Opened 3 days ago
Closed 11 hours ago
#19449 closed defect (limitation)
KVFinder on old MacOS
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Surface/Binding Analysis | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-12.7.6-x86_64-i386-64bit
ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 UTC)
Description
Replace this text with list of actions that caused this problem to occur
Log:
UCSF ChimeraX version: 1.10.1 (2025-07-24)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 9f33
9f33 title:
Cryo-EM structure of Dopamine 3 Receptor:Go complex bound to bitopic FOB02-04A
- Conformation A [more info...]
Chain information for 9f33 #1
---
Chain | Description | UniProt
A | Guanine nucleotide-binding protein G(o) subunit alpha | GNAO_HUMAN 1-354
B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | GBB1_RAT 2-340
C | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | GBG2_HUMAN 1-71
E | Antibody scFv16 |
R | Green fluorescent protein,D(3) dopamine receptor | GFP_AEQVI -243--7, DRD3_HUMAN 4-400
Non-standard residues in 9f33 #1
---
A1H9N — N-[2-[(1R,2S)-2-[[(2S,5S)-2-(6-azanylpyridin-3-yl)-5-methyl-
morpholin-4-yl]methyl]cyclopropyl]ethyl]-1H-indole-2-carboxamide
8 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> show #1 atoms
> info models
model id #1 type AtomicStructure name 9f33
model id #1.1 type PseudobondGroup name "missing structure"
> delete #1.1
[Repeated 1 time(s)]
> show #1 atoms
> cartoon #1
> style #1 cartoon
Expected a keyword
> hide spheres
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> style #1 stick
Changed 8658 atom styles
> hide stick
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> list
Unknown command: modelcif list
> models list
Unknown command: models list
> undo
[Repeated 2 time(s)]
> style #1 stick
Changed 8658 atom styles
> info models
model id #1 type AtomicStructure name 9f33
model id #1.1 type PseudobondGroup name "missing structure"
> show #1
> info chains #1
chain id /A chain_id A
chain id /B chain_id B
chain id /C chain_id C
chain id /E chain_id E
chain id /R chain_id R
> name #1 receptor_9f33
"receptor_9f33": invalid atom specifier
> name #1 receptor_9f33
"receptor_9f33": invalid atom specifier
> rename #1 id 10
> rename #1 model 10
Expected a keyword
> ui tool show "Model Panel"
> style #10 cartoon
Expected a keyword
> cartoon #10
> reset
Unknown command: ui reset
> tool show "Model Panel"
> ui tool show "Model Panel"
> ui tool show "Show Sequence Viewer"
> modelpanel update
Unknown command: modelpanel update
> tool new modelpanel
> new modelpanel
Unknown command: ui tool new modelpanel
> ui tool show "Show Sequence Viewer"
> sequence chain /R
Alignment identifier is 10/R
> select /R:30-57,62-92,99-139,142-170,185-223,324-354,361-384,387-398
1854 atoms, 1893 bonds, 235 residues, 1 model selected
> hide #10 & ~:/R
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide #10/A
> hide #10/B
> hide #10/C
> hide #10/E
> select #10 & ~:/R
Expected a keyword
> hide #10
> hide #!10 models
> show #!10 models
> hide #10.1 models
> show #10.1 models
> hide #10.1 models
> show #10.1 models
> hide #10.1 models
> show #10.1 models
> hide #10.1 models
> show #10.1 models
> hide #!10 models
> show #!10 models
> info chains #10
chain id /A chain_id A
chain id /B chain_id B
chain id /C chain_id C
chain id /E chain_id E
chain id /R chain_id R
> info models
model id #10 type AtomicStructure name 9f33
model id #10.1 type PseudobondGroup name "missing structure"
> close #*
> open 9f33
9f33 title:
Cryo-EM structure of Dopamine 3 Receptor:Go complex bound to bitopic FOB02-04A
- Conformation A [more info...]
Chain information for 9f33 #1
---
Chain | Description | UniProt
A | Guanine nucleotide-binding protein G(o) subunit alpha | GNAO_HUMAN 1-354
B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | GBB1_RAT 2-340
C | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | GBG2_HUMAN 1-71
E | Antibody scFv16 |
R | Green fluorescent protein,D(3) dopamine receptor | GFP_AEQVI -243--7, DRD3_HUMAN 4-400
Non-standard residues in 9f33 #1
---
A1H9N — N-[2-[(1R,2S)-2-[[(2S,5S)-2-(6-azanylpyridin-3-yl)-5-methyl-
morpholin-4-yl]methyl]cyclopropyl]ethyl]-1H-indole-2-carboxamide
8 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> hide #!1 models
> show #1/R
> show #!1 models
> hide #1
> show #1/R
> cartoon #1/R
> style #1/R cartoon
Expected a keyword
> cartoon #1
> ~display #1
> display #1
> ~display #1
> hide #1
> ~display #1/R
> cartoon #1/R
> ~atoms
Unknown command: ~atoms
> hide #1 & ~:/R
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide #1
> delete #1/A
> delete #1/B
> delete #1/C
> delete #1/E
> hide #1.1 models
> show #1.1 models
> hide atoms
> show cartoons
> show atoms
[Repeated 1 time(s)]
> hide atoms
> hide cartoons
> show cartoons
> ui tool show "Show Sequence Viewer"
> sequence chain /R
Alignment identifier is 1/R
> show :A1H9N
> open 3pbl
3pbl title:
Structure of the human dopamine D3 receptor in complex with eticlopride [more
info...]
Chain information for 3pbl #2
---
Chain | Description | UniProt
A B | D(3) dopamine receptor, Lysozyme chimera | DRD3_HUMAN 2-221 319-400, LYS_BPT4 1002-1161
Non-standard residues in 3pbl #2
---
ETQ —
3-chloro-5-ethyl-N-{[(2S)-1-ethylpyrrolidin-2-yl]methyl}-6-hydroxy-2-methoxybenzamide
GLC — alpha-D-glucopyranose (alpha-D-glucose; D-glucose; glucose)
3pbl mmCIF Assemblies
---
1| software_defined_assembly
2| software_defined_assembly
> delete #2/B
> select subtract #2.1
Nothing selected
> select add #2.1
Nothing selected
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> info residues #2
residue id #2/A:32 name TYR index 40
residue id #2/A:33 name ALA index 41
residue id #2/A:34 name LEU index 42
residue id #2/A:35 name SER index 43
residue id #2/A:36 name TYR index 44
residue id #2/A:37 name CYS index 45
residue id #2/A:38 name ALA index 46
residue id #2/A:39 name LEU index 47
residue id #2/A:40 name ILE index 48
residue id #2/A:41 name LEU index 49
residue id #2/A:42 name ALA index 50
residue id #2/A:43 name ILE index 51
residue id #2/A:44 name VAL index 52
residue id #2/A:45 name PHE index 53
residue id #2/A:46 name GLY index 54
residue id #2/A:47 name ASN index 55
residue id #2/A:48 name GLY index 56
residue id #2/A:49 name LEU index 57
residue id #2/A:50 name VAL index 58
residue id #2/A:51 name CYS index 59
residue id #2/A:52 name MET index 60
residue id #2/A:53 name ALA index 61
residue id #2/A:54 name VAL index 62
residue id #2/A:55 name LEU index 63
residue id #2/A:56 name LYS index 64
residue id #2/A:57 name GLU index 65
residue id #2/A:58 name ARG index 66
residue id #2/A:59 name ALA index 67
