Opened 2 days ago

Closed 22 hours ago

#20856 closed defect (nonchimerax)

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-13.5-arm64-arm-64bit
ChimeraX Version: 1.12 (2026-06-12 03:42:34 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.12 (2026-06-12)  
© 2016-2026 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 1KD7

Summary of feedback from opening 1KD7 fetched from pdb  
---  
note | Fetching compressed mmCIF 1kd7 from http://files.rcsb.org/download/1kd7.cif  
  
1kd7 title:  
Crystal structure of an extracellular domain fragment of human BAFF [more
info...]  
  
Chain information for 1kd7 #1  
---  
Chain | Description | UniProt  
A B C K L M | TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 13B | TN13B_HUMAN 122-285  
  
1kd7 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  

> open 1KD7hide atoms

'1KD7hide' has no suffix  

> hide atoms

> show cartoons

> hide #1 atoms

> show #1 cartoons

> color #1 bychain

> view #1

> save "/Users/seviljafarzadeh/Desktop/BAFF 3mer CHIMERAX 1KD7.gif" width 389
> height 409 supersample 3

> hide #1

> show #1/A cartoons

> view #1/A

[Repeated 1 time(s)]

> hide #1 cartoons

> show #1/A cartoons

> view #1/A

> save "/Users/seviljafarzadeh/Desktop/BAFF A MONOMER.gif" width 538 height
> 528 supersample 3

> show #1/A:122 atoms

> color #1/A:122 red

> show #1/A:285 atoms

> color #1/A:285 yellow

> color #1/A:122 red

> hide #1 cartoons

> show #1/A-C cartoons

> color #1/A-C bychain

> view #1/A-C

> hide #1 atoms

> open 4V46

Summary of feedback from opening 4V46 fetched from pdb  
---  
notes | Fetching compressed mmCIF 4v46 from http://files.rcsb.org/download/4v46.cif  
Fetching CCD MG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/MG/MG.cif  
  
4v46 title:  
Crystal structure of the BAFF-BAFF-R complex [more info...]  
  
Chain information for 4v46 #2  
---  
Chain | Description | UniProt  
A0 A1 A2 A3 A4 A5 A6 A7 A8 A9 AA AB AC AD AE AF AG AH AI AJ AK AL AM AN AO AP AQ AR AS AT AU AV AW AX AY AZ Aa Ab Ac Ad Ae Af Ag Ah Ai Aj Ak Al Am An Ao Ap Aq Ar As At Au Av Aw Ax | Tumor necrosis factor ligand superfamily member 13B | T13B_HUMAN 138-285  
B0 B1 B2 B3 B4 B5 B6 B7 B8 B9 BA BB BC BD BE BF BG BH BI BJ BK BL BM BN BO BP BQ BR BS BT BU BV BW BX BY BZ Ba Bb Bc Bd Be Bf Bg Bh Bi Bj Bk Bl Bm Bn Bo Bp Bq Br Bs Bt Bu Bv Bw Bx | Tumor necrosis factor receptor superfamily member 13C | TR13C_HUMAN 1-63  
  
Non-standard residues in 4v46 #2  
---  
MG — magnesium ion  
  

> hide #1 models

> hide #2 atoms

> show #2 cartoons

> color #2 bychain

> view #2

> save /Users/seviljafarzadeh/Desktop/baffr.gif width 538 height 528
> supersample 3

> color #!2 bynucleotide

> hide #2 cartoons

> show #2/A cartoons

> show #1 models

> color #2/A cornflowerblue

> hide #1 models

> show #2 cartoons

> view #2

> info chains #2

chain id #2/AA chain_id AA  
chain id #2/AB chain_id AB  
chain id #2/AC chain_id AC  
chain id #2/AD chain_id AD  
chain id #2/AE chain_id AE  
chain id #2/AF chain_id AF  
chain id #2/AG chain_id AG  
chain id #2/AH chain_id AH  
chain id #2/AI chain_id AI  
chain id #2/AJ chain_id AJ  
chain id #2/AK chain_id AK  
chain id #2/AL chain_id AL  
chain id #2/AM chain_id AM  
chain id #2/AN chain_id AN  
chain id #2/AO chain_id AO  
chain id #2/AP chain_id AP  
chain id #2/AQ chain_id AQ  
chain id #2/AR chain_id AR  
chain id #2/AS chain_id AS  
chain id #2/AT chain_id AT  
chain id #2/AU chain_id AU  
chain id #2/AV chain_id AV  
chain id #2/AW chain_id AW  
chain id #2/AX chain_id AX  
chain id #2/AY chain_id AY  
chain id #2/AZ chain_id AZ  
chain id #2/A0 chain_id A0  
chain id #2/A1 chain_id A1  
chain id #2/A2 chain_id A2  
chain id #2/A3 chain_id A3  
chain id #2/A4 chain_id A4  
chain id #2/A5 chain_id A5  
chain id #2/A6 chain_id A6  
chain id #2/A7 chain_id A7  
chain id #2/A8 chain_id A8  
chain id #2/A9 chain_id A9  
chain id #2/Aa chain_id Aa  
chain id #2/Ab chain_id Ab  
chain id #2/Ac chain_id Ac  
chain id #2/Ad chain_id Ad  
chain id #2/Ae chain_id Ae  
chain id #2/Af chain_id Af  
chain id #2/Ag chain_id Ag  
chain id #2/Ah chain_id Ah  
chain id #2/Ai chain_id Ai  
chain id #2/Aj chain_id Aj  
chain id #2/Ak chain_id Ak  
chain id #2/Al chain_id Al  
chain id #2/Am chain_id Am  
chain id #2/An chain_id An  
chain id #2/Ao chain_id Ao  
chain id #2/Ap chain_id Ap  
chain id #2/Aq chain_id Aq  
chain id #2/Ar chain_id Ar  
chain id #2/As chain_id As  
chain id #2/At chain_id At  
chain id #2/Au chain_id Au  
chain id #2/Av chain_id Av  
chain id #2/Aw chain_id Aw  
chain id #2/Ax chain_id Ax  
chain id #2/BA chain_id BA  
chain id #2/BB chain_id BB  
chain id #2/BC chain_id BC  
chain id #2/BD chain_id BD  
chain id #2/BE chain_id BE  
chain id #2/BF chain_id BF  
chain id #2/BG chain_id BG  
chain id #2/BH chain_id BH  
chain id #2/BI chain_id BI  
chain id #2/BJ chain_id BJ  
chain id #2/BK chain_id BK  
chain id #2/BL chain_id BL  
chain id #2/BM chain_id BM  
chain id #2/BN chain_id BN  
chain id #2/BO chain_id BO  
chain id #2/BP chain_id BP  
chain id #2/BQ chain_id BQ  
chain id #2/BR chain_id BR  
chain id #2/BS chain_id BS  
chain id #2/BT chain_id BT  
chain id #2/BU chain_id BU  
chain id #2/BV chain_id BV  
chain id #2/BW chain_id BW  
chain id #2/BX chain_id BX  
chain id #2/BY chain_id BY  
chain id #2/BZ chain_id BZ  
chain id #2/B0 chain_id B0  
chain id #2/B1 chain_id B1  
chain id #2/B2 chain_id B2  
chain id #2/B3 chain_id B3  
chain id #2/B4 chain_id B4  
chain id #2/B5 chain_id B5  
chain id #2/B6 chain_id B6  
chain id #2/B7 chain_id B7  
chain id #2/B8 chain_id B8  
chain id #2/B9 chain_id B9  
chain id #2/Ba chain_id Ba  
chain id #2/Bb chain_id Bb  
chain id #2/Bc chain_id Bc  
chain id #2/Bd chain_id Bd  
chain id #2/Be chain_id Be  
chain id #2/Bf chain_id Bf  
chain id #2/Bg chain_id Bg  
chain id #2/Bh chain_id Bh  
chain id #2/Bi chain_id Bi  
chain id #2/Bj chain_id Bj  
chain id #2/Bk chain_id Bk  
chain id #2/Bl chain_id Bl  
chain id #2/Bm chain_id Bm  
chain id #2/Bn chain_id Bn  
chain id #2/Bo chain_id Bo  
chain id #2/Bp chain_id Bp  
chain id #2/Bq chain_id Bq  
chain id #2/Br chain_id Br  
chain id #2/Bs chain_id Bs  
chain id #2/Bt chain_id Bt  
chain id #2/Bu chain_id Bu  
chain id #2/Bv chain_id Bv  
chain id #2/Bw chain_id Bw  
chain id #2/Bx chain_id Bx  

