id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 10304 Crash after computing/showing surface chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-13.1-arm64-arm-64bit ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC) Description Last time you used ChimeraX it crashed. 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All rights reserved. How to cite UCSF ChimeraX > open /Users/lamiawahba/Downloads/AF-P90786-F1-model_v4.pdb format pdb AF-P90786-F1-model_v4.pdb title: Alphafold monomer V2.0 prediction for piwi-like protein (P90786) [more info...] Chain information for AF-P90786-F1-model_v4.pdb #1 --- Chain | Description | UniProt A | piwi-like protein | P90786_CAEEL 1-824 > style sphere Changed 6589 atom styles > show atoms > hide atoms > show atoms > hide atoms > label #1 text ""{0.name} {0.number}{0.insertion_code}"" > ~label #1 residues > select 6589 atoms, 6721 bonds, 824 residues, 1 model selected > help help:user/menu.html#selectzone > style sel stick Changed 6589 atom styles > style sel stick Changed 6589 atom styles > style sel sphere Changed 6589 atom styles > select nucleic-acid Nothing selected > nucleotides atoms > style nucleic stick Changed 0 atom styles > volume style surface No volumes specified > volume step 1 No volumes specified > ui mousemode right select > ui mousemode right rotate > ui mousemode right label Alignment identifier is 1/A > select > /A:31-33,82-90,92-98,147-163,183-185,220-230,235-246,284-292,324-326,334-338,340-348,354-370,372-381,416-421,441-461,478-492,509-522,532-534,539-541,548-562,619-640,658-660,662-687,767-780,793-809,815-817 2263 atoms, 2278 bonds, 277 residues, 1 model selected > select /A:315 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:315-376 507 atoms, 515 bonds, 62 residues, 1 model selected > select /A:311 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:311-415 851 atoms, 868 bonds, 105 residues, 1 model selected > select /A:215-216 18 atoms, 17 bonds, 2 residues, 1 model selected > select /A:215-217 27 atoms, 26 bonds, 3 residues, 1 model selected > select /A:217 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:217-269 455 atoms, 463 bonds, 53 residues, 1 model selected > select /A:217 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:217-354 1134 atoms, 1159 bonds, 138 residues, 1 model selected > select /A:217 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:217-354 1134 atoms, 1159 bonds, 138 residues, 1 model selected > select /A:217-354 1134 atoms, 1159 bonds, 138 residues, 1 model selected > select > /A:48-54,56-61,67-76,108-111,119-124,131-143,167-169,172-174,180-182,187-200,203-216,250-253,258-261,264-266,274-277,280-283,303-307,319-322,327-329,383-385,390-396,401-403,407-409,433-438,469-473,499-504,527-531,577-586,594-601,609-616,648-654,695-702,709-711,726-728,738-743,755-762 1767 atoms, 1773 bonds, 213 residues, 1 model selected > select /A:217-354 1134 atoms, 1159 bonds, 138 residues, 1 model selected > select > /A:48-54,56-61,67-76,108-111,119-124,131-143,167-169,172-174,180-182,187-200,203-216,250-253,258-261,264-266,274-277,280-283,303-307,319-322,327-329,383-385,390-396,401-403,407-409,433-438,469-473,499-504,527-531,577-586,594-601,609-616,648-654,695-702,709-711,726-728,738-743,755-762 1767 atoms, 1773 bonds, 213 residues, 1 model selected > select /A:217-354 1134 atoms, 1159 bonds, 138 residues, 1 model selected > color sel red > select /A:489 8 atoms, 7 bonds, 1 residue, 1 model selected > select /A:489 8 atoms, 7 bonds, 1 residue, 1 model selected > select > /A:48-54,56-61,67-76,108-111,119-124,131-143,167-169,172-174,180-182,187-200,203-216,250-253,258-261,264-266,274-277,280-283,303-307,319-322,327-329,383-385,390-396,401-403,407-409,433-438,469-473,499-504,527-531,577-586,594-601,609-616,648-654,695-702,709-711,726-728,738-743,755-762 1767 atoms, 1773 bonds, 213 residues, 1 model selected > ui mousemode right select > ui mousemode right rotate > ui mousemode right zoom > ui mousemode right translate > ui mousemode right select > select > /A:31-33,82-90,92-98,147-163,183-185,220-230,235-246,284-292,324-326,334-338,340-348,354-370,372-381,416-421,441-461,478-492,509-522,532-534,539-541,548-562,619-640,658-660,662-687,767-780,793-809,815-817 2263 atoms, 2278 bonds, 277 residues, 1 model selected > select /A:498 10 atoms, 10 bonds, 1 residue, 1 model selected > select /A:498-822 2560 atoms, 2610 bonds, 325 residues, 1 model selected > color sel