residue id #2/A:60 name LEU index 68
residue id #2/A:61 name GLN index 69
residue id #2/A:62 name THR index 70
residue id #2/A:63 name THR index 71
residue id #2/A:64 name THR index 72
residue id #2/A:65 name ASN index 73
residue id #2/A:66 name TYR index 74
residue id #2/A:67 name LEU index 75
residue id #2/A:68 name VAL index 76
residue id #2/A:69 name VAL index 77
residue id #2/A:70 name SER index 78
residue id #2/A:71 name LEU index 79
residue id #2/A:72 name ALA index 80
residue id #2/A:73 name VAL index 81
residue id #2/A:74 name ALA index 82
residue id #2/A:75 name ASP index 83
residue id #2/A:76 name LEU index 84
residue id #2/A:77 name LEU index 85
residue id #2/A:78 name VAL index 86
residue id #2/A:79 name ALA index 87
residue id #2/A:80 name THR index 88
residue id #2/A:81 name LEU index 89
residue id #2/A:82 name VAL index 90
residue id #2/A:83 name MET index 91
residue id #2/A:84 name PRO index 92
residue id #2/A:85 name TRP index 93
residue id #2/A:86 name VAL index 94
residue id #2/A:87 name VAL index 95
residue id #2/A:88 name TYR index 96
residue id #2/A:89 name LEU index 97
residue id #2/A:90 name GLU index 98
residue id #2/A:91 name VAL index 99
residue id #2/A:92 name THR index 100
residue id #2/A:93 name GLY index 101
residue id #2/A:94 name GLY index 102
residue id #2/A:95 name VAL index 103
residue id #2/A:96 name TRP index 104
residue id #2/A:97 name ASN index 105
residue id #2/A:98 name PHE index 106
residue id #2/A:99 name SER index 107
residue id #2/A:100 name ARG index 108
residue id #2/A:101 name ILE index 109
residue id #2/A:102 name CYS index 110
residue id #2/A:103 name CYS index 111
residue id #2/A:104 name ASP index 112
residue id #2/A:105 name VAL index 113
residue id #2/A:106 name PHE index 114
residue id #2/A:107 name VAL index 115
residue id #2/A:108 name THR index 116
residue id #2/A:109 name LEU index 117
residue id #2/A:110 name ASP index 118
residue id #2/A:111 name VAL index 119
residue id #2/A:112 name MET index 120
residue id #2/A:113 name MET index 121
residue id #2/A:114 name CYS index 122
residue id #2/A:115 name THR index 123
residue id #2/A:116 name ALA index 124
residue id #2/A:117 name SER index 125
residue id #2/A:118 name ILE index 126
residue id #2/A:119 name TRP index 127
residue id #2/A:120 name ASN index 128
residue id #2/A:121 name LEU index 129
residue id #2/A:122 name CYS index 130
residue id #2/A:123 name ALA index 131
residue id #2/A:124 name ILE index 132
residue id #2/A:125 name SER index 133
residue id #2/A:126 name ILE index 134
residue id #2/A:127 name ASP index 135
residue id #2/A:128 name ARG index 136
residue id #2/A:129 name TYR index 137
residue id #2/A:130 name THR index 138
residue id #2/A:131 name ALA index 139
residue id #2/A:132 name VAL index 140
residue id #2/A:133 name VAL index 141
residue id #2/A:134 name MET index 142
residue id #2/A:135 name PRO index 143
residue id #2/A:136 name VAL index 144
residue id #2/A:137 name HIS index 145
residue id #2/A:138 name TYR index 146
residue id #2/A:139 name GLN index 147
residue id #2/A:140 name HIS index 148
residue id #2/A:141 name GLY index 149
residue id #2/A:142 name THR index 150
residue id #2/A:143 name GLY index 151
residue id #2/A:144 name GLN index 152
residue id #2/A:145 name SER index 153
residue id #2/A:146 name SER index 154
residue id #2/A:147 name CYS index 155
residue id #2/A:148 name ARG index 156
residue id #2/A:149 name ARG index 157
residue id #2/A:150 name VAL index 158
residue id #2/A:151 name ALA index 159
residue id #2/A:152 name LEU index 160
residue id #2/A:153 name MET index 161
residue id #2/A:154 name ILE index 162
residue id #2/A:155 name THR index 163
residue id #2/A:156 name ALA index 164
residue id #2/A:157 name VAL index 165
residue id #2/A:158 name TRP index 166
residue id #2/A:159 name VAL index 167
residue id #2/A:160 name LEU index 168
residue id #2/A:161 name ALA index 169
residue id #2/A:162 name PHE index 170
residue id #2/A:163 name ALA index 171
residue id #2/A:164 name VAL index 172
residue id #2/A:165 name SER index 173
residue id #2/A:166 name CYS index 174
residue id #2/A:167 name PRO index 175
residue id #2/A:168 name LEU index 176
residue id #2/A:169 name LEU index 177
residue id #2/A:170 name PHE index 178
residue id #2/A:171 name GLY index 179
residue id #2/A:172 name PHE index 180
residue id #2/A:173 name ASN index 181
residue id #2/A:174 name THR index 182
residue id #2/A:175 name THR index 183
residue id #2/A:176 name GLY index 184
residue id #2/A:177 name ASP index 185
residue id #2/A:178 name PRO index 186
residue id #2/A:179 name THR index 187
residue id #2/A:180 name VAL index 188
residue id #2/A:181 name CYS index 189
residue id #2/A:182 name SER index 190
residue id #2/A:183 name ILE index 191
residue id #2/A:184 name SER index 192
residue id #2/A:185 name ASN index 193
residue id #2/A:186 name PRO index 194
residue id #2/A:187 name ASP index 195
residue id #2/A:188 name PHE index 196
residue id #2/A:189 name VAL index 197
residue id #2/A:190 name ILE index 198
residue id #2/A:191 name TYR index 199
residue id #2/A:192 name SER index 200
residue id #2/A:193 name SER index 201
residue id #2/A:194 name VAL index 202
residue id #2/A:195 name VAL index 203
residue id #2/A:196 name SER index 204
residue id #2/A:197 name PHE index 205
residue id #2/A:198 name TYR index 206
residue id #2/A:199 name LEU index 207
residue id #2/A:200 name PRO index 208
residue id #2/A:201 name PHE index 209
residue id #2/A:202 name GLY index 210
residue id #2/A:203 name VAL index 211
residue id #2/A:204 name THR index 212
residue id #2/A:205 name VAL index 213
residue id #2/A:206 name LEU index 214
residue id #2/A:207 name VAL index 215
residue id #2/A:208 name TYR index 216
residue id #2/A:209 name ALA index 217
residue id #2/A:210 name ARG index 218
residue id #2/A:211 name ILE index 219
residue id #2/A:212 name TYR index 220
residue id #2/A:213 name VAL index 221
residue id #2/A:214 name VAL index 222
residue id #2/A:215 name LEU index 223
residue id #2/A:216 name LYS index 224
residue id #2/A:217 name GLN index 225
residue id #2/A:218 name ARG index 226
residue id #2/A:219 name ARG index 227
residue id #2/A:220 name ARG index 228
residue id #2/A:221 name LYS index 229
residue id #2/A:1002 name ASN index 230
residue id #2/A:1003 name ILE index 231
residue id #2/A:1004 name PHE index 232
residue id #2/A:1005 name GLU index 233
residue id #2/A:1006 name MET index 234
residue id #2/A:1007 name LEU index 235
residue id #2/A:1008 name ARG index 236
residue id #2/A:1009 name ILE index 237
residue id #2/A:1010 name ASP index 238