> hide #2 cartoons

> show #2/AA cartoons

> color #2/AA cornflowerblue

> view #2/AA

> select (#2/AA :<4) & ~#2/AA

1235 atoms, 1211 bonds, 152 residues, 2 models selected  

> info residues sel

residue id #1/K:156 name PRO index 34  
residue id #1/K:157 name THR index 35  
residue id #1/K:158 name ILE index 36  
residue id #1/K:159 name GLN index 37  
residue id #1/K:160 name LYS index 38  
residue id #1/K:161 name GLY index 39  
residue id #1/K:162 name SER index 40  
residue id #1/K:163 name TYR index 41  
residue id #1/K:164 name THR index 42  
residue id #1/K:165 name PHE index 43  
residue id #1/K:166 name VAL index 44  
residue id #1/K:195 name ILE index 73  
residue id #1/K:199 name VAL index 77  
residue id #1/K:201 name TYR index 79  
residue id #1/K:209 name GLY index 87  
residue id #1/K:210 name HIS index 88  
residue id #1/K:211 name LEU index 89  
residue id #1/K:212 name ILE index 90  
residue id #1/K:213 name GLN index 91  
residue id #1/K:214 name ARG index 92  
residue id #1/K:215 name LYS index 93  
residue id #1/K:216 name LYS index 94  
residue id #1/K:217 name VAL index 95  
residue id #1/K:218 name HIS index 96  
residue id #1/K:219 name VAL index 97  
residue id #1/K:220 name PHE index 98  
residue id #1/K:221 name GLY index 99  
residue id #1/K:222 name ASP index 100  
residue id #1/K:223 name GLU index 101  
residue id #1/K:224 name LEU index 102  
residue id #1/K:225 name SER index 103  
residue id #1/K:226 name LEU index 104  
residue id #1/K:227 name VAL index 105  
residue id #1/K:228 name THR index 106  
residue id #1/K:229 name LEU index 107  
residue id #1/K:230 name PHE index 108  
residue id #1/K:231 name ARG index 109  
residue id #1/K:232 name CYS index 110  
residue id #1/K:250 name ILE index 128  
residue id #1/K:251 name ALA index 129  
residue id #1/K:252 name LYS index 130  
residue id #1/K:253 name LEU index 131  
residue id #1/K:254 name GLU index 132  
residue id #1/K:257 name ASP index 135  
residue id #1/K:258 name GLU index 136  
residue id #1/K:259 name LEU index 137  
residue id #1/K:260 name GLN index 138  
residue id #1/K:261 name LEU index 139  
residue id #1/K:262 name ALA index 140  
residue id #1/K:263 name ILE index 141  
residue id #1/K:264 name PRO index 142  
residue id #1/K:265 name ARG index 143  
residue id #1/K:266 name GLU index 144  
residue id #1/K:267 name ASN index 145  
residue id #1/K:268 name ALA index 146  
residue id #1/K:270 name ILE index 148  
residue id #1/K:279 name PHE index 157  
residue id #1/M:147 name LEU index 25  
residue id #1/M:148 name GLN index 26  
residue id #1/M:150 name ILE index 28  
residue id #1/M:151 name ALA index 29  
residue id #1/M:152 name ASP index 30  
residue id #1/M:153 name SER index 31  
residue id #1/M:154 name GLU index 32  
residue id #1/M:169 name LEU index 47  
residue id #1/M:170 name LEU index 48  
residue id #1/M:171 name SER index 49  
residue id #1/M:172 name PHE index 50  
residue id #1/M:173 name LYS index 51  
residue id #1/M:180 name GLU index 58  
residue id #1/M:200 name LEU index 78  
residue id #1/M:272 name LEU index 150  
residue id #1/M:273 name ASP index 151  
residue id #1/M:274 name GLY index 152  
residue id #1/M:275 name ASP index 153  
residue id #1/M:276 name VAL index 154  
residue id #2/AE:216 name LYS index 78  
residue id #2/AE:220 name PHE index 82  
residue id #2/AE:221 name GLY index 83  
residue id #2/AE:222 name ASP index 84  
residue id #2/AE:223 name GLU index 85  
residue id #2/AE:227 name VAL index 89  
residue id #2/AE:228 name THR index 90  
residue id #2/AE:229 name LEU index 91  
residue id #2/AE:250 name ILE index 112  
residue id #2/AE:251 name ALA index 113  
residue id #2/AE:252 name LYS index 114  
residue id #2/AG:142 name VAL index 4  
residue id #2/AG:143 name THR index 5  
residue id #2/AG:144 name GLN index 6  
residue id #2/AG:148 name GLN index 10  
residue id #2/AG:172 name PHE index 34  
residue id #2/AG:174 name ARG index 36  
residue id #2/AG:194 name PHE index 56  
residue id #2/AG:196 name TYR index 58  
residue id #2/AG:198 name GLN index 60  
residue id #2/AG:200 name LEU index 62  
residue id #2/AG:234 name GLN index 96  
residue id #2/AG:235 name ASN index 97  
residue id #2/AG:237 name PRO index 99  
residue id #2/AG:240 name LEU index 102  
residue id #2/AG:241 name PRO index 103  
residue id #2/AG:242 name ASN index 104  
residue id #2/AG:243 name ASN index 105  
residue id #2/AG:244 name SER index 106  
residue id #2/AG:246 name TYR index 108  
residue id #2/AG:273 name ASP index 135  
residue id #2/AG:275 name ASP index 137  
residue id #2/AG:276 name VAL index 138  
residue id #2/AG:278 name PHE index 140  
residue id #2/AG:282 name LEU index 144  
residue id #2/AG:285 name LEU index 147  
residue id #2/AK:150 name ILE index 12  
residue id #2/AK:170 name LEU index 32  
residue id #2/AK:171 name SER index 33  
residue id #2/AK:172 name PHE index 34  
residue id #2/AK:274 name GLY index 136  
residue id #2/AK:275 name ASP index 137  
residue id #2/AM:144 name GLN index 6  
residue id #2/AM:192 name TYR index 54  
residue id #2/AM:194 name PHE index 56  
residue id #2/AM:206 name TYR index 68  
residue id #2/AM:228 name THR index 90  
residue id #2/AM:229 name LEU index 91  
residue id #2/AM:230 name PHE index 92  
residue id #2/AM:231 name ARG index 93  
residue id #2/AM:232 name CYS index 94  
residue id #2/AM:233 name ILE index 95  
residue id #2/AM:234 name GLN index 96  
residue id #2/AM:235 name ASN index 97  
residue id #2/AM:246 name TYR index 108  
residue id #2/AM:247 name SER index 109  
residue id #2/AM:248 name ALA index 110  
residue id #2/AM:249 name GLY index 111  
residue id #2/AM:250 name ILE index 112  
residue id #2/AM:284 name LEU index 146  
residue id #2/AM:285 name LEU index 147  
residue id #2/Aa:217 name VAL index 79  
residue id #2/Aa:218 name HIS index 80  
residue id #2/Aa:219 name VAL index 81  
residue id #2/Aa:220 name PHE index 82  
residue id #2/Aa:221 name GLY index 83  
residue id #2/Aa:222 name ASP index 84  
residue id #2/BA:26 name ASP index 25  
residue id #2/BA:27 name LEU index 26  
residue id #2/BA:28 name LEU index 27  
residue id #2/BA:29 name VAL index 28  
residue id #2/BA:33 name VAL index 32  
residue id #2/BA:40 name THR index 39  
residue id #2/BA:41 name PRO index 40  
residue id #2/BM:29 name VAL index 28  
residue id #2/BM:37 name LEU index 36  

> close #1

> hide #2 cartoons

> show #2/AA,BA,BM cartoons

> color #2/AA cornflowerblue

> color #2/BA,BM red

> view #2/AA,BA,BM

> save "/Users/seviljafarzadeh/Desktop/baff baffr.gif" width 538 height 528
> supersample 3

> show #2/BA:26-27 atoms

> color #2/BA:26-27 yellow

> open 4V46 format mmcif fromDatabase pdb

4v46 title:  
Crystal structure of the BAFF-BAFF-R complex [more info...]  
  
