spacing_factor
See log for complete Python traceback.
> show cartoons
> show cartoons
> hide cartoons
> tile #1-2 columns 1
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 258, in execute
cmd.run(cmd_text)
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\std_commands\tile.py", line 27, in tile
spacing = max([m.bounds().radius() for m in models]) * spacing_factor
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\std_commands\tile.py", line 27, in <listcomp>
spacing = max([m.bounds().radius() for m in models]) * spacing_factor
AttributeError: 'NoneType' object has no attribute 'radius'
AttributeError: 'NoneType' object has no attribute 'radius'
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\std_commands\tile.py", line 27, in
spacing = max([m.bounds().radius() for m in models]) * spacing_factor
See log for complete Python traceback.
> show cartoons
> show cartoons
> hide cartoons
> undo
> undo
> undo
> undo
> undo
> undo
> undo
> undo
> undo
> undo
> undo
No undo action is available
> undo
No undo action is available
> undo
No undo action is available
> undo
No undo action is available
> undo
No undo action is available
> undo
No undo action is available
> undo
No undo action is available
> undo
No undo action is available
> matchmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3fe4, chain B (#1) with 5cjf, chain A (#2), sequence alignment
score = 635.5
RMSD between 187 pruned atom pairs is 0.915 angstroms; (across all 237 pairs:
2.791)
> turn
> turn y -90
> cofr #1-2
> turn
> turn
> turn
> turn
> turn
> turn
> ~ribbon #2
> tile
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 258, in execute
cmd.run(cmd_text)
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\std_commands\tile.py", line 27, in tile
spacing = max([m.bounds().radius() for m in models]) * spacing_factor
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\std_commands\tile.py", line 27, in <listcomp>
spacing = max([m.bounds().radius() for m in models]) * spacing_factor
AttributeError: 'NoneType' object has no attribute 'radius'
AttributeError: 'NoneType' object has no attribute 'radius'
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\std_commands\tile.py", line 27, in
spacing = max([m.bounds().radius() for m in models]) * spacing_factor
See log for complete Python traceback.
> select clear
> show cartoons
> ~ribbon #2
> tile
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 258, in execute
cmd.run(cmd_text)
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\std_commands\tile.py", line 27, in tile
spacing = max([m.bounds().radius() for m in models]) * spacing_factor
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\std_commands\tile.py", line 27, in <listcomp>
spacing = max([m.bounds().radius() for m in models]) * spacing_factor
AttributeError: 'NoneType' object has no attribute 'radius'
AttributeError: 'NoneType' object has no attribute 'radius'
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\std_commands\tile.py", line 27, in
spacing = max([m.bounds().radius() for m in models]) * spacing_factor
See log for complete Python traceback.
> show cartoons
> tile
> undo
> ~ribbon #2
> tile columns =2
Invalid "columns" argument: Expected an integer
> tile columns 2
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 258, in execute
cmd.run(cmd_text)
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\std_commands\tile.py", line 27, in tile
spacing = max([m.bounds().radius() for m in models]) * spacing_factor
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\std_commands\tile.py", line 27, in <listcomp>
spacing = max([m.bounds().radius() for m in models]) * spacing_factor
AttributeError: 'NoneType' object has no attribute 'radius'
AttributeError: 'NoneType' object has no attribute 'radius'
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\std_commands\tile.py", line 27, in
spacing = max([m.bounds().radius() for m in models]) * spacing_factor
See log for complete Python traceback.