residue id #2/A:1011 name GLU index 239
residue id #2/A:1012 name GLY index 240
residue id #2/A:1013 name LEU index 241
residue id #2/A:1014 name ARG index 242
residue id #2/A:1015 name LEU index 243
residue id #2/A:1016 name LYS index 244
residue id #2/A:1017 name ILE index 245
residue id #2/A:1018 name TYR index 246
residue id #2/A:1019 name LYS index 247
residue id #2/A:1020 name ASP index 248
residue id #2/A:1021 name THR index 249
residue id #2/A:1022 name GLU index 250
residue id #2/A:1023 name GLY index 251
residue id #2/A:1024 name TYR index 252
residue id #2/A:1025 name TYR index 253
residue id #2/A:1026 name THR index 254
residue id #2/A:1027 name ILE index 255
residue id #2/A:1028 name GLY index 256
residue id #2/A:1029 name ILE index 257
residue id #2/A:1030 name GLY index 258
residue id #2/A:1031 name HIS index 259
residue id #2/A:1032 name LEU index 260
residue id #2/A:1033 name LEU index 261
residue id #2/A:1034 name THR index 262
residue id #2/A:1035 name LYS index 263
residue id #2/A:1036 name SER index 264
residue id #2/A:1037 name PRO index 265
residue id #2/A:1038 name SER index 266
residue id #2/A:1039 name LEU index 267
residue id #2/A:1040 name ASN index 268
residue id #2/A:1041 name ALA index 269
residue id #2/A:1042 name ALA index 270
residue id #2/A:1043 name LYS index 271
residue id #2/A:1044 name SER index 272
residue id #2/A:1045 name GLU index 273
residue id #2/A:1046 name LEU index 274
residue id #2/A:1047 name ASP index 275
residue id #2/A:1048 name LYS index 276
residue id #2/A:1049 name ALA index 277
residue id #2/A:1050 name ILE index 278
residue id #2/A:1051 name GLY index 279
residue id #2/A:1052 name ARG index 280
residue id #2/A:1053 name ASN index 281
residue id #2/A:1054 name THR index 282
residue id #2/A:1055 name ASN index 283
residue id #2/A:1056 name GLY index 284
residue id #2/A:1057 name VAL index 285
residue id #2/A:1058 name ILE index 286
residue id #2/A:1059 name THR index 287
residue id #2/A:1060 name LYS index 288
residue id #2/A:1061 name ASP index 289
residue id #2/A:1062 name GLU index 290
residue id #2/A:1063 name ALA index 291
residue id #2/A:1064 name GLU index 292
residue id #2/A:1065 name LYS index 293
residue id #2/A:1066 name LEU index 294
residue id #2/A:1067 name PHE index 295
residue id #2/A:1068 name ASN index 296
residue id #2/A:1069 name GLN index 297
residue id #2/A:1070 name ASP index 298
residue id #2/A:1071 name VAL index 299
residue id #2/A:1072 name ASP index 300
residue id #2/A:1073 name ALA index 301
residue id #2/A:1074 name ALA index 302
residue id #2/A:1075 name VAL index 303
residue id #2/A:1076 name ARG index 304
residue id #2/A:1077 name GLY index 305
residue id #2/A:1078 name ILE index 306
residue id #2/A:1079 name LEU index 307
residue id #2/A:1080 name ARG index 308
residue id #2/A:1081 name ASN index 309
residue id #2/A:1082 name ALA index 310
residue id #2/A:1083 name LYS index 311
residue id #2/A:1084 name LEU index 312
residue id #2/A:1085 name LYS index 313
residue id #2/A:1086 name PRO index 314
residue id #2/A:1087 name VAL index 315
residue id #2/A:1088 name TYR index 316
residue id #2/A:1089 name ASP index 317
residue id #2/A:1090 name SER index 318
residue id #2/A:1091 name LEU index 319
residue id #2/A:1092 name ASP index 320
residue id #2/A:1093 name ALA index 321
residue id #2/A:1094 name VAL index 322
residue id #2/A:1095 name ARG index 323
residue id #2/A:1096 name ARG index 324
residue id #2/A:1097 name ALA index 325
residue id #2/A:1098 name ALA index 326
residue id #2/A:1099 name LEU index 327
residue id #2/A:1100 name ILE index 328
residue id #2/A:1101 name ASN index 329
residue id #2/A:1102 name MET index 330
residue id #2/A:1103 name VAL index 331
residue id #2/A:1104 name PHE index 332
residue id #2/A:1105 name GLN index 333
residue id #2/A:1106 name MET index 334
residue id #2/A:1107 name GLY index 335
residue id #2/A:1108 name GLU index 336
residue id #2/A:1109 name THR index 337
residue id #2/A:1110 name GLY index 338
residue id #2/A:1111 name VAL index 339
residue id #2/A:1112 name ALA index 340
residue id #2/A:1113 name GLY index 341
residue id #2/A:1114 name PHE index 342
residue id #2/A:1115 name THR index 343
residue id #2/A:1116 name ASN index 344
residue id #2/A:1117 name SER index 345
residue id #2/A:1118 name LEU index 346
residue id #2/A:1119 name ARG index 347
residue id #2/A:1120 name MET index 348
residue id #2/A:1121 name LEU index 349
residue id #2/A:1122 name GLN index 350
residue id #2/A:1123 name GLN index 351
residue id #2/A:1124 name LYS index 352
residue id #2/A:1125 name ARG index 353
residue id #2/A:1126 name TRP index 354
residue id #2/A:1127 name ASP index 355
residue id #2/A:1128 name GLU index 356
residue id #2/A:1129 name ALA index 357
residue id #2/A:1130 name ALA index 358
residue id #2/A:1131 name VAL index 359
residue id #2/A:1132 name ASN index 360
residue id #2/A:1133 name LEU index 361
residue id #2/A:1134 name ALA index 362
residue id #2/A:1135 name LYS index 363
residue id #2/A:1136 name SER index 364
residue id #2/A:1137 name ARG index 365
residue id #2/A:1138 name TRP index 366
residue id #2/A:1139 name TYR index 367
residue id #2/A:1140 name ASN index 368
residue id #2/A:1141 name GLN index 369
residue id #2/A:1142 name THR index 370
residue id #2/A:1143 name PRO index 371
residue id #2/A:1144 name ASN index 372
residue id #2/A:1145 name ARG index 373
residue id #2/A:1146 name ALA index 374
residue id #2/A:1147 name LYS index 375
residue id #2/A:1148 name ARG index 376
residue id #2/A:1149 name VAL index 377
residue id #2/A:1150 name ILE index 378
residue id #2/A:1151 name THR index 379
residue id #2/A:1152 name THR index 380
residue id #2/A:1153 name PHE index 381
residue id #2/A:1154 name ARG index 382
residue id #2/A:1155 name THR index 383
residue id #2/A:1156 name GLY index 384
residue id #2/A:1157 name THR index 385
residue id #2/A:1158 name TRP index 386
residue id #2/A:1159 name ASP index 387
residue id #2/A:1160 name ALA index 388
residue id #2/A:1161 name TYR index 389
residue id #2/A:319 name GLY index 390
residue id #2/A:320 name VAL index 391
residue id #2/A:321 name PRO index 392
residue id #2/A:322 name LEU index 393
residue id #2/A:323 name ARG index 394
residue id #2/A:324 name GLU index 395
residue id #2/A:325 name LYS index 396
residue id #2/A:326 name LYS index 397
residue id #2/A:327 name ALA index 398
residue id #2/A:328 name THR index 399
residue id #2/A:329 name GLN index 400
residue id #2/A:330 name MET index 401
residue id #2/A:331 name VAL index 402
residue id #2/A:332 name ALA index 403
residue id #2/A:333 name ILE index 404