Chain information for 4v46 #1  
---  
Chain | Description | UniProt  
A0 A1 A2 A3 A4 A5 A6 A7 A8 A9 AA AB AC AD AE AF AG AH AI AJ AK AL AM AN AO AP AQ AR AS AT AU AV AW AX AY AZ Aa Ab Ac Ad Ae Af Ag Ah Ai Aj Ak Al Am An Ao Ap Aq Ar As At Au Av Aw Ax | Tumor necrosis factor ligand superfamily member 13B | T13B_HUMAN 138-285  
B0 B1 B2 B3 B4 B5 B6 B7 B8 B9 BA BB BC BD BE BF BG BH BI BJ BK BL BM BN BO BP BQ BR BS BT BU BV BW BX BY BZ Ba Bb Bc Bd Be Bf Bg Bh Bi Bj Bk Bl Bm Bn Bo Bp Bq Br Bs Bt Bu Bv Bw Bx | Tumor necrosis factor receptor superfamily member 13C | TR13C_HUMAN 1-63  
  
Non-standard residues in 4v46 #1  
---  
MG — magnesium ion  
  

> color #2/BA:26-27 yellow

> open 4V46 format mmcif fromDatabase pdb

4v46 title:  
Crystal structure of the BAFF-BAFF-R complex [more info...]  
  
Chain information for 4v46 #3  
---  
Chain | Description | UniProt  
A0 A1 A2 A3 A4 A5 A6 A7 A8 A9 AA AB AC AD AE AF AG AH AI AJ AK AL AM AN AO AP AQ AR AS AT AU AV AW AX AY AZ Aa Ab Ac Ad Ae Af Ag Ah Ai Aj Ak Al Am An Ao Ap Aq Ar As At Au Av Aw Ax | Tumor necrosis factor ligand superfamily member 13B | T13B_HUMAN 138-285  
B0 B1 B2 B3 B4 B5 B6 B7 B8 B9 BA BB BC BD BE BF BG BH BI BJ BK BL BM BN BO BP BQ BR BS BT BU BV BW BX BY BZ Ba Bb Bc Bd Be Bf Bg Bh Bi Bj Bk Bl Bm Bn Bo Bp Bq Br Bs Bt Bu Bv Bw Bx | Tumor necrosis factor receptor superfamily member 13C | TR13C_HUMAN 1-63  
  
Non-standard residues in 4v46 #3  
---  
MG — magnesium ion  
  

> open 1KD7 format mmcif fromDatabase pdb

1kd7 title:  
Crystal structure of an extracellular domain fragment of human BAFF [more
info...]  
  
Chain information for 1kd7 #4  
---  
Chain | Description | UniProt  
A B C K L M | TUMOR NECROSIS FACTOR LIGAND SUPERFAMILY MEMBER 13B | TN13B_HUMAN 122-285  
  
1kd7 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  

> open 4V46 format mmcif fromDatabase pdb

4v46 title:  
Crystal structure of the BAFF-BAFF-R complex [more info...]  
  
Chain information for 4v46 #5  
---  
Chain | Description | UniProt  
A0 A1 A2 A3 A4 A5 A6 A7 A8 A9 AA AB AC AD AE AF AG AH AI AJ AK AL AM AN AO AP AQ AR AS AT AU AV AW AX AY AZ Aa Ab Ac Ad Ae Af Ag Ah Ai Aj Ak Al Am An Ao Ap Aq Ar As At Au Av Aw Ax | Tumor necrosis factor ligand superfamily member 13B | T13B_HUMAN 138-285  
B0 B1 B2 B3 B4 B5 B6 B7 B8 B9 BA BB BC BD BE BF BG BH BI BJ BK BL BM BN BO BP BQ BR BS BT BU BV BW BX BY BZ Ba Bb Bc Bd Be Bf Bg Bh Bi Bj Bk Bl Bm Bn Bo Bp Bq Br Bs Bt Bu Bv Bw Bx | Tumor necrosis factor receptor superfamily member 13C | TR13C_HUMAN 1-63  
  
Non-standard residues in 4v46 #5  
---  
MG — magnesium ion  
  

> hide #!1 models

> hide #!2 models

> hide #!3 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> hide #4 models

> show #!1 models

> hide #!1 models

> show #!2 models

> select add #2

79720 atoms, 81420 bonds, 80 pseudobonds, 10180 residues, 2 models selected  

> close all

> open 4V46

4v46 title:  
Crystal structure of the BAFF-BAFF-R complex [more info...]  
  
Chain information for 4v46 #1  
---  
Chain | Description | UniProt  
A0 A1 A2 A3 A4 A5 A6 A7 A8 A9 AA AB AC AD AE AF AG AH AI AJ AK AL AM AN AO AP AQ AR AS AT AU AV AW AX AY AZ Aa Ab Ac Ad Ae Af Ag Ah Ai Aj Ak Al Am An Ao Ap Aq Ar As At Au Av Aw Ax | Tumor necrosis factor ligand superfamily member 13B | T13B_HUMAN 138-285  
B0 B1 B2 B3 B4 B5 B6 B7 B8 B9 BA BB BC BD BE BF BG BH BI BJ BK BL BM BN BO BP BQ BR BS BT BU BV BW BX BY BZ Ba Bb Bc Bd Be Bf Bg Bh Bi Bj Bk Bl Bm Bn Bo Bp Bq Br Bs Bt Bu Bv Bw Bx | Tumor necrosis factor receptor superfamily member 13C | TR13C_HUMAN 1-63  
  
Non-standard residues in 4v46 #1  
---  
MG — magnesium ion  
  

> hide #1 atoms

> show #1 cartoons

> color #1 bychain

> view #1

> hide #1 cartoons

> show #1/AA cartoons

> color #1/AA cornflowerblue

> view #1/AA

> select (#1 & ~#1/AA) & (#1/AA :<4)

625 atoms, 605 bonds, 76 residues, 1 model selected  

> info residues sel

residue id /AE:216 name LYS index 78  
residue id /AE:220 name PHE index 82  
residue id /AE:221 name GLY index 83  
residue id /AE:222 name ASP index 84  
residue id /AE:223 name GLU index 85  
residue id /AE:227 name VAL index 89  
residue id /AE:228 name THR index 90  
residue id /AE:229 name LEU index 91  
residue id /AE:250 name ILE index 112  
residue id /AE:251 name ALA index 113  
residue id /AE:252 name LYS index 114  
residue id /AG:142 name VAL index 4  
residue id /AG:143 name THR index 5  
residue id /AG:144 name GLN index 6  
residue id /AG:148 name GLN index 10  
residue id /AG:172 name PHE index 34  
residue id /AG:174 name ARG index 36  
residue id /AG:194 name PHE index 56  
residue id /AG:196 name TYR index 58  
residue id /AG:198 name GLN index 60  
residue id /AG:200 name LEU index 62  
residue id /AG:234 name GLN index 96  
residue id /AG:235 name ASN index 97  
residue id /AG:237 name PRO index 99  
residue id /AG:240 name LEU index 102  
residue id /AG:241 name PRO index 103  
residue id /AG:242 name ASN index 104  
residue id /AG:243 name ASN index 105  
residue id /AG:244 name SER index 106  
residue id /AG:246 name TYR index 108  
residue id /AG:273 name ASP index 135  
residue id /AG:275 name ASP index 137  
residue id /AG:276 name VAL index 138  
residue id /AG:278 name PHE index 140  
residue id /AG:282 name LEU index 144  
residue id /AG:285 name LEU index 147  
residue id /AK:150 name ILE index 12  
residue id /AK:170 name LEU index 32  
residue id /AK:171 name SER index 33  
residue id /AK:172 name PHE index 34  
residue id /AK:274 name GLY index 136  
residue id /AK:275 name ASP index 137  
residue id /AM:144 name GLN index 6  
residue id /AM:192 name TYR index 54  
residue id /AM:194 name PHE index 56  
residue id /AM:206 name TYR index 68  
residue id /AM:228 name THR index 90  
residue id /AM:229 name LEU index 91  
residue id /AM:230 name PHE index 92  
residue id /AM:231 name ARG index 93  
residue id /AM:232 name CYS index 94  
residue id /AM:233 name ILE index 95  
residue id /AM:234 name GLN index 96  
residue id /AM:235 name ASN index 97  
residue id /AM:246 name TYR index 108  
residue id /AM:247 name SER index 109  
residue id /AM:248 name ALA index 110  
residue id /AM:249 name GLY index 111  
residue id /AM:250 name ILE index 112  
residue id /AM:284 name LEU index 146  
residue id /AM:285 name LEU index 147  
residue id /Aa:217 name VAL index 79  
residue id /Aa:218 name HIS index 80  
residue id /Aa:219 name VAL index 81  
residue id /Aa:220 name PHE index 82  
residue id /Aa:221 name GLY index 83  
residue id /Aa:222 name ASP index 84  
residue id /BA:26 name ASP index 25  
residue id /BA:27 name LEU index 26  
residue id /BA:28 name LEU index 27  
residue id /BA:29 name VAL index 28  
residue id /BA:33 name VAL index 32  
residue id /BA:40 name THR index 39  
residue id /BA:41 name PRO index 40  
residue id /BM:29 name VAL index 28  
residue id /BM:37 name LEU index 36  