blue > select > /A:48-54,56-61,67-76,108-111,119-124,131-143,167-169,172-174,180-182,187-200,203-216,250-253,258-261,264-266,274-277,280-283,303-307,319-322,327-329,383-385,390-396,401-403,407-409,433-438,469-473,499-504,527-531,577-586,594-601,609-616,648-654,695-702,709-711,726-728,738-743,755-762 1767 atoms, 1773 bonds, 213 residues, 1 model selected > select > /A:31-33,82-90,92-98,147-163,183-185,220-230,235-246,284-292,324-326,334-338,340-348,354-370,372-381,416-421,441-461,478-492,509-522,532-534,539-541,548-562,619-640,658-660,662-687,767-780,793-809,815-817 2263 atoms, 2278 bonds, 277 residues, 1 model selected > style sel sphere Changed 2263 atom styles > color sel bychain > save /Users/lamiawahba/Desktop/prg-1.cxs > color sel bychain > style sel sphere Changed 2263 atom styles > hide target m > show target m > view clip false > view orient > view clip false > show target m > log metadata #1 Metadata for AF-P90786-F1-model_v4.pdb #1 --- Title | Alphafold monomer V2.0 prediction for piwi-like protein (P90786) Source (natural) | Caenorhabditis elegans > log chains #1 Chain information for AF-P90786-F1-model_v4.pdb #1 --- Chain | Description | UniProt A | piwi-like protein | P90786_CAEEL 1-824 > ui tool show ""Show Sequence Viewer"" > sequence chain /A Alignment identifier is 1/A > select > /A:48-54,56-61,67-76,108-111,119-124,131-143,167-169,172-174,180-182,187-200,203-216,250-253,258-261,264-266,274-277,280-283,303-307,319-322,327-329,383-385,390-396,401-403,407-409,433-438,469-473,499-504,527-531,577-586,594-601,609-616,648-654,695-702,709-711,726-728,738-743,755-762 1767 atoms, 1773 bonds, 213 residues, 1 model selected > select /A:13 6 atoms, 5 bonds, 1 residue, 1 model selected > select /A:13-51 289 atoms, 292 bonds, 39 residues, 1 model selected > select > /A:31-33,82-90,92-98,147-163,183-185,220-230,235-246,284-292,324-326,334-338,340-348,354-370,372-381,416-421,441-461,478-492,509-522,532-534,539-541,548-562,619-640,658-660,662-687,767-780,793-809,815-817 2263 atoms, 2278 bonds, 277 residues, 1 model selected > select /A:220 8 atoms, 7 bonds, 1 residue, 1 model selected > select /A:220-228 83 atoms, 85 bonds, 9 residues, 1 model selected > select /A:312-313 16 atoms, 16 bonds, 2 residues, 1 model selected > select /A:312-319 59 atoms, 61 bonds, 8 residues, 1 model selected > select /A:367-403 296 atoms, 300 bonds, 37 residues, 1 model selected > select /A:367-407 325 atoms, 329 bonds, 41 residues, 1 model selected > select /A:311 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:311-402 742 atoms, 756 bonds, 92 residues, 1 model selected > color #1 #ebe0d1ff > color #1 #ebe4d2ff > ui tool show AlphaFold > color sel byelement > select /A:217 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:217-394 1458 atoms, 1487 bonds, 178 residues, 1 model selected > select /A:217 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:217-360 1187 atoms, 1212 bonds, 144 residues, 1 model selected > select /A:217 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:217-354 1134 atoms, 1159 bonds, 138 residues, 1 model selected > color sel red > select sequence EESMY 44 atoms, 44 bonds, 5 residues, 1 model selected > select /A:498 10 atoms, 10 bonds, 1 residue, 1 model selected > select /A:498-821 2549 atoms, 2598 bonds, 324 residues, 1 model selected > color sel medium blue > save /Users/lamiawahba/Desktop/prg-1.cxs > select ::name=""LYS"" 540 atoms, 482 bonds, 60 residues, 1 model selected > color sel yellow > color sel bychain > select > /A:48-54,56-61,67-76,108-111,119-124,131-143,167-169,172-174,180-182,187-200,203-216,250-253,258-261,264-266,274-277,280-283,303-307,319-322,327-329,383-385,390-396,401-403,407-409,433-438,469-473,499-504,527-531,577-586,594-601,609-616,648-654,695-702,709-711,726-728,738-743,755-762 1767 atoms, 1773 bonds, 213 residues, 1 model selected > select /A:498-821 2549 atoms, 2598 bonds, 324 residues, 1 model selected > view clip false > log metadata #1 Metadata for AF-P90786-F1-model_v4.pdb #1 --- Title | Alphafold monomer V2.0 prediction for piwi-like protein (P90786) Source (natural) | Caenorhabditis elegans > log chains #1 Chain information for AF-P90786-F1-model_v4.pdb #1 --- Chain | Description | UniProt A | piwi-like protein | P90786_CAEEL 1-824 > view clip false > select /A:636 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:636 9 atoms, 8 bonds, 1 residue, 1 model selected > select > /A:48-54,56-61,67-76,108-111,119-124,131-143,167-169,172-174,180-182,187-200,203-216,250-253,258-261,264-266,274-277,280-283,303-307,319-322,327-329,383-385,390-396,401-403,407-409,433-438,469-473,499-504,527-531,577-586,594-601,609-616,648-654,695-702,709-711,726-728,738-743,755-762 1767 atoms, 1773 bonds, 213 residues, 1 model selected > select /A:537-538 13 atoms, 12 bonds, 2 residues, 1 model selected > select /A:537-538 13 atoms, 12 bonds, 2 residues, 1 model selected > select /A:583-584 16 atoms, 15 bonds, 2 residues, 1 model selected > select /A:583-584 16 atoms, 15 bonds, 2 residues, 1 model selected > style sel stick Changed 16 atom styles > style sel stick Changed 16 atom styles > style sel ball Changed 16 atom styles > nucleotides sel atoms > style nucleic & sel stick Changed 0 atom styles > nucleotides sel fill > style nucleic & sel stick Changed 0 atom styles > style sel ball Changed 16 atom styles > rainbow sel > style sel ball Changed 16 atom styles > style sel stick Changed 16 atom styles > style sel sphere Changed 16 atom styles > color sel bychain > color sel byhetero > color sel bypolymer > rainbow sel > coulombic sel Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for AF-P90786-F1-model_v4.pdb_A SES surface #1.1: minimum, -19.72, mean 0.46, maximum 16.36 To also show corresponding color key, enter the above coulombic command and add key true > color sel bynucleotide > color sel byhetero > color bfactor sel 16 atoms, 2 residues, 1 surfaces, atom bfactor range 89.8 to 94.4 > interfaces select & ~solvent Missing or invalid ""atoms"" argument: invalid atoms specifier Destroying pre-existing alignment with identifier 1/A Alignment identifier is 1/A > style sel sphere Changed 16 atom styles > select /A:824 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A 6589 atoms, 6721 bonds, 824 residues, 1 model selected > style sel sphere Changed 6589 atom styles > lighting full > set bgColor black > set bgColor white > set bgColor black > show sel surfaces > show sel cartoons > show sel atoms > show sel cartoons > hide sel atoms > hide sel cartoons > hide sel surfaces > show sel surfaces > show sel cartoons > hide sel surfaces > hide sel cartoons > show sel cartoons > show sel atoms > hide sel cartoons > show sel cartoons > hide sel cartoons > show sel cartoons > hide sel cartoons > show sel cartoons > hide sel surfaces > hide sel cartoons > hide sel atoms > show sel atoms > show sel surfaces > hide sel surfaces > save /Users/lamiawahba/Desktop/image1.png supersample 3 > ui tool show ""Side View"" > view orient > view > view sel > ui mousemode right ""rotate selected models"" > ui mousemode right rotate > save /Users/lamiawahba/Desktop/image2.png supersample 3 > save /Users/lamiawahba/Desktop/image3.png supersample 3 > hide sel surfaces > hide sel cartoons > hide sel atoms > show sel atoms > style sel stick Changed 6589 atom styles > style sel ball Changed 6589 atom styles > show sel cartoons > select /A 6589 atoms, 6721 bonds, 824 residues, 1 model selected > select /A:824 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:824 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:824 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:596-642 380 atoms, 389 bonds, 47 residues, 1 model selected > select /A:596-643 389 atoms, 398 bonds, 48 residues, 1 model selected > select /A 6589 atoms, 6721 bonds, 824 residues, 1 model selected > select /A:462 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:462-507 346 atoms, 350 bonds, 46 residues, 1 model selected > select /A 6589 atoms, 6721 bonds, 824 residues, 1 model selected > select /A:641 8 atoms, 7 bonds, 1 residue, 1 model selected > select /A:641-642 16 atoms, 15 bonds, 2 residues, 1 model selected > style sel stick Changed 16 atom styles > style sel ball Changed 16 atom styles > style sel ball Changed 16 atom styles > hide sel atoms > show sel atoms > show sel cartoons > show sel surfaces > style sel stick Changed 16 atom styles > nucleotides sel fill > style nucleic & sel stick Changed 0 atom styles > nucleotides sel atoms > style nucleic & sel stick Changed 0 atom styles > nucleotides sel tube/slab shape box > select /A 6589 atoms, 6721 bonds, 824 residues, 1 model selected > style sel ball Changed 6589 atom styles > style sel ball Changed 6589 atom styles > style sel sphere Changed 6589 atom styles > style sel sphere Changed 6589 atom styles > style sel stick Changed 6589 atom styles > nucleotides sel tube/slab