residue id #2/A:334 name VAL index 405
residue id #2/A:335 name LEU index 406
residue id #2/A:336 name GLY index 407
residue id #2/A:337 name ALA index 408
residue id #2/A:338 name PHE index 409
residue id #2/A:339 name ILE index 410
residue id #2/A:340 name VAL index 411
residue id #2/A:341 name CYS index 412
residue id #2/A:342 name TRP index 413
residue id #2/A:343 name LEU index 414
residue id #2/A:344 name PRO index 415
residue id #2/A:345 name PHE index 416
residue id #2/A:346 name PHE index 417
residue id #2/A:347 name LEU index 418
residue id #2/A:348 name THR index 419
residue id #2/A:349 name HIS index 420
residue id #2/A:350 name VAL index 421
residue id #2/A:351 name LEU index 422
residue id #2/A:352 name ASN index 423
residue id #2/A:353 name THR index 424
residue id #2/A:354 name HIS index 425
residue id #2/A:355 name CYS index 426
residue id #2/A:356 name GLN index 427
residue id #2/A:357 name THR index 428
residue id #2/A:358 name CYS index 429
residue id #2/A:359 name HIS index 430
residue id #2/A:360 name VAL index 431
residue id #2/A:361 name SER index 432
residue id #2/A:362 name PRO index 433
residue id #2/A:363 name GLU index 434
residue id #2/A:364 name LEU index 435
residue id #2/A:365 name TYR index 436
residue id #2/A:366 name SER index 437
residue id #2/A:367 name ALA index 438
residue id #2/A:368 name THR index 439
residue id #2/A:369 name THR index 440
residue id #2/A:370 name TRP index 441
residue id #2/A:371 name LEU index 442
residue id #2/A:372 name GLY index 443
residue id #2/A:373 name TYR index 444
residue id #2/A:374 name VAL index 445
residue id #2/A:375 name ASN index 446
residue id #2/A:376 name SER index 447
residue id #2/A:377 name ALA index 448
residue id #2/A:378 name LEU index 449
residue id #2/A:379 name ASN index 450
residue id #2/A:380 name PRO index 451
residue id #2/A:381 name VAL index 452
residue id #2/A:382 name ILE index 453
residue id #2/A:383 name TYR index 454
residue id #2/A:384 name THR index 455
residue id #2/A:385 name THR index 456
residue id #2/A:386 name PHE index 457
residue id #2/A:387 name ASN index 458
residue id #2/A:388 name ILE index 459
residue id #2/A:389 name GLU index 460
residue id #2/A:390 name PHE index 461
residue id #2/A:391 name ARG index 462
residue id #2/A:392 name LYS index 463
residue id #2/A:393 name ALA index 464
residue id #2/A:394 name PHE index 465
residue id #2/A:395 name LEU index 466
residue id #2/A:396 name LYS index 467
residue id #2/A:397 name ILE index 468
residue id #2/A:398 name LEU index 469
residue id #2/A:399 name SER index 470
residue id #2/A:400 name CYS index 471
residue id #2/C:1 name GLC
residue id #2/C:2 name GLC
residue id #2/D:1 name GLC
residue id #2/D:2 name GLC
residue id #2/A:1200 name ETQ
> delete #2/ETQ
> delete #2/GLC
> delete #2/C:1
> delete #2/D:1
> delete #2/A:1200
> select #2 & ~protein
22 atoms, 22 bonds, 2 residues, 1 model selected
> delete sel
> select #2 & ~protein
Nothing selected
> delete #2 & ~protein
> select #2/A:1-219
1447 atoms, 1482 bonds, 188 residues, 1 model selected
> log metadata #1
Metadata for 9f33 #1
---
Title | Cryo-EM structure of Dopamine 3 Receptor:Go complex bound to bitopic FOB02-04A - Conformation A
Citation | Arroyo-Urea, S., Nazarova, A.L., Carrion-Antoli, A., Bonifazi, A., Battiti, F.O., Lam, J.H., Newman, A.H., Katritch, V., Garcia-Nafria, J. (2024). A bitopic agonist bound to the dopamine 3 receptor reveals a selectivity site. Nat Commun, 15, 7759-7759. PMID: 39237617. DOI: 10.1038/s41467-024-51993-4
Non-standard residue | A1H9N — N-[2-[(1R,2S)-2-[[(2S,5S)-2-(6-azanylpyridin-3-yl)-5-methyl-morpholin-4-yl]methyl]cyclopropyl]ethyl]-1H-indole-2-carboxamide
Gene sources | Mus musculus (house mouse)
Aequorea victoria
Homo sapiens (human)
Rattus norvegicus (norway rat)
CryoEM Map | EMDB 50168 — open map
Experimental method | Electron microscopy
Resolution | 3.05Å
> log chains #1
Chain information for 9f33 #1
---
Chain | Description | UniProt
R | Green fluorescent protein,D(3) dopamine receptor | GFP_AEQVI -243--7, DRD3_HUMAN 4-400
> sym #2
3pbl mmCIF Assemblies
---
1| software_defined_assembly| 1 copy of chain A
2| software_defined_assembly| 1 copy of chain
> log metadata #2
Metadata for 3pbl #2
---
Title | Structure of the human dopamine D3 receptor in complex with eticlopride
Citation | Chien, E.Y., Liu, W., Zhao, Q., Katritch, V., Han, G.W., Hanson, M.A., Shi, L., Newman, A.H., Javitch, J.A., Cherezov, V., Stevens, R.C. (2010). Structure of the human dopamine d3 receptor in complex with a d2/d3 selective antagonist. Science, 330, 1091-1095. PMID: 21097933. DOI: 10.1126/science.1197410
Gene sources | Enterobacteria phage T4 (human, bacteriophage t4)
Homo sapiens (human, bacteriophage t4)
Experimental method | X-ray diffraction
Resolution | 2.9Å
> log chains #2
Chain information for 3pbl #2
---
Chain | Description | UniProt
A | D(3) dopamine receptor, Lysozyme chimera | DRD3_HUMAN 2-221 319-400, LYS_BPT4 1002-1161
> select #2/A:1002-1161
1271 atoms, 1291 bonds, 160 residues, 1 model selected
> open P00720 fromDatabase uniprot associate #2/A
Summary of feedback from opening P00720 fetched from uniprot
---
notes | Fetching compressed P00720 UniProt info from https://www.uniprot.org/uniprot/P00720.xml
Alignment identifier is P00720
Associated 3pbl chain A to P00720 with 8 mismatches
Opened UniProt P00720
> delete #2 & ~protein
> select subtract #2.1
1271 atoms, 1291 bonds, 160 residues, 1 model selected
> select add #2.1
1271 atoms, 1291 bonds, 160 residues, 1 model selected
> select add #2
3389 atoms, 3466 bonds, 432 residues, 1 model selected
> select subtract #2
Nothing selected
> select subtract #2.1
Nothing selected
> select add #2.1
Nothing selected
> select subtract #2.1
Nothing selected
> matchmaker #1/R #2/A
Missing required "to" argument
> matchmaker #2/A to #1/R
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 9f33, chain R (#1) with 3pbl, chain A (#2), sequence alignment
score = 1418.9
RMSD between 219 pruned atom pairs is 0.941 angstroms; (across all 270 pairs:
2.521)
> color #1/A1H9N hotpink
> color #1/R limegreen
> transparency #1/R 40
> color #2/A cornflowerblue
> transparency #2/A 0
> transparency #2/A 80
> transparency #2/A 200
> color #2/A cornflowerblue:a50
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #2/A cornflowerblue alpha=0.5
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> graphics ribbons translucency true
Expected a keyword
> transparency #2/A 50
> transparency #1/A 0
> transparency #1/A 50
> color #1/R limegreen
> color #2/A cornflowerblue
> color #1/A1H9N hotpink
> select #1 & ligand