> hide #1

> show #1/AA,BA,BM cartoons

> color #1/AA cornflowerblue

> color #1/BA,BM red

> view #1/AA,BA,BM

> show #1/BA:26-29 atoms

> color #1/BA:26-29 yellow

> show #1/BM:29,37 atoms

> color #1/BM:29,37 orange

> save /Users/seviljafarzadeh/Desktop/1.gif width 538 height 528 supersample 3

> hide #1/BM

> view #1/AA,BA

> select (#1/AA & (#1/BA :<4))

101 atoms, 101 bonds, 12 residues, 1 model selected  

> info residues sel

residue id /AA:162 name SER index 24  
residue id /AA:163 name TYR index 25  
residue id /AA:206 name TYR index 68  
residue id /AA:207 name ALA index 69  
residue id /AA:208 name MET index 70  
residue id /AA:209 name GLY index 71  
residue id /AA:210 name HIS index 72  
residue id /AA:231 name ARG index 93  
residue id /AA:232 name CYS index 94  
residue id /AA:264 name PRO index 126  
residue id /AA:265 name ARG index 127  
residue id /AA:266 name GLU index 128  

> show #1/AA:162,163,206-210,231,232,264-266 atoms

> color #1/AA:162,163,206-210,231,232,264-266 magenta

> view #1/AA,BA

> save /Users/seviljafarzadeh/Desktop/2.gif width 538 height 528 supersample 3

> hide #1/BA

> surface #1/AA

> color #1/AA:162,163,206-210,231,232,264-266 magenta target s

> view #1/AA

> save /Users/seviljafarzadeh/Desktop/3.gif width 538 height 528 supersample 3

> show #1/BA cartoons

> color #1/BA red

> hbonds #1/AA restrict #1/BA

5 hydrogen bonds found  

> hbonds #1/AA restrict #1/BA

5 hydrogen bonds found  

> hbonds #1/AA restrict #1/BA log true
    
    
    Finding intermodel H-bonds
    Finding intramodel H-bonds
    Constraints relaxed by 0.4 angstroms and 20 degrees
    Models used:
    	1 4v46
    
    5 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    /AA TYR 206 OH   /BA ASP 26 OD2  no hydrogen  2.613  N/A
    /AA ARG 231 NE   /BA LEU 28 O    no hydrogen  3.196  N/A
    /AA ARG 265 NH1  /BA ASP 26 OD1  no hydrogen  3.037  N/A
    /AA ARG 265 NH2  /BA ASP 26 OD1  no hydrogen  2.867  N/A
    /AA ARG 265 NH2  /BA ASP 26 OD2  no hydrogen  2.777  N/A
    

  
5 hydrogen bonds found  

> hide #1/AA atoms

> show #1/AA:206,231,265 atoms

> color #1/AA:206,231,265 magenta

> show #1/BA:26,28 atoms

> color #1/BA:26,28 yellow

> hbonds #1/AA restrict #1/BA

5 hydrogen bonds found  

> view #1/AA:206,231,265 | #1/BA:26,28

> save /Users/seviljafarzadeh/Desktop/4.gif width 1012 height 723 supersample
> 3

> save /Users/seviljafarzadeh/Desktop/BAFF_interface_analysis.cxs

> open 4V46

4v46 title:  
Crystal structure of the BAFF-BAFF-R complex [more info...]  
  
Chain information for 4v46 #2  
---  
Chain | Description | UniProt  
A0 A1 A2 A3 A4 A5 A6 A7 A8 A9 AA AB AC AD AE AF AG AH AI AJ AK AL AM AN AO AP AQ AR AS AT AU AV AW AX AY AZ Aa Ab Ac Ad Ae Af Ag Ah Ai Aj Ak Al Am An Ao Ap Aq Ar As At Au Av Aw Ax | Tumor necrosis factor ligand superfamily member 13B | T13B_HUMAN 138-285  
B0 B1 B2 B3 B4 B5 B6 B7 B8 B9 BA BB BC BD BE BF BG BH BI BJ BK BL BM BN BO BP BQ BR BS BT BU BV BW BX BY BZ Ba Bb Bc Bd Be Bf Bg Bh Bi Bj Bk Bl Bm Bn Bo Bp Bq Br Bs Bt Bu Bv Bw Bx | Tumor necrosis factor receptor superfamily member 13C | TR13C_HUMAN 1-63  
  
Non-standard residues in 4v46 #2  
---  
MG — magnesium ion  
  

> hide #1 models

> hide #2

> show #2/AA cartoons

> view #2/AA

No displayed objects specified.  

> surface #2/AA

> color #2/AA cornflowerblue

> show #2/AA:162,163,206-210,231,232,264-266 atoms

> color #2/AA:162,163,206-210,231,232,264-266 magenta

> save /Users/seviljafarzadeh/Desktop/BAFF_interface_surface.png width 1600
> height 1600 supersample 3

> ui tool show "Find Cavities"

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  
╰─> [57 lines of output]  
running bdist_wheel  
running build  
running build_py  
creating 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  
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/hydropathy.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/__init__.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/export.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/spatial.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/depth.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/constitutional.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/geometry.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/cavity.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/openings.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/detect.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
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  
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/WimleyWhite.toml ->
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/ZhaoLondon.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/MoonFleming.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/HessaHeijne.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/ADN.pdb ->
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/PKI.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.KVFinder.output.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/1FMO.xyz ->
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/ADN.xyz ->
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  
running build_ext  
building 'pyKVFinder._pyKVFinder' extension  
swigging C/pyKVFinder.i to C/pyKVFinder_wrap.c  
swig -python -o C/pyKVFinder_wrap.c C/pyKVFinder.i  
clang -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g
-fwrapv -O3 -Wall -arch arm64 -arch x86_64 -g
-I/private/var/folders/b_/dq2yjg5x5dn3nrxz040fqcqh0000gn/T/pip-build-
env-0huy03wv/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/private/var/folders/b_/dq2yjg5x5dn3nrxz040fqcqh0000gn/T/AppTranslocation/E3FA49AA-678F-49DC-9E4A-4B6406914F24/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/private/var/folders/b_/dq2yjg5x5dn3nrxz040fqcqh0000gn/T/AppTranslocation/E3FA49AA-678F-49DC-9E4A-4B6406914F24/d/ChimeraX-1.12.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 '['clang', '-Wsign-compare', '-Wunreachable-code', '-fno-
common', '-dynamic', '-DNDEBUG', '-g', '-fwrapv', '-O3', '-Wall', '-arch',
'arm64', '-arch', 'x86_64', '-g',
'-I/private/var/folders/b_/dq2yjg5x5dn3nrxz040fqcqh0000gn/T/pip-build-
env-0huy03wv/overlay/lib/python3.11/site-packages/numpy/_core/include', '-IC',
'-I/private/var/folders/b_/dq2yjg5x5dn3nrxz040fqcqh0000gn/T/AppTranslocation/E3FA49AA-678F-49DC-9E4A-4B6406914F24/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11',
'-I/private/var/folders/b_/dq2yjg5x5dn3nrxz040fqcqh0000gn/T/AppTranslocation/E3FA49AA-678F-49DC-9E4A-4B6406914F24/d/ChimeraX-1.12.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']' returned non-zero
exit status 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-wheel-build-for-install  
  