shape box > nucleotides sel atoms > style nucleic & sel stick Changed 0 atom styles > nucleotides sel atoms > style nucleic & sel stick Changed 0 atom styles > nucleotides sel atoms > style nucleic & sel stick Changed 0 atom styles > nucleotides sel fill > style nucleic & sel stick Changed 0 atom styles > hide sel atoms > select /A:824 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:823-824 20 atoms, 20 bonds, 2 residues, 1 model selected > select /A:639 8 atoms, 7 bonds, 1 residue, 1 model selected > select /A:639-640 14 atoms, 13 bonds, 2 residues, 1 model selected > select /A 6589 atoms, 6721 bonds, 824 residues, 1 model selected > select /A:643-644 16 atoms, 15 bonds, 2 residues, 1 model selected > select /A:642-644 24 atoms, 23 bonds, 3 residues, 1 model selected > show sel surfaces > hide sel surfaces > select /A:641 8 atoms, 7 bonds, 1 residue, 1 model selected > select /A:641 8 atoms, 7 bonds, 1 residue, 1 model selected > hide sel surfaces > interfaces select & ~solvent Missing or invalid ""atoms"" argument: invalid atoms specifier > show sel surfaces > hide sel surfaces > select /A:561 6 atoms, 5 bonds, 1 residue, 1 model selected > select /A:561 6 atoms, 5 bonds, 1 residue, 1 model selected > select /A:824 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A 6589 atoms, 6721 bonds, 824 residues, 1 model selected > show sel surfaces > select /A:24 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:24 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:42 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:42 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:51 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:51 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:82 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:82-83 14 atoms, 13 bonds, 2 residues, 1 model selected > select /A:81-82 15 atoms, 14 bonds, 2 residues, 1 model selected > select /A:81-82 15 atoms, 14 bonds, 2 residues, 1 model selected > select /A:82-83 14 atoms, 13 bonds, 2 residues, 1 model selected > select /A:83 5 atoms, 4 bonds, 1 residue, 1 model selected > select /A:82 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:82 9 atoms, 8 bonds, 1 residue, 1 model selected > hide sel surfaces > show sel surfaces > select /A:87 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:87 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:112 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:112 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:137-138 18 atoms, 17 bonds, 2 residues, 1 model selected > select /A:137-138 18 atoms, 17 bonds, 2 residues, 1 model selected > select /A:213 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:213 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:226 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:226 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:241 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:241 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:258 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:258 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:277 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:277 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:285 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:285 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:289 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:289 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:309 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:309 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:311 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:311 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:338 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:338 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:341 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:341 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:348 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:348 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:370 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:370 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:373 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:373 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:379 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:379 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:398 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:398 