Opened 3 days ago

Closed 11 hours ago

#19449 closed defect (limitation)

KVFinder on old MacOS

Reported by: chimerax-bug-report@… 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  
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atom id #1/R:128@NH2 idatm_type Ng+  
atom id #1/R:129@N idatm_type Npl  
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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
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    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 Eric Pettersen, 11 hours ago

Component: UnassignedSurface/Binding Analysis
Owner: set to Eric Pettersen
Platform: all
Project: ChimeraX
Status: newaccepted
Summary: ChimeraX bug report submissionKVFinder on old MacOS

comment:2 by Eric Pettersen, 11 hours ago

Resolution: limitation
Status: acceptedclosed
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