× Failed to build installable wheels for some pyproject.toml based projects  
╰─> pyKVFinder  
  
Traceback (most recent call last):  
File
"/private/var/folders/b_/dq2yjg5x5dn3nrxz040fqcqh0000gn/T/AppTranslocation/E3FA49AA-678F-49DC-9E4A-4B6406914F24/d/ChimeraX-1.12.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
"/private/var/folders/b_/dq2yjg5x5dn3nrxz040fqcqh0000gn/T/AppTranslocation/E3FA49AA-678F-49DC-9E4A-4B6406914F24/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 571, in start_tool  
ti = api._api_caller.start_tool(api, session, self, tool_info)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/private/var/folders/b_/dq2yjg5x5dn3nrxz040fqcqh0000gn/T/AppTranslocation/E3FA49AA-678F-49DC-9E4A-4B6406914F24/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1400, in start_tool  
return cls._get_func(api, "start_tool")(session, ti.name)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/private/var/folders/b_/dq2yjg5x5dn3nrxz040fqcqh0000gn/T/AppTranslocation/E3FA49AA-678F-49DC-9E4A-4B6406914F24/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/kvfinder/__init__.py", line 42, in start_tool  
check_pyKVFinder(session.logger)  
File
"/private/var/folders/b_/dq2yjg5x5dn3nrxz040fqcqh0000gn/T/AppTranslocation/E3FA49AA-678F-49DC-9E4A-4B6406914F24/d/ChimeraX-1.12.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
"/private/var/folders/b_/dq2yjg5x5dn3nrxz040fqcqh0000gn/T/AppTranslocation/E3FA49AA-678F-49DC-9E4A-4B6406914F24/d/ChimeraX-1.12.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
"/private/var/folders/b_/dq2yjg5x5dn3nrxz040fqcqh0000gn/T/AppTranslocation/E3FA49AA-678F-49DC-9E4A-4B6406914F24/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3245, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/private/var/folders/b_/dq2yjg5x5dn3nrxz040fqcqh0000gn/T/AppTranslocation/E3FA49AA-678F-49DC-9E4A-4B6406914F24/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/pip.py", line 84, in pip  
run_logged_pip(pip_cmd, session.logger)  
File
"/private/var/folders/b_/dq2yjg5x5dn3nrxz040fqcqh0000gn/T/AppTranslocation/E3FA49AA-678F-49DC-9E4A-4B6406914F24/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/python_utils.py", line 148, 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  
╰─> [57 lines of output]  
running bdist_wheel  
running build  
running build_py  
creating 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  
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/hydropathy.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/__init__.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/export.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/spatial.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/depth.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/constitutional.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/geometry.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/cavity.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/openings.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/detect.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
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  
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/WimleyWhite.toml ->
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/ZhaoLondon.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/MoonFleming.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/HessaHeijne.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/ADN.pdb ->
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/PKI.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.KVFinder.output.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/1FMO.xyz ->
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/ADN.xyz ->
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  
running build_ext  
building 'pyKVFinder._pyKVFinder' extension  
swigging C/pyKVFinder.i to C/pyKVFinder_wrap.c  
swig -python -o C/pyKVFinder_wrap.c C/pyKVFinder.i  
clang -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g
-fwrapv -O3 -Wall -arch arm64 -arch x86_64 -g
-I/private/var/folders/b_/dq2yjg5x5dn3nrxz040fqcqh0000gn/T/pip-build-
env-0huy03wv/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/private/var/folders/b_/dq2yjg5x5dn3nrxz040fqcqh0000gn/T/AppTranslocation/E3FA49AA-678F-49DC-9E4A-4B6406914F24/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/private/var/folders/b_/dq2yjg5x5dn3nrxz040fqcqh0000gn/T/AppTranslocation/E3FA49AA-678F-49DC-9E4A-4B6406914F24/d/ChimeraX-1.12.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 '['clang', '-Wsign-compare', '-Wunreachable-code', '-fno-
common', '-dynamic', '-DNDEBUG', '-g', '-fwrapv', '-O3', '-Wall', '-arch',
'arm64', '-arch', 'x86_64', '-g',
'-I/private/var/folders/b_/dq2yjg5x5dn3nrxz040fqcqh0000gn/T/pip-build-
env-0huy03wv/overlay/lib/python3.11/site-packages/numpy/_core/include', '-IC',
'-I/private/var/folders/b_/dq2yjg5x5dn3nrxz040fqcqh0000gn/T/AppTranslocation/E3FA49AA-678F-49DC-9E4A-4B6406914F24/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11',
'-I/private/var/folders/b_/dq2yjg5x5dn3nrxz040fqcqh0000gn/T/AppTranslocation/E3FA49AA-678F-49DC-9E4A-4B6406914F24/d/ChimeraX-1.12.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']' returned non-zero
exit status 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-wheel-build-for-install  
  
× 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
"/private/var/folders/b_/dq2yjg5x5dn3nrxz040fqcqh0000gn/T/AppTranslocation/E3FA49AA-678F-49DC-9E4A-4B6406914F24/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1955, in <lambda>  
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/private/var/folders/b_/dq2yjg5x5dn3nrxz040fqcqh0000gn/T/AppTranslocation/E3FA49AA-678F-49DC-9E4A-4B6406914F24/d/ChimeraX-1.12.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
"/private/var/folders/b_/dq2yjg5x5dn3nrxz040fqcqh0000gn/T/AppTranslocation/E3FA49AA-678F-49DC-9E4A-4B6406914F24/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3245, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/private/var/folders/b_/dq2yjg5x5dn3nrxz040fqcqh0000gn/T/AppTranslocation/E3FA49AA-678F-49DC-9E4A-4B6406914F24/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/cmd.py", line 219, in ui_tool_show  
return bi.start_tool(session, name)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/private/var/folders/b_/dq2yjg5x5dn3nrxz040fqcqh0000gn/T/AppTranslocation/E3FA49AA-678F-49DC-9E4A-4B6406914F24/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 578, in start_tool  
raise ToolshedError(  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Find
Cavities in bundle ChimeraX-KVFinder:  
error: subprocess-exited-with-error  
  
× Building wheel for pyKVFinder (pyproject.toml) did not run successfully.  
│ exit code: 1  
╰─> [57 lines of output]  
running bdist_wheel  
running build  
running build_py  
creating 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  
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/hydropathy.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/__init__.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/export.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/spatial.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/depth.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/constitutional.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/geometry.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/cavity.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/openings.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/detect.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
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  
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/WimleyWhite.toml ->
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/ZhaoLondon.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/MoonFleming.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/HessaHeijne.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/ADN.pdb ->
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/PKI.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.KVFinder.output.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/1FMO.xyz ->
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/ADN.xyz ->
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  
running build_ext  
building 'pyKVFinder._pyKVFinder' extension  
swigging C/pyKVFinder.i to C/pyKVFinder_wrap.c  
swig -python -o C/pyKVFinder_wrap.c C/pyKVFinder.i  
clang -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g
-fwrapv -O3 -Wall -arch arm64 -arch x86_64 -g
-I/private/var/folders/b_/dq2yjg5x5dn3nrxz040fqcqh0000gn/T/pip-build-
env-0huy03wv/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/private/var/folders/b_/dq2yjg5x5dn3nrxz040fqcqh0000gn/T/AppTranslocation/E3FA49AA-678F-49DC-9E4A-4B6406914F24/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/private/var/folders/b_/dq2yjg5x5dn3nrxz040fqcqh0000gn/T/AppTranslocation/E3FA49AA-678F-49DC-9E4A-4B6406914F24/d/ChimeraX-1.12.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 '['clang', '-Wsign-compare', '-Wunreachable-code', '-fno-
common', '-dynamic', '-DNDEBUG', '-g', '-fwrapv', '-O3', '-Wall', '-arch',
'arm64', '-arch', 'x86_64', '-g',
'-I/private/var/folders/b_/dq2yjg5x5dn3nrxz040fqcqh0000gn/T/pip-build-
env-0huy03wv/overlay/lib/python3.11/site-packages/numpy/_core/include', '-IC',
'-I/private/var/folders/b_/dq2yjg5x5dn3nrxz040fqcqh0000gn/T/AppTranslocation/E3FA49AA-678F-49DC-9E4A-4B6406914F24/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11',
'-I/private/var/folders/b_/dq2yjg5x5dn3nrxz040fqcqh0000gn/T/AppTranslocation/E3FA49AA-678F-49DC-9E4A-4B6406914F24/d/ChimeraX-1.12.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']' returned non-zero
exit status 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-wheel-build-for-install  
  