32 atoms, 36 bonds, 1 residue, 1 model selected
> select subtract #2.1
32 atoms, 36 bonds, 1 residue, 1 model selected
> color hotpink sel
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> select #1 & ligand
32 atoms, 36 bonds, 1 residue, 1 model selected
> color sel hotpink
> transparency #1/R 60
> graphics silhouettes false
> graphics cartoons translucency on
Expected a keyword
> graphics ribbons translucency on
Expected a keyword
> style ribbons transparency
Expected a keyword
> transparency #1/R 60
> select subtract #2.1
32 atoms, 36 bonds, 1 residue, 1 model selected
> select helix
4589 atoms, 4675 bonds, 582 residues, 2 models selected
> info selection
atom id #1/R:30@N idatm_type Npl
atom id #1/R:30@CA idatm_type C3
atom id #1/R:30@C idatm_type C2
atom id #1/R:30@O idatm_type O2
atom id #1/R:30@CB idatm_type C3
atom id #1/R:31@N idatm_type Npl
atom id #1/R:31@CA idatm_type C3
atom id #1/R:31@C idatm_type C2
atom id #1/R:31@O idatm_type O2
atom id #1/R:31@CB idatm_type C3
atom id #1/R:31@CG idatm_type Car
atom id #1/R:31@CD1 idatm_type Car
atom id #1/R:31@CD2 idatm_type Car
atom id #1/R:31@CE1 idatm_type Car
atom id #1/R:31@CE2 idatm_type Car
atom id #1/R:31@CZ idatm_type Car
atom id #1/R:31@OH idatm_type O3
atom id #1/R:32@N idatm_type Npl
atom id #1/R:32@CA idatm_type C3
atom id #1/R:32@C idatm_type C2
atom id #1/R:32@O idatm_type O2
atom id #1/R:32@CB idatm_type C3
atom id #1/R:32@CG idatm_type Car
atom id #1/R:32@CD1 idatm_type Car
atom id #1/R:32@CD2 idatm_type Car
atom id #1/R:32@CE1 idatm_type Car
atom id #1/R:32@CE2 idatm_type Car
atom id #1/R:32@CZ idatm_type Car
atom id #1/R:32@OH idatm_type O3
atom id #1/R:33@N idatm_type Npl
atom id #1/R:33@CA idatm_type C3
atom id #1/R:33@C idatm_type C2
atom id #1/R:33@O idatm_type O2
atom id #1/R:33@CB idatm_type C3
atom id #1/R:34@N idatm_type Npl
atom id #1/R:34@CA idatm_type C3
atom id #1/R:34@C idatm_type C2
atom id #1/R:34@O idatm_type O2
atom id #1/R:34@CB idatm_type C3
atom id #1/R:34@CG idatm_type C3
atom id #1/R:34@CD1 idatm_type C3
atom id #1/R:34@CD2 idatm_type C3
atom id #1/R:35@N idatm_type Npl
atom id #1/R:35@CA idatm_type C3
atom id #1/R:35@C idatm_type C2
atom id #1/R:35@O idatm_type O2
atom id #1/R:35@CB idatm_type C3
atom id #1/R:35@OG idatm_type O3
atom id #1/R:36@N idatm_type Npl
atom id #1/R:36@CA idatm_type C3
atom id #1/R:36@C idatm_type C2
atom id #1/R:36@O idatm_type O2
atom id #1/R:36@CB idatm_type C3
atom id #1/R:36@CG idatm_type Car
atom id #1/R:36@CD1 idatm_type Car
atom id #1/R:36@CD2 idatm_type Car
atom id #1/R:36@CE1 idatm_type Car
atom id #1/R:36@CE2 idatm_type Car
atom id #1/R:36@CZ idatm_type Car
atom id #1/R:36@OH idatm_type O3
atom id #1/R:37@N idatm_type Npl
atom id #1/R:37@CA idatm_type C3
atom id #1/R:37@C idatm_type C2
atom id #1/R:37@O idatm_type O2
atom id #1/R:37@CB idatm_type C3
atom id #1/R:37@SG idatm_type S3
atom id #1/R:38@N idatm_type Npl
atom id #1/R:38@CA idatm_type C3
atom id #1/R:38@C idatm_type C2
atom id #1/R:38@O idatm_type O2
atom id #1/R:38@CB idatm_type C3
atom id #1/R:39@N idatm_type Npl
atom id #1/R:39@CA idatm_type C3
atom id #1/R:39@C idatm_type C2
atom id #1/R:39@O idatm_type O2
atom id #1/R:39@CB idatm_type C3
atom id #1/R:39@CG idatm_type C3
atom id #1/R:39@CD1 idatm_type C3
atom id #1/R:39@CD2 idatm_type C3
atom id #1/R:40@N idatm_type Npl
atom id #1/R:40@CA idatm_type C3
atom id #1/R:40@C idatm_type C2
atom id #1/R:40@O idatm_type O2
atom id #1/R:40@CB idatm_type C3
atom id #1/R:40@CG1 idatm_type C3
atom id #1/R:40@CG2 idatm_type C3
atom id #1/R:40@CD1 idatm_type C3
atom id #1/R:41@N idatm_type Npl
atom id #1/R:41@CA idatm_type C3
atom id #1/R:41@C idatm_type C2
atom id #1/R:41@O idatm_type O2
atom id #1/R:41@CB idatm_type C3
atom id #1/R:41@CG idatm_type C3
atom id #1/R:41@CD1 idatm_type C3
atom id #1/R:41@CD2 idatm_type C3
atom id #1/R:42@N idatm_type Npl
atom id #1/R:42@CA idatm_type C3
atom id #1/R:42@C idatm_type C2
atom id #1/R:42@O idatm_type O2
atom id #1/R:42@CB idatm_type C3
atom id #1/R:43@N idatm_type Npl
atom id #1/R:43@CA idatm_type C3
atom id #1/R:43@C idatm_type C2
atom id #1/R:43@O idatm_type O2
atom id #1/R:43@CB idatm_type C3
atom id #1/R:43@CG1 idatm_type C3
atom id #1/R:43@CG2 idatm_type C3
atom id #1/R:43@CD1 idatm_type C3
atom id #1/R:44@N idatm_type Npl
atom id #1/R:44@CA idatm_type C3
atom id #1/R:44@C idatm_type C2
atom id #1/R:44@O idatm_type O2
atom id #1/R:44@CB idatm_type C3
atom id #1/R:44@CG1 idatm_type C3
atom id #1/R:44@CG2 idatm_type C3
atom id #1/R:45@N idatm_type Npl
atom id #1/R:45@CA idatm_type C3
atom id #1/R:45@C idatm_type C2
atom id #1/R:45@O idatm_type O2
atom id #1/R:45@CB idatm_type C3
atom id #1/R:45@CG idatm_type Car
atom id #1/R:45@CD1 idatm_type Car
atom id #1/R:45@CD2 idatm_type Car
atom id #1/R:45@CE1 idatm_type Car
atom id #1/R:45@CE2 idatm_type Car
atom id #1/R:45@CZ idatm_type Car
atom id #1/R:46@N idatm_type Npl
atom id #1/R:46@CA idatm_type C3
atom id #1/R:46@C idatm_type C2
atom id #1/R:46@O idatm_type O2
atom id #1/R:47@N idatm_type Npl
atom id #1/R:47@CA idatm_type C3
atom id #1/R:47@C idatm_type C2
atom id #1/R:47@O idatm_type O2
atom id #1/R:47@CB idatm_type C3
atom id #1/R:47@CG idatm_type C2
atom id #1/R:47@OD1 idatm_type O2
atom id #1/R:47@ND2 idatm_type Npl
atom id #1/R:48@N idatm_type Npl
atom id #1/R:48@CA idatm_type C3
atom id #1/R:48@C idatm_type C2
atom id #1/R:48@O idatm_type O2
atom id #1/R:49@N idatm_type Npl
atom id #1/R:49@CA idatm_type C3
atom id #1/R:49@C idatm_type C2
atom id #1/R:49@O idatm_type O2
atom id #1/R:49@CB idatm_type C3
atom id #1/R:49@CG idatm_type C3
atom id #1/R:49@CD1 idatm_type C3
atom id #1/R:49@CD2 idatm_type C3
atom id #1/R:50@N idatm_type Npl
atom id #1/R:50@CA idatm_type C3
atom id #1/R:50@C idatm_type C2
atom id #1/R:50@O idatm_type O2
atom id #1/R:50@CB idatm_type C3
atom id #1/R:50@CG1 idatm_type C3
atom id #1/R:50@CG2 idatm_type C3
atom id #1/R:51@N idatm_type Npl
atom id #1/R:51@CA idatm_type C3
atom id #1/R:51@C idatm_type C2
atom id #1/R:51@O idatm_type O2
atom id #1/R:51@CB idatm_type C3
atom id #1/R:51@SG idatm_type S3
atom id #1/R:52@N idatm_type Npl
atom id #1/R:52@CA idatm_type C3
atom id #1/R:52@C idatm_type C2
atom id #1/R:52@O idatm_type O2
atom id #1/R:52@CB idatm_type C3
atom id #1/R:52@CG idatm_type C3
atom id #1/R:52@SD idatm_type S3
atom id #1/R:52@CE idatm_type C3
atom id #1/R:53@N idatm_type Npl
atom id #1/R:53@CA idatm_type C3
atom id #1/R:53@C idatm_type C2
atom id #1/R:53@O idatm_type O2
atom id #1/R:53@CB idatm_type C3
atom id #1/R:54@N idatm_type Npl
atom id #1/R:54@CA idatm_type C3
atom id #1/R:54@C idatm_type C2
atom id #1/R:54@O idatm_type O2