> show cartoons
> show cartoons
> hide cartoons
> show cartoons
> ~ribbon #2
Alignment identifier is 1.B
Alignment identifier is 2.A
> help findclash
No help found for 'findclash'
> ui tool show Clashes
> help clash
> help info
> help defattr
No help found for 'defattr'
> help list
> help define
No help found for 'define'
> ui tool show Contacts
> help ui
> transparency 30
> transparency 10
> help transparency
> functionkey F1 mousemode right 'rotate selected models'
> functionkey F1 mousemode right 'zoom'
> functionkey F2 mousemode right 'translate selected models'
> mousemode rightMode "translate selected models"
> mousemode rightMode zoom
> mousemode rightMode "translate selected models"
> select :233
17 atoms, 15 bonds, 2 models selected
> 237
Unknown command: 237
> 212
Unknown command: 212
> 112
Unknown command: 112
> 231
Unknown command: 231
> 227
Unknown command: 227
> 277
Unknown command: 277
> 171
Unknown command: 171
> 149
Unknown command: 149
> 266
Unknown command: 266
> 101
Unknown command: 101
> tile
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 258, in execute
cmd.run(cmd_text)
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\std_commands\tile.py", line 27, in tile
spacing = max([m.bounds().radius() for m in models]) * spacing_factor
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\std_commands\tile.py", line 27, in <listcomp>
spacing = max([m.bounds().radius() for m in models]) * spacing_factor
AttributeError: 'NoneType' object has no attribute 'radius'
AttributeError: 'NoneType' object has no attribute 'radius'
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\std_commands\tile.py", line 27, in
spacing = max([m.bounds().radius() for m in models]) * spacing_factor
See log for complete Python traceback.
> tile #1-2
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 258, in execute
cmd.run(cmd_text)
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\std_commands\tile.py", line 27, in tile
spacing = max([m.bounds().radius() for m in models]) * spacing_factor
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\std_commands\tile.py", line 27, in <listcomp>
spacing = max([m.bounds().radius() for m in models]) * spacing_factor
AttributeError: 'NoneType' object has no attribute 'radius'
AttributeError: 'NoneType' object has no attribute 'radius'
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\std_commands\tile.py", line 27, in
spacing = max([m.bounds().radius() for m in models]) * spacing_factor
See log for complete Python traceback.
> save "C:/Users/meetol/Documents/opetus/Structural Bioinformatics/chimera
> tests/tiling fails.cxs"
opened ChimeraX session
> tile #1-2
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 258, in execute
cmd.run(cmd_text)
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/std_commands/tile.py", line 27, in tile
spacing = max([m.bounds().radius() for m in models]) * spacing_factor
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/std_commands/tile.py", line 27, in <listcomp>
spacing = max([m.bounds().radius() for m in models]) * spacing_factor
AttributeError: 'NoneType' object has no attribute 'radius'
AttributeError: 'NoneType' object has no attribute 'radius'
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/std_commands/tile.py", line 27, in
spacing = max([m.bounds().radius() for m in models]) * spacing_factor
See log for complete Python traceback.
OpenGL version: 4.1 INTEL-12.10.16
OpenGL renderer: Intel(R) Iris(TM) Pro Graphics 6200
OpenGL vendor: Intel Inc.Hardware:
Hardware Overview:
Model Name: iMac
Model Identifier: iMac16,2
Processor Name: Intel Core i5
Processor Speed: 2.8 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 256 KB
L3 Cache: 4 MB
Memory: 16 GB
Boot ROM Version: 232.0.0.0.0
SMC Version (system): 2.32f20
Software:
System Software Overview:
System Version: macOS 10.14.6 (18G3020)
Kernel Version: Darwin 18.7.0
Time since boot: 10:05
Graphics/Displays:
Intel Iris Pro Graphics 6200:
Chipset Model: Intel Iris Pro Graphics 6200
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x1622
Revision ID: 0x000a
Metal: Supported, feature set macOS GPUFamily1 v4
Displays:
iMac:
Display Type: LCD
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Automatically Adjust Brightness: No
Connection Type: DisplayPort
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.8
File attachment: tiling fails.cxs
Attachments (1)
Change History (3)
by , 5 years ago
| Attachment: | tiling fails.cxs added |
|---|
comment:1 by , 5 years ago
| Component: | Unassigned → Structure Comparison |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
Additional info from emails:
Tiling of two models fails in ChimeraX 1.0 if one of the models to be tiled does not have a visible representation. (I did not try this with more than two.)
By "no visible representation", I mean one that has no atoms/bonds, cartoon or surface representation visible. The way I read the error message would indicate that problem is zero size of one object when spacing is figured out. I attach a session file to reproduce this. In addition to the error message, #2 remains in its superimposed starting position if I try tiling when it's invisible. If I display a ribbon or a surface of #2, tiling works fine.
comment:2 by , 5 years ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
Fixed in 04ec502b1.
Only models that are displayed (have bounding boxes) are tiled now.
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