× Failed to build installable wheels for some pyproject.toml based projects  
╰─> pyKVFinder  
  
  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Find
Cavities in bundle ChimeraX-KVFinder:  
error: subprocess-exited-with-error  
  
× Building wheel for pyKVFinder (pyproject.toml) did not run successfully.  
│ exit code: 1  
╰─> [57 lines of output]  
running bdist_wheel  
running build  
running build_py  
creating 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  
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/hydropathy.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/__init__.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/export.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/spatial.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/depth.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/constitutional.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/geometry.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/cavity.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/openings.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/detect.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
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  
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/WimleyWhite.toml ->
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/ZhaoLondon.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/MoonFleming.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/HessaHeijne.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/ADN.pdb ->
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/PKI.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.KVFinder.output.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/1FMO.xyz ->
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/ADN.xyz ->
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  
running build_ext  
building 'pyKVFinder._pyKVFinder' extension  
swigging C/pyKVFinder.i to C/pyKVFinder_wrap.c  
swig -python -o C/pyKVFinder_wrap.c C/pyKVFinder.i  
clang -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g
-fwrapv -O3 -Wall -arch arm64 -arch x86_64 -g
-I/private/var/folders/b_/dq2yjg5x5dn3nrxz040fqcqh0000gn/T/pip-build-
env-0huy03wv/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/private/var/folders/b_/dq2yjg5x5dn3nrxz040fqcqh0000gn/T/AppTranslocation/E3FA49AA-678F-49DC-9E4A-4B6406914F24/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/private/var/folders/b_/dq2yjg5x5dn3nrxz040fqcqh0000gn/T/AppTranslocation/E3FA49AA-678F-49DC-9E4A-4B6406914F24/d/ChimeraX-1.12.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 '['clang', '-Wsign-compare', '-Wunreachable-code', '-fno-
common', '-dynamic', '-DNDEBUG', '-g', '-fwrapv', '-O3', '-Wall', '-arch',
'arm64', '-arch', 'x86_64', '-g',
'-I/private/var/folders/b_/dq2yjg5x5dn3nrxz040fqcqh0000gn/T/pip-build-
env-0huy03wv/overlay/lib/python3.11/site-packages/numpy/_core/include', '-IC',
'-I/private/var/folders/b_/dq2yjg5x5dn3nrxz040fqcqh0000gn/T/AppTranslocation/E3FA49AA-678F-49DC-9E4A-4B6406914F24/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11',
'-I/private/var/folders/b_/dq2yjg5x5dn3nrxz040fqcqh0000gn/T/AppTranslocation/E3FA49AA-678F-49DC-9E4A-4B6406914F24/d/ChimeraX-1.12.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']' returned non-zero
exit status 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-wheel-build-for-install  
  
× Failed to build installable wheels for some pyproject.toml based projects  
╰─> pyKVFinder  
  
  
File
"/private/var/folders/b_/dq2yjg5x5dn3nrxz040fqcqh0000gn/T/AppTranslocation/E3FA49AA-678F-49DC-9E4A-4B6406914F24/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 578, in start_tool  
raise ToolshedError(  
  
See log for complete Python traceback.  
  

> ui tool show "Find Cavities"

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  
╰─> [57 lines of output]  
running bdist_wheel  
running build  
running build_py  
creating 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  
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/hydropathy.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/__init__.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/export.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/spatial.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/depth.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/constitutional.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/geometry.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/cavity.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/openings.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/detect.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
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  
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/WimleyWhite.toml ->
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/ZhaoLondon.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/MoonFleming.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/HessaHeijne.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/ADN.pdb ->
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/PKI.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.KVFinder.output.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/1FMO.xyz ->
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/ADN.xyz ->
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  
running build_ext  
building 'pyKVFinder._pyKVFinder' extension  
swigging C/pyKVFinder.i to C/pyKVFinder_wrap.c  
swig -python -o C/pyKVFinder_wrap.c C/pyKVFinder.i  
clang -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g
-fwrapv -O3 -Wall -arch arm64 -arch x86_64 -g
-I/private/var/folders/b_/dq2yjg5x5dn3nrxz040fqcqh0000gn/T/pip-build-
env-4l67ahu6/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/private/var/folders/b_/dq2yjg5x5dn3nrxz040fqcqh0000gn/T/AppTranslocation/E3FA49AA-678F-49DC-9E4A-4B6406914F24/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/private/var/folders/b_/dq2yjg5x5dn3nrxz040fqcqh0000gn/T/AppTranslocation/E3FA49AA-678F-49DC-9E4A-4B6406914F24/d/ChimeraX-1.12.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 '['clang', '-Wsign-compare', '-Wunreachable-code', '-fno-
common', '-dynamic', '-DNDEBUG', '-g', '-fwrapv', '-O3', '-Wall', '-arch',
'arm64', '-arch', 'x86_64', '-g',
'-I/private/var/folders/b_/dq2yjg5x5dn3nrxz040fqcqh0000gn/T/pip-build-
env-4l67ahu6/overlay/lib/python3.11/site-packages/numpy/_core/include', '-IC',
'-I/private/var/folders/b_/dq2yjg5x5dn3nrxz040fqcqh0000gn/T/AppTranslocation/E3FA49AA-678F-49DC-9E4A-4B6406914F24/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11',
'-I/private/var/folders/b_/dq2yjg5x5dn3nrxz040fqcqh0000gn/T/AppTranslocation/E3FA49AA-678F-49DC-9E4A-4B6406914F24/d/ChimeraX-1.12.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']' returned non-zero
exit status 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-wheel-build-for-install  
  
× Failed to build installable wheels for some pyproject.toml based projects  
╰─> pyKVFinder  
  
Traceback (most recent call last):  
File
"/private/var/folders/b_/dq2yjg5x5dn3nrxz040fqcqh0000gn/T/AppTranslocation/E3FA49AA-678F-49DC-9E4A-4B6406914F24/d/ChimeraX-1.12.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
"/private/var/folders/b_/dq2yjg5x5dn3nrxz040fqcqh0000gn/T/AppTranslocation/E3FA49AA-678F-49DC-9E4A-4B6406914F24/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 571, in start_tool  
ti = api._api_caller.start_tool(api, session, self, tool_info)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/private/var/folders/b_/dq2yjg5x5dn3nrxz040fqcqh0000gn/T/AppTranslocation/E3FA49AA-678F-49DC-9E4A-4B6406914F24/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1400, in start_tool  
return cls._get_func(api, "start_tool")(session, ti.name)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/private/var/folders/b_/dq2yjg5x5dn3nrxz040fqcqh0000gn/T/AppTranslocation/E3FA49AA-678F-49DC-9E4A-4B6406914F24/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/kvfinder/__init__.py", line 42, in start_tool  
check_pyKVFinder(session.logger)  
File
"/private/var/folders/b_/dq2yjg5x5dn3nrxz040fqcqh0000gn/T/AppTranslocation/E3FA49AA-678F-49DC-9E4A-4B6406914F24/d/ChimeraX-1.12.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
"/private/var/folders/b_/dq2yjg5x5dn3nrxz040fqcqh0000gn/T/AppTranslocation/E3FA49AA-678F-49DC-9E4A-4B6406914F24/d/ChimeraX-1.12.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
"/private/var/folders/b_/dq2yjg5x5dn3nrxz040fqcqh0000gn/T/AppTranslocation/E3FA49AA-678F-49DC-9E4A-4B6406914F24/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3245, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/private/var/folders/b_/dq2yjg5x5dn3nrxz040fqcqh0000gn/T/AppTranslocation/E3FA49AA-678F-49DC-9E4A-4B6406914F24/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/pip.py", line 84, in pip  
run_logged_pip(pip_cmd, session.logger)  
File
"/private/var/folders/b_/dq2yjg5x5dn3nrxz040fqcqh0000gn/T/AppTranslocation/E3FA49AA-678F-49DC-9E4A-4B6406914F24/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/python_utils.py", line 148, 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  
╰─> [57 lines of output]  
running bdist_wheel  
running build  
running build_py  
creating 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  
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/hydropathy.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/__init__.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/export.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/spatial.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/depth.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/constitutional.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/geometry.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/cavity.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/openings.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/detect.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
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  
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/WimleyWhite.toml ->
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/ZhaoLondon.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/MoonFleming.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/HessaHeijne.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/ADN.pdb ->
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/PKI.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.KVFinder.output.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/1FMO.xyz ->
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/ADN.xyz ->
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  
running build_ext  
building 'pyKVFinder._pyKVFinder' extension  
swigging C/pyKVFinder.i to C/pyKVFinder_wrap.c  
swig -python -o C/pyKVFinder_wrap.c C/pyKVFinder.i  
clang -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g
-fwrapv -O3 -Wall -arch arm64 -arch x86_64 -g
-I/private/var/folders/b_/dq2yjg5x5dn3nrxz040fqcqh0000gn/T/pip-build-
env-4l67ahu6/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/private/var/folders/b_/dq2yjg5x5dn3nrxz040fqcqh0000gn/T/AppTranslocation/E3FA49AA-678F-49DC-9E4A-4B6406914F24/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/private/var/folders/b_/dq2yjg5x5dn3nrxz040fqcqh0000gn/T/AppTranslocation/E3FA49AA-678F-49DC-9E4A-4B6406914F24/d/ChimeraX-1.12.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 '['clang', '-Wsign-compare', '-Wunreachable-code', '-fno-
common', '-dynamic', '-DNDEBUG', '-g', '-fwrapv', '-O3', '-Wall', '-arch',
'arm64', '-arch', 'x86_64', '-g',
'-I/private/var/folders/b_/dq2yjg5x5dn3nrxz040fqcqh0000gn/T/pip-build-
env-4l67ahu6/overlay/lib/python3.11/site-packages/numpy/_core/include', '-IC',
'-I/private/var/folders/b_/dq2yjg5x5dn3nrxz040fqcqh0000gn/T/AppTranslocation/E3FA49AA-678F-49DC-9E4A-4B6406914F24/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11',
'-I/private/var/folders/b_/dq2yjg5x5dn3nrxz040fqcqh0000gn/T/AppTranslocation/E3FA49AA-678F-49DC-9E4A-4B6406914F24/d/ChimeraX-1.12.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']' returned non-zero
exit status 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-wheel-build-for-install  
  