atom id #1/R:54@CB idatm_type C3
atom id #1/R:54@CG1 idatm_type C3
atom id #1/R:54@CG2 idatm_type C3
atom id #1/R:55@N idatm_type Npl
atom id #1/R:55@CA idatm_type C3
atom id #1/R:55@C idatm_type C2
atom id #1/R:55@O idatm_type O2
atom id #1/R:55@CB idatm_type C3
atom id #1/R:55@CG idatm_type C3
atom id #1/R:55@CD1 idatm_type C3
atom id #1/R:55@CD2 idatm_type C3
atom id #1/R:56@N idatm_type Npl
atom id #1/R:56@CA idatm_type C3
atom id #1/R:56@C idatm_type C2
atom id #1/R:56@O idatm_type O2
atom id #1/R:56@CB idatm_type C3
atom id #1/R:56@CG idatm_type C3
atom id #1/R:56@CD idatm_type C3
atom id #1/R:56@CE idatm_type C3
atom id #1/R:56@NZ idatm_type N3+
atom id #1/R:57@N idatm_type Npl
atom id #1/R:57@CA idatm_type C3
atom id #1/R:57@C idatm_type C2
atom id #1/R:57@O idatm_type O2
atom id #1/R:57@CB idatm_type C3
atom id #1/R:57@CG idatm_type C3
atom id #1/R:57@CD idatm_type Cac
atom id #1/R:57@OE1 idatm_type O2-
atom id #1/R:57@OE2 idatm_type O2-
atom id #1/R:62@N idatm_type Npl
atom id #1/R:62@CA idatm_type C3
atom id #1/R:62@C idatm_type C2
atom id #1/R:62@O idatm_type O2
atom id #1/R:62@CB idatm_type C3
atom id #1/R:62@OG1 idatm_type O3
atom id #1/R:62@CG2 idatm_type C3
atom id #1/R:63@N idatm_type Npl
atom id #1/R:63@CA idatm_type C3
atom id #1/R:63@C idatm_type C2
atom id #1/R:63@O idatm_type O2
atom id #1/R:63@CB idatm_type C3
atom id #1/R:63@OG1 idatm_type O3
atom id #1/R:63@CG2 idatm_type C3
atom id #1/R:64@N idatm_type Npl
atom id #1/R:64@CA idatm_type C3
atom id #1/R:64@C idatm_type C2
atom id #1/R:64@O idatm_type O2
atom id #1/R:64@CB idatm_type C3
atom id #1/R:64@OG1 idatm_type O3
atom id #1/R:64@CG2 idatm_type C3
atom id #1/R:65@N idatm_type Npl
atom id #1/R:65@CA idatm_type C3
atom id #1/R:65@C idatm_type C2
atom id #1/R:65@O idatm_type O2
atom id #1/R:65@CB idatm_type C3
atom id #1/R:65@CG idatm_type C2
atom id #1/R:65@OD1 idatm_type O2
atom id #1/R:65@ND2 idatm_type Npl
atom id #1/R:66@N idatm_type Npl
atom id #1/R:66@CA idatm_type C3
atom id #1/R:66@C idatm_type C2
atom id #1/R:66@O idatm_type O2
atom id #1/R:66@CB idatm_type C3
atom id #1/R:66@CG idatm_type Car
atom id #1/R:66@CD1 idatm_type Car
atom id #1/R:66@CD2 idatm_type Car
atom id #1/R:66@CE1 idatm_type Car
atom id #1/R:66@CE2 idatm_type Car
atom id #1/R:66@CZ idatm_type Car
atom id #1/R:66@OH idatm_type O3
atom id #1/R:67@N idatm_type Npl
atom id #1/R:67@CA idatm_type C3
atom id #1/R:67@C idatm_type C2
atom id #1/R:67@O idatm_type O2
atom id #1/R:67@CB idatm_type C3
atom id #1/R:67@CG idatm_type C3
atom id #1/R:67@CD1 idatm_type C3
atom id #1/R:67@CD2 idatm_type C3
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> info structure #1
Expected a models specifier or a keyword
> info secondary_structure #1
Expected a models specifier or a keyword
> info ss #1
Expected a models specifier or a keyword
> select secondary_structure
Expected an objects specifier or a keyword
> structureassign #1
Unknown command: structureassign #1
> structureassign #2
Unknown command: structureassign #2
> dssp #1
> dssp #2
>
Unknown command: sequence #1/R
>
Unknown command: sequence #2/A
pyKVFinder module not installed; fetching from PyPi repository...
'pip install pyKVFinder' failed. Error from pip: error: subprocess-exited-
with-error
× Building wheel for pyKVFinder (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [51 lines of output]
running bdist_wheel
running build
running build_py
file _pyKVFinder.py (for module _pyKVFinder) not found
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder
copying pyKVFinder/grid.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder
copying pyKVFinder/__init__.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder
copying pyKVFinder/utils.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder
copying pyKVFinder/main.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder
copying pyKVFinder/argparser.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder
running egg_info
writing pyKVFinder.egg-info/PKG-INFO
writing dependency_links to pyKVFinder.egg-info/dependency_links.txt
writing entry points to pyKVFinder.egg-info/entry_points.txt
writing requirements to pyKVFinder.egg-info/requires.txt
writing top-level names to pyKVFinder.egg-info/top_level.txt
file _pyKVFinder.py (for module _pyKVFinder) not found
reading manifest file 'pyKVFinder.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching 'requirements.txt'
adding license file 'LICENSE'
writing manifest file 'pyKVFinder.egg-info/SOURCES.txt'
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/EisenbergWeiss.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/HessaHeijne.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/KyteDoolittle.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/MoonFleming.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/RadzickaWolfenden.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/WimleyWhite.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/ZhaoLondon.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/vdw.dat ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/1FMO.KVFinder.output.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/1FMO.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/1FMO.xyz ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/ADN.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/ADN.xyz ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/C1.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/ClO4.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/PKI.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/custom-box.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/residues-box.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
file _pyKVFinder.py (for module _pyKVFinder) not found
running build_ext
building '_pyKVFinder' extension
swigging C/pyKVFinder.i to C/pyKVFinder_wrap.c
swig -python -o C/pyKVFinder_wrap.c C/pyKVFinder.i
creating build/temp.macosx-10.9-universal2-cpython-311/C
clang -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g
-fwrapv -O3 -Wall -arch arm64 -arch x86_64 -g
-I/private/var/folders/nk/scpz8r4s6zb13_j698r0h52m0000gp/T/pip-build-env-
mclrhu12/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/Applications/ChimeraX-1.10.1.app/Contents/include/python3.11 -c
C/pyKVFinder.c -o build/temp.macosx-10.9-universal2-cpython-311/C/pyKVFinder.o
-Xpreprocessor -fopenmp=libomp -O3 -ffast-math
error: unknown argument: '-fopenmp=libomp'
error: command '/usr/bin/clang' failed with exit code 1
[end of output]
note: This error originates from a subprocess, and is likely not a problem
with pip.