× 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
"/private/var/folders/b_/dq2yjg5x5dn3nrxz040fqcqh0000gn/T/AppTranslocation/E3FA49AA-678F-49DC-9E4A-4B6406914F24/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1955, in <lambda>  
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/private/var/folders/b_/dq2yjg5x5dn3nrxz040fqcqh0000gn/T/AppTranslocation/E3FA49AA-678F-49DC-9E4A-4B6406914F24/d/ChimeraX-1.12.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
"/private/var/folders/b_/dq2yjg5x5dn3nrxz040fqcqh0000gn/T/AppTranslocation/E3FA49AA-678F-49DC-9E4A-4B6406914F24/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3245, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/private/var/folders/b_/dq2yjg5x5dn3nrxz040fqcqh0000gn/T/AppTranslocation/E3FA49AA-678F-49DC-9E4A-4B6406914F24/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/cmd.py", line 219, in ui_tool_show  
return bi.start_tool(session, name)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/private/var/folders/b_/dq2yjg5x5dn3nrxz040fqcqh0000gn/T/AppTranslocation/E3FA49AA-678F-49DC-9E4A-4B6406914F24/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 578, in start_tool  
raise ToolshedError(  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Find
Cavities in bundle ChimeraX-KVFinder:  
error: subprocess-exited-with-error  
  
× Building wheel for pyKVFinder (pyproject.toml) did not run successfully.  
│ exit code: 1  
╰─> [57 lines of output]  
running bdist_wheel  
running build  
running build_py  
creating 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  
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/hydropathy.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/__init__.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/export.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/spatial.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/depth.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/constitutional.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/geometry.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/cavity.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/openings.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/detect.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
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  
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/WimleyWhite.toml ->
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/ZhaoLondon.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/MoonFleming.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/HessaHeijne.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/ADN.pdb ->
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/PKI.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.KVFinder.output.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/1FMO.xyz ->
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/ADN.xyz ->
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  
running build_ext  
building 'pyKVFinder._pyKVFinder' extension  
swigging C/pyKVFinder.i to C/pyKVFinder_wrap.c  
swig -python -o C/pyKVFinder_wrap.c C/pyKVFinder.i  
clang -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g
-fwrapv -O3 -Wall -arch arm64 -arch x86_64 -g
-I/private/var/folders/b_/dq2yjg5x5dn3nrxz040fqcqh0000gn/T/pip-build-
env-4l67ahu6/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/private/var/folders/b_/dq2yjg5x5dn3nrxz040fqcqh0000gn/T/AppTranslocation/E3FA49AA-678F-49DC-9E4A-4B6406914F24/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/private/var/folders/b_/dq2yjg5x5dn3nrxz040fqcqh0000gn/T/AppTranslocation/E3FA49AA-678F-49DC-9E4A-4B6406914F24/d/ChimeraX-1.12.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 '['clang', '-Wsign-compare', '-Wunreachable-code', '-fno-
common', '-dynamic', '-DNDEBUG', '-g', '-fwrapv', '-O3', '-Wall', '-arch',
'arm64', '-arch', 'x86_64', '-g',
'-I/private/var/folders/b_/dq2yjg5x5dn3nrxz040fqcqh0000gn/T/pip-build-
env-4l67ahu6/overlay/lib/python3.11/site-packages/numpy/_core/include', '-IC',
'-I/private/var/folders/b_/dq2yjg5x5dn3nrxz040fqcqh0000gn/T/AppTranslocation/E3FA49AA-678F-49DC-9E4A-4B6406914F24/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11',
'-I/private/var/folders/b_/dq2yjg5x5dn3nrxz040fqcqh0000gn/T/AppTranslocation/E3FA49AA-678F-49DC-9E4A-4B6406914F24/d/ChimeraX-1.12.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']' returned non-zero
exit status 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-wheel-build-for-install  
  
× Failed to build installable wheels for some pyproject.toml based projects  
╰─> pyKVFinder  
  
  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Find
Cavities in bundle ChimeraX-KVFinder:  
error: subprocess-exited-with-error  
  
× Building wheel for pyKVFinder (pyproject.toml) did not run successfully.  
│ exit code: 1  
╰─> [57 lines of output]  
running bdist_wheel  
running build  
running build_py  
creating 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  
creating build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/hydropathy.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/__init__.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/export.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/spatial.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/depth.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/constitutional.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/geometry.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/cavity.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/openings.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
copying pyKVFinder/grid/detect.py ->
build/lib.macosx-10.9-universal2-cpython-311/pyKVFinder/grid  
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  
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/WimleyWhite.toml ->
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/ZhaoLondon.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/MoonFleming.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/HessaHeijne.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/ADN.pdb ->
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/PKI.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.KVFinder.output.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/1FMO.xyz ->
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/ADN.xyz ->
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  
running build_ext  
building 'pyKVFinder._pyKVFinder' extension  
swigging C/pyKVFinder.i to C/pyKVFinder_wrap.c  
swig -python -o C/pyKVFinder_wrap.c C/pyKVFinder.i  
clang -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g
-fwrapv -O3 -Wall -arch arm64 -arch x86_64 -g
-I/private/var/folders/b_/dq2yjg5x5dn3nrxz040fqcqh0000gn/T/pip-build-
env-4l67ahu6/overlay/lib/python3.11/site-packages/numpy/_core/include -IC
-I/private/var/folders/b_/dq2yjg5x5dn3nrxz040fqcqh0000gn/T/AppTranslocation/E3FA49AA-678F-49DC-9E4A-4B6406914F24/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
-I/private/var/folders/b_/dq2yjg5x5dn3nrxz040fqcqh0000gn/T/AppTranslocation/E3FA49AA-678F-49DC-9E4A-4B6406914F24/d/ChimeraX-1.12.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 '['clang', '-Wsign-compare', '-Wunreachable-code', '-fno-
common', '-dynamic', '-DNDEBUG', '-g', '-fwrapv', '-O3', '-Wall', '-arch',
'arm64', '-arch', 'x86_64', '-g',
'-I/private/var/folders/b_/dq2yjg5x5dn3nrxz040fqcqh0000gn/T/pip-build-
env-4l67ahu6/overlay/lib/python3.11/site-packages/numpy/_core/include', '-IC',
'-I/private/var/folders/b_/dq2yjg5x5dn3nrxz040fqcqh0000gn/T/AppTranslocation/E3FA49AA-678F-49DC-9E4A-4B6406914F24/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/include/python3.11',
'-I/private/var/folders/b_/dq2yjg5x5dn3nrxz040fqcqh0000gn/T/AppTranslocation/E3FA49AA-678F-49DC-9E4A-4B6406914F24/d/ChimeraX-1.12.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']' returned non-zero
exit status 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-wheel-build-for-install  
  
× Failed to build installable wheels for some pyproject.toml based projects  
╰─> pyKVFinder  
  
  
File
"/private/var/folders/b_/dq2yjg5x5dn3nrxz040fqcqh0000gn/T/AppTranslocation/E3FA49AA-678F-49DC-9E4A-4B6406914F24/d/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 578, in start_tool  
raise ToolshedError(  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 83.1
OpenGL renderer: Apple M1
OpenGL vendor: Apple

Python: 3.11.9
Locale: UTF-8
Qt version: PyQt6 6.10.2, Qt 6.10.0
Qt runtime version: 6.10.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Air
      Model Identifier: MacBookAir10,1
      Model Number: Z1240009KTU/A
      Chip: Apple M1
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 16 GB
      System Firmware Version: 8422.141.2
      OS Loader Version: 8422.141.2

Software:

    System Software Overview:

      System Version: macOS 13.5 (22G74)
      Kernel Version: Darwin 22.6.0
      Time since boot: 15 gün 21 saat 40 dakika

Graphics/Displays:

    Apple M1:

      Chipset Model: Apple M1
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 7
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    accessible-pygments: 0.0.5
    aiohappyeyeballs: 2.6.2
    aiohttp: 3.13.4
    aiosignal: 1.4.0
    alabaster: 1.0.0
    annotated-types: 0.7.0
    anyio: 4.13.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.1
    attrs: 26.1.0
    babel: 2.18.0
    beautifulsoup4: 4.13.5
    blockdiag: 3.0.0
    blosc2: 4.4.3
    bs4: 0.0.2
    build: 1.3.0
    certifi: 2025.7.14
    cftime: 1.6.5
    charset-normalizer: 3.4.7
    ChimeraX-AddCharge: 1.5.20
    ChimeraX-AddH: 2.2.8
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.2
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 3.2
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Animations: 1.0
    ChimeraX-Aniso: 1.3.2
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.67.1
    ChimeraX-AtomicLibrary: 14.4
    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: 1.1
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.6.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4.1
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.4
    ChimeraX-Cluster: 1.0
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3.1
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.12
    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: 1.2.2
    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: 2.5.3
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.4
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.8.2
    ChimeraX-Label: 1.5
    ChimeraX-LightingGUI: 1.0
    ChimeraX-ListInfo: 1.3.1
    ChimeraX-Log: 1.2.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.3
    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-MatchAlign: 1.2
    ChimeraX-MatchMaker: 2.4.1
    ChimeraX-MCopy: 1.0
    ChimeraX-MCPServer: 0.2.0
    ChimeraX-MDcrds: 2.19
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-Minimize: 1.3.9
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.23
    ChimeraX-ModelPanel: 1.6.1
    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: 1.0.1
    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: 1.15.4
    ChimeraX-OpenFold: 1.0
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.13
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.5
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.4
    ChimeraX-ProfileGrids: 1.6
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.8.2
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.3
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.2
    ChimeraX-Scenes: 0.3.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.12
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.18
    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-SNFG: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.19.3
    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: 2.5.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.4
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.50.8
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDock: 1.6.2
    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
    click: 8.4.1
    colorama: 0.4.6
    comm: 0.2.3
    contourpy: 1.3.3
    coverage: 7.14.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.2.4
    debugpy: 1.8.21
    decorator: 5.3.1
    docutils: 0.21.2
    executing: 2.2.1
    filelock: 3.19.1
    fonttools: 4.63.0
    frozenlist: 1.8.0
    funcparserlib: 2.0.0a0
    glfw: 2.10.0
    grako: 3.16.5
    h11: 0.16.0
    h5py: 3.16.0
    html2text: 2025.4.15
    httpcore: 1.0.9
    httpx: 0.28.1
    httpx-sse: 0.4.3
    idna: 3.18
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 2.0.0
    iniconfig: 2.3.0
    ipykernel: 7.1.0
    ipython: 9.9.0
    ipython_pygments_lexers: 1.1.1
    jedi: 0.19.2
    Jinja2: 3.1.6
    jsonschema: 4.26.0
    jsonschema-specifications: 2025.9.1
    jupyter_client: 8.8.0
    jupyter_core: 5.9.1
    kiwisolver: 1.5.0
    line_profiler: 5.0.0
    lxml: 6.0.2
    lz4: 4.3.2
    Markdown: 3.8.2
    MarkupSafe: 3.0.3
    matplotlib: 3.10.7
    matplotlib-inline: 0.2.2
    mcp: 1.18.0
    msgpack: 1.1.1
    multidict: 6.7.1
    narwhals: 2.22.1
    ndindex: 1.10.1
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.14.1
    numpy: 1.26.4
    OpenMM: 8.4.0
    openvr: 1.26.701
    packaging: 25.0
    ParmEd: 4.2.2
    parso: 0.8.7
    pep517: 0.13.1
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 11.3.0
    pip: 25.2
    pkginfo: 1.12.1.2
    platformdirs: 4.10.0
    plotly: 6.8.0
    pluggy: 1.6.0
    prompt_toolkit: 3.0.52
    propcache: 0.5.2
    psutil: 7.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pybind11: 3.0.1
    pycollada: 0.8
    pydantic: 2.13.4
    pydantic-settings: 2.14.1
    pydantic_core: 2.46.4
    pydata-sphinx-theme: 0.18.0
    pydicom: 2.4.4
    Pygments: 2.18.0
    pynmrstar: 3.5.1
    pynrrd: 1.0.0
    PyOpenGL: 3.1.10
    PyOpenGL-accelerate: 3.1.10
    pyopenxr: 1.1.4501
    pyparsing: 3.3.2
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.10.2
    PyQt6-Qt6: 6.10.2
    PyQt6-WebEngine-commercial: 6.10.0
    PyQt6-WebEngine-Qt6: 6.10.2
    PyQt6_sip: 13.10.3
    pytest: 9.0.3
    pytest-cov: 7.1.0
    python-dateutil: 2.9.0.post0
    python-dotenv: 1.2.2
    python-multipart: 0.0.32
    pyzmq: 27.1.0
    qtconsole: 5.7.0
    QtPy: 2.4.3
    qtshim: 1.2.2
    RandomWords: 0.4.0
    referencing: 0.37.0
    requests: 2.32.5
    roman-numerals: 4.1.0
    rpds-py: 2026.5.1
    scipy: 1.14.0
    setuptools: 80.9.0
    sfftk-rw: 0.8.1
    six: 1.17.0
    snowballstemmer: 3.1.1
    sortedcontainers: 2.4.0
    soupsieve: 2.8.4
    Sphinx: 9.0.4
    sphinx-autodoc-typehints: 3.6.1
    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
    sse-starlette: 3.4.4
    stack-data: 0.6.3
    starlette: 1.3.0
    superqt: 0.7.6
    tables: 3.10.2
    tcia_utils: 3.2.1
    threadpoolctl: 3.6.0
    tifffile: 2025.3.13
    tinyarray: 1.2.5
    tornado: 6.5.7
    tqdm: 4.68.2
    traitlets: 5.14.3
    typing-inspection: 0.4.2
    typing_extensions: 4.15.0
    Unidecode: 1.4.0
    urllib3: 2.7.0
    uvicorn: 0.49.0
    wcwidth: 0.8.1
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    yarl: 1.24.2

Change History (2)

comment:1 by Eric Pettersen, 22 hours ago

Component: Unassigned → Surface/Binding Analysis
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → KVFinder on old MacOS

comment:2 by Eric Pettersen, 22 hours ago

Resolution: → nonchimerax
Status: accepted → closed
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