ERROR: Failed building wheel for pyKVFinder
ERROR: Failed to build installable wheels for some pyproject.toml based
projects (pyKVFinder)
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/kvfinder/__init__.py", line 48, in check_pyKVFinder
import pyKVFinder
ModuleNotFoundError: No module named 'pyKVFinder'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 330, in _register_cmd
api._api_caller.register_command(api, self, ci, logger)
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1403, in register_command
return cls._get_func(api, "register_command")(ci.name, logger)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/kvfinder/__init__.py", line 36, in register_command
check_pyKVFinder(logger)
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/kvfinder/__init__.py", line 54, in check_pyKVFinder
run(logger.session, pip_cmd, log=False)
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3221, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/pip.py", line 88, in pip
run_logged_pip(pip_cmd, session.logger)
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/python_utils.py", line 143, in run_logged_pip
raise RuntimeError(s)
RuntimeError: error: subprocess-exited-with-error
× Building wheel for pyKVFinder (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [51 lines of output]
running bdist_wheel
running build
running build_py
file _pyKVFinder.py (for module _pyKVFinder) not found
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder
copying pyKVFinder/grid.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder
copying pyKVFinder/__init__.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder
copying pyKVFinder/utils.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder
copying pyKVFinder/main.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder
copying pyKVFinder/argparser.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder
running egg_info
writing pyKVFinder.egg-info/PKG-INFO
writing dependency_links to pyKVFinder.egg-info/dependency_links.txt
writing entry points to pyKVFinder.egg-info/entry_points.txt
writing requirements to pyKVFinder.egg-info/requires.txt
writing top-level names to pyKVFinder.egg-info/top_level.txt
file _pyKVFinder.py (for module _pyKVFinder) not found
reading manifest file 'pyKVFinder.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching 'requirements.txt'
adding license file 'LICENSE'
writing manifest file 'pyKVFinder.egg-info/SOURCES.txt'
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/EisenbergWeiss.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/HessaHeijne.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/KyteDoolittle.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/MoonFleming.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/RadzickaWolfenden.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/WimleyWhite.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/ZhaoLondon.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/vdw.dat ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/1FMO.KVFinder.output.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/1FMO.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/1FMO.xyz ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/ADN.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/ADN.xyz ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/C1.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/ClO4.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/PKI.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/custom-box.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/residues-box.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
file _pyKVFinder.py (for module _pyKVFinder) not found
running build_ext
building '_pyKVFinder' extension
swigging C/pyKVFinder.i to C/pyKVFinder_wrap.c
swig -python -o C/pyKVFinder_wrap.c C/pyKVFinder.i
creating build/temp.macosx-10.9-universal2-cpython-311/C
clang -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g
-fwrapv -O3 -Wall -arch arm64 -arch x86_64 -g
-I/private/var/folders/nk/scpz8r4s6zb13_j698r0h52m0000gp/T/pip-build-env-
mclrhu12/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/Applications/ChimeraX-1.10.1.app/Contents/include/python3.11 -c
C/pyKVFinder.c -o build/temp.macosx-10.9-universal2-cpython-311/C/pyKVFinder.o
-Xpreprocessor -fopenmp=libomp -O3 -ffast-math
error: unknown argument: '-fopenmp=libomp'
error: command '/usr/bin/clang' failed with exit code 1
[end of output]
note: This error originates from a subprocess, and is likely not a problem
with pip.
ERROR: Failed building wheel for pyKVFinder
ERROR: Failed to build installable wheels for some pyproject.toml based
projects (pyKVFinder)
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2479, in lazy_register
deferred.call()
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2407, in call
return self.proxy()
^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 320, in cb
s._register_cmd(ci, logger)
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 332, in _register_cmd
raise ToolshedError(
chimerax.core.toolshed.ToolshedError: register_command() failed for command
kvfinder in bundle ChimeraX-KVFinder:
error: subprocess-exited-with-error
× Building wheel for pyKVFinder (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [51 lines of output]
running bdist_wheel
running build
running build_py
file _pyKVFinder.py (for module _pyKVFinder) not found
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder
copying pyKVFinder/grid.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder
copying pyKVFinder/__init__.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder
copying pyKVFinder/utils.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder
copying pyKVFinder/main.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder
copying pyKVFinder/argparser.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder
running egg_info
writing pyKVFinder.egg-info/PKG-INFO
writing dependency_links to pyKVFinder.egg-info/dependency_links.txt
writing entry points to pyKVFinder.egg-info/entry_points.txt
writing requirements to pyKVFinder.egg-info/requires.txt
writing top-level names to pyKVFinder.egg-info/top_level.txt
file _pyKVFinder.py (for module _pyKVFinder) not found
reading manifest file 'pyKVFinder.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching 'requirements.txt'
adding license file 'LICENSE'
writing manifest file 'pyKVFinder.egg-info/SOURCES.txt'
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/EisenbergWeiss.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/HessaHeijne.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/KyteDoolittle.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/MoonFleming.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/RadzickaWolfenden.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/WimleyWhite.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/ZhaoLondon.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/vdw.dat ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/1FMO.KVFinder.output.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/1FMO.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/1FMO.xyz ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/ADN.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/ADN.xyz ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/C1.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/ClO4.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/PKI.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/custom-box.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/residues-box.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
file _pyKVFinder.py (for module _pyKVFinder) not found
running build_ext
building '_pyKVFinder' extension
swigging C/pyKVFinder.i to C/pyKVFinder_wrap.c
swig -python -o C/pyKVFinder_wrap.c C/pyKVFinder.i
creating build/temp.macosx-10.9-universal2-cpython-311/C
clang -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g
-fwrapv -O3 -Wall -arch arm64 -arch x86_64 -g
-I/private/var/folders/nk/scpz8r4s6zb13_j698r0h52m0000gp/T/pip-build-env-
mclrhu12/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/Applications/ChimeraX-1.10.1.app/Contents/include/python3.11 -c
C/pyKVFinder.c -o build/temp.macosx-10.9-universal2-cpython-311/C/pyKVFinder.o
-Xpreprocessor -fopenmp=libomp -O3 -ffast-math
error: unknown argument: '-fopenmp=libomp'
error: command '/usr/bin/clang' failed with exit code 1
[end of output]
note: This error originates from a subprocess, and is likely not a problem
with pip.
ERROR: Failed building wheel for pyKVFinder
ERROR: Failed to build installable wheels for some pyproject.toml based
projects (pyKVFinder)
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute
cmd.run(cmd_text)
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3147, in run
self._find_command_name(final, used_aliases=_used_aliases)
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2867, in _find_command_name
what.lazy_register(cmd_name)
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2481, in lazy_register
raise RuntimeError(
RuntimeError: delayed command registration for 'kvfinder' failed
(register_command() failed for command kvfinder in bundle ChimeraX-KVFinder:
error: subprocess-exited-with-error
× Building wheel for pyKVFinder (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [51 lines of output]
running bdist_wheel
running build
running build_py
file _pyKVFinder.py (for module _pyKVFinder) not found
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder
copying pyKVFinder/grid.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder
copying pyKVFinder/__init__.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder
copying pyKVFinder/utils.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder
copying pyKVFinder/main.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder
copying pyKVFinder/argparser.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder
running egg_info
writing pyKVFinder.egg-info/PKG-INFO
writing dependency_links to pyKVFinder.egg-info/dependency_links.txt
writing entry points to pyKVFinder.egg-info/entry_points.txt
writing requirements to pyKVFinder.egg-info/requires.txt
writing top-level names to pyKVFinder.egg-info/top_level.txt
file _pyKVFinder.py (for module _pyKVFinder) not found
reading manifest file 'pyKVFinder.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching 'requirements.txt'
adding license file 'LICENSE'
writing manifest file 'pyKVFinder.egg-info/SOURCES.txt'
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/EisenbergWeiss.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/HessaHeijne.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/KyteDoolittle.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/MoonFleming.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/RadzickaWolfenden.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/WimleyWhite.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/ZhaoLondon.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/vdw.dat ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/1FMO.KVFinder.output.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/1FMO.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/1FMO.xyz ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/ADN.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/ADN.xyz ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/C1.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/ClO4.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/PKI.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/custom-box.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/residues-box.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
file _pyKVFinder.py (for module _pyKVFinder) not found
running build_ext
building '_pyKVFinder' extension
swigging C/pyKVFinder.i to C/pyKVFinder_wrap.c
swig -python -o C/pyKVFinder_wrap.c C/pyKVFinder.i
creating build/temp.macosx-10.9-universal2-cpython-311/C
clang -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g
-fwrapv -O3 -Wall -arch arm64 -arch x86_64 -g
-I/private/var/folders/nk/scpz8r4s6zb13_j698r0h52m0000gp/T/pip-build-env-
mclrhu12/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/Applications/ChimeraX-1.10.1.app/Contents/include/python3.11 -c
C/pyKVFinder.c -o build/temp.macosx-10.9-universal2-cpython-311/C/pyKVFinder.o
-Xpreprocessor -fopenmp=libomp -O3 -ffast-math
error: unknown argument: '-fopenmp=libomp'
error: command '/usr/bin/clang' failed with exit code 1
[end of output]
note: This error originates from a subprocess, and is likely not a problem
with pip.
ERROR: Failed building wheel for pyKVFinder
ERROR: Failed to build installable wheels for some pyproject.toml based
projects (pyKVFinder)
)
RuntimeError: delayed command registration for 'kvfinder' failed
(register_command() failed for command kvfinder in bundle ChimeraX-KVFinder:
error: subprocess-exited-with-error
× Building wheel for pyKVFinder (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [51 lines of output]
running bdist_wheel
running build
running build_py
file _pyKVFinder.py (for module _pyKVFinder) not found
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder
copying pyKVFinder/grid.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder
copying pyKVFinder/__init__.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder
copying pyKVFinder/utils.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder
copying pyKVFinder/main.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder
copying pyKVFinder/argparser.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder
running egg_info
writing pyKVFinder.egg-info/PKG-INFO
writing dependency_links to pyKVFinder.egg-info/dependency_links.txt
writing entry points to pyKVFinder.egg-info/entry_points.txt
writing requirements to pyKVFinder.egg-info/requires.txt
writing top-level names to pyKVFinder.egg-info/top_level.txt
file _pyKVFinder.py (for module _pyKVFinder) not found
reading manifest file 'pyKVFinder.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching 'requirements.txt'
adding license file 'LICENSE'
writing manifest file 'pyKVFinder.egg-info/SOURCES.txt'
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/EisenbergWeiss.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/HessaHeijne.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/KyteDoolittle.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/MoonFleming.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/RadzickaWolfenden.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/WimleyWhite.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/ZhaoLondon.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
copying pyKVFinder/data/vdw.dat ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/1FMO.KVFinder.output.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/1FMO.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/1FMO.xyz ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/ADN.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/ADN.xyz ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/C1.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/ClO4.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/PKI.pdb ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/custom-box.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
copying pyKVFinder/data/tests/residues-box.toml ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/data/tests
file _pyKVFinder.py (for module _pyKVFinder) not found
running build_ext
building '_pyKVFinder' extension
swigging C/pyKVFinder.i to C/pyKVFinder_wrap.c
swig -python -o C/pyKVFinder_wrap.c C/pyKVFinder.i
creating build/temp.macosx-10.9-universal2-cpython-311/C
clang -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g
-fwrapv -O3 -Wall -arch arm64 -arch x86_64 -g
-I/private/var/folders/nk/scpz8r4s6zb13_j698r0h52m0000gp/T/pip-build-env-
mclrhu12/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/Applications/ChimeraX-1.10.1.app/Contents/include/python3.11 -c
C/pyKVFinder.c -o build/temp.macosx-10.9-universal2-cpython-311/C/pyKVFinder.o
-Xpreprocessor -fopenmp=libomp -O3 -ffast-math
error: unknown argument: '-fopenmp=libomp'
error: command '/usr/bin/clang' failed with exit code 1
[end of output]
note: This error originates from a subprocess, and is likely not a problem
with pip.
ERROR: Failed building wheel for pyKVFinder
ERROR: Failed to build installable wheels for some pyproject.toml based
projects (pyKVFinder)
)
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2481, in lazy_register
raise RuntimeError(
See log for complete Python traceback.
OpenGL version: 4.1 INTEL-18.8.16
OpenGL renderer: Intel(R) HD Graphics 6000
OpenGL vendor: Intel Inc.
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: MacBookAir7,2
Processor Name: Dual-Core Intel Core i5
Processor Speed: 1.8 GHz
Number of Processors: 1
Total Number of Cores: 2
L2 Cache (per Core): 256 KB
L3 Cache: 3 MB
Hyper-Threading Technology: Enabled
Memory: 8 GB
System Firmware Version: 489.0.0.0.0
OS Loader Version: 540.120.3~37
SMC Version (system): 2.27f2
Software:
System Software Overview:
System Version: macOS 12.7.6 (21H1320)
Kernel Version: Darwin 21.6.0
Time since boot: 11:08
Graphics/Displays:
Intel HD Graphics 6000:
Chipset Model: Intel HD Graphics 6000
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x1626
Revision ID: 0x0009
Metal Family: Supported, Metal GPUFamily macOS 1
Displays:
Color LCD:
Display Type: LCD
Resolution: 1440 x 900 (Widescreen eXtended Graphics Array Plus)
UI Looks like: 1440 x 900
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
HP 27vx:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Framebuffer Depth: 24-Bit Color (ARGB8888)
Display Serial Number: 3CM5170FZ1
Mirror: Off
Online: Yes
Rotation: Supported
Adapter Type: Apple Mini DisplayPort To VGA Adapter
Adapter Firmware Version: 1.03
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
babel: 2.17.0
beautifulsoup4: 4.13.3
blockdiag: 3.0.0
blosc2: 3.6.1
build: 1.2.2.post1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.2
ChimeraX-AddCharge: 1.5.19
ChimeraX-AddH: 2.2.7
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.20.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.1.4
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.7
ChimeraX-AtomicLibrary: 14.1.19
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.5.1
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.10.1
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5.1
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.6.2
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.10.1
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.19
ChimeraX-ModelPanel: 1.5.1
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14.1
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.10
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.3
ChimeraX-ProfileGrids: 1.1.3
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.3
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.1
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.45.2
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.5
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.2
coverage: 7.10.0
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.12
debugpy: 1.8.15
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.0
filelock: 3.18.0
fonttools: 4.59.0
funcparserlib: 2.0.0a0
glfw: 2.9.0
grako: 3.16.5
h5py: 3.14.0
html2text: 2024.2.26
idna: 3.10
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.1.0
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.7
jedi: 0.19.1
Jinja2: 3.1.6
jupyter_client: 8.6.3
jupyter_core: 5.8.1
jupyterlab_widgets: 3.0.15
kiwisolver: 1.4.8
line_profiler: 4.2.0
lxml: 5.3.1
lz4: 4.3.2
MarkupSafe: 3.0.2
matplotlib: 3.10.1
matplotlib-inline: 0.1.7
msgpack: 1.1.0
ndindex: 1.10.0
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.11.0
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 24.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.4.0
pip: 25.0.1
pkginfo: 1.11.1
platformdirs: 4.3.8
pluggy: 1.6.0
prompt_toolkit: 3.0.51
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.9
PyOpenGL-accelerate: 3.1.9
pyopenxr: 1.1.4501
pyparsing: 3.2.3
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.8.1
PyQt6-Qt6: 6.8.2
PyQt6-WebEngine-commercial: 6.8.0
PyQt6-WebEngine-Qt6: 6.8.2
PyQt6_sip: 13.10.0
pytest: 8.4.1
pytest-cov: 6.2.1
python-dateutil: 2.9.0.post0
pytz: 2025.2
pyzmq: 27.0.0
qtconsole: 5.5.2
QtPy: 2.4.3
qtshim: 1.1
RandomWords: 0.4.0
requests: 2.32.3
roman-numerals-py: 3.1.0
scipy: 1.14.0
setuptools: 78.1.0
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.7
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.1.0
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.7.1
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.4
tornado: 6.5.1
traitlets: 5.14.3
typing_extensions: 4.14.1
tzdata: 2025.2
urllib3: 2.5.0
wcwidth: 0.2.13
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.14
Change History (2)
comment:1 by , 11 hours ago
| Component: | Unassigned → Surface/Binding Analysis |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → KVFinder on old MacOS |
comment:2 by , 11 hours ago
| Resolution: | → limitation |
|---|---|
| Status: | accepted → closed |
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