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:405 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:405 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:406 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:406 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:411 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:411 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:420 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:420 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:449 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:449 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:459 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:459 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:490-491 18 atoms, 17 bonds, 2 residues, 1 model selected > select /A:490-491 18 atoms, 17 bonds, 2 residues, 1 model selected > select /A:509 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:509 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:516 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:516-517 18 atoms, 17 bonds, 2 residues, 1 model selected > select /A:538 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:538-539 15 atoms, 14 bonds, 2 residues, 1 model selected > select /A:540 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:540 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:546 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:546 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:554 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:554 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:562 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:562 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A 6589 atoms, 6721 bonds, 824 residues, 1 model selected > select /A:569 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:569 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:575 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:575 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:591 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:591 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:593 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:593 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:632 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:632 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:665 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:665 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:670 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:670 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:682 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:682 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:689 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:689 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:695 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:695 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:703 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:703 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:711 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:711 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:770 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:770 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:777 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:777 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:800 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:800 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:820 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:820 9 atoms, 8 bonds, 1 residue, 1 model selected > open ""/Users/lamiawahba/Library/Containers/com.apple.mail/Data/Library/Mail > Downloads/753B9663-26C1-4821-942F-2BD094A26B5E/Undefined.pdb"" Chain information for Undefined.pdb #2 --- Chain | Description ? | No description available > open ""/Users/lamiawahba/Library/Containers/com.apple.mail/Data/Library/Mail > Downloads/753B9663-26C1-4821-942F-2BD094A26B5E/Undefined.pdb"" Chain information for Undefined.pdb #3 --- Chain | Description ? | No description available > show #2 target m > select add #2 6376 atoms, 6505 bonds, 793 residues, 3 models selected > show #2 target m > hide #!1 models > show #!1 models > hide #!1 models > log metadata #2 The model has no metadata > log chains #2 Chain information for Undefined.pdb #2 --- Chain | Description ? | No description available > ui tool show ""Show Sequence Viewer"" > sequence chain #2/? #3/? Alignment identifier is 1 > select #2/*:84 #3/*:84 16 atoms, 14 bonds, 2 residues, 2 models selected > select #2/*:84-134 #3/*:84-134 866 atoms, 882 bonds, 102 residues, 2 models selected 1 [ID: 1] region 2 chains [52-102] RMSD: 0.000 > select #2/*:33 #3/*:33 16 atoms, 14 bonds, 2 residues, 2 models selected > select #2/*:33-37 #3/*:33-37 94 atoms, 94 bonds, 10 residues, 2 models selected 1 [ID: 1] region 2 chains [1-5] RMSD: 0.000 > select add #1 6683 atoms, 6815 bonds, 834 residues, 3 models selected > select add #3 13003 atoms, 13265 bonds, 1621 residues, 4 models selected > close #3 > select add #2 12956 atoms, 13218 bonds, 1616 residues, 3 models selected > show #!1 models > hide #2 models > select ::name=""LYS"" 1062 atoms, 948 bonds, 118 residues, 2 models selected > select #1/A:779-824 376 atoms, 388 bonds, 46 residues, 1 model selected > select #1/A 6589 atoms, 6721 bonds, 824 residues, 1 model selected > select #1/A:310 7 atoms, 7 bonds, 1 residue, 1 model selected > select #1/A:309-310 16 atoms, 16 bonds, 2 residues, 1 model selected > select #1/A 6589 atoms, 6721 bonds, 824 residues, 1 model selected > select #1/A:309 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/A:309-310 16 atoms, 16 bonds, 2 residues, 1 model selected > select #1/A:311 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/A:310 7 atoms, 7 bonds, 1 residue, 1 model selected > select #1/A:309-310 16 atoms, 16 bonds, 2 residues, 1 model selected > select #1/A:309 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/A:309 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/A:309 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/A:309-311 25 atoms, 25 bonds, 3 residues, 1 model selected > coulombic sel Coulombic values for AF-P90786-F1-model_v4.pdb_A SES surface #1.1: minimum, -19.72, mean 0.46, maximum 16.36 To also show corresponding color key, enter the above coulombic command and add key true > coulombic sel Coulombic values for AF-P90786-F1-model_v4.pdb_A SES surface #1.1: minimum, -19.72, mean 0.46, maximum 16.36 To also show corresponding color key, enter the above coulombic command and add key true > coulombic sel Coulombic values for AF-P90786-F1-model_v4.pdb_A SES surface #1.1: minimum, -19.72, mean 0.46, maximum 16.36 To also show corresponding color key, enter the above coulombic command and add key true > coulombic sel Coulombic values for AF-P90786-F1-model_v4.pdb_A SES surface #1.1: minimum, -19.72, mean 0.46, maximum 16.36 To also show corresponding color key, enter the above coulombic command and add key true > coulombic sel Coulombic values for AF-P90786-F1-model_v4.pdb_A SES surface #1.1: minimum, -19.72, mean 0.46, maximum 16.36 To also show corresponding color key, enter the above coulombic command and add key true > mlp sel Map values for surface ""AF-P90786-F1-model_v4.pdb_A SES surface"": minimum -29.33, mean -5.891, maximum 22.8 To also show corresponding color key, enter the above mlp command and add key true > mlp sel Map values for surface ""AF-P90786-F1-model_v4.pdb_A SES surface"": minimum -29.33, mean -5.891, maximum 22.8 To also show corresponding color key, enter the above mlp command and add key true > color bfactor sel 25 atoms, 3 residues, 1 surfaces, atom bfactor range 73.4 to 79.5 > rainbow sel > color sel bypolymer > rainbow sel > color sel byhetero > coulombic sel Coulombic values for AF-P90786-F1-model_v4.pdb_A SES surface #1.1: minimum, -19.72, mean 0.46, maximum 16.36 To also show corresponding color key, enter the above coulombic command and add key true > coulombic sel Coulombic values for AF-P90786-F1-model_v4.pdb_A SES surface #1.1: minimum, -19.72, mean 0.46, maximum 16.36 To also show corresponding color key, enter the above coulombic command and add key true > select #1/A 6589 atoms, 6721 bonds, 824 residues, 1 model selected > coulombic sel Coulombic values for AF-P90786-F1-model_v4.pdb_A SES surface #1.1: minimum, -19.72, mean 0.46, maximum 16.36 To also show corresponding color key, enter the above coulombic command and add key true > color sel bychain > select #1/A:217 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/A:217-337 992 atoms, 1014 bonds, 121 residues, 1 model selected > select #1/A:217 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/A:217-354 1134 atoms, 1159 bonds, 138 residues, 1 model selected > color (#!1 & sel) forest green > select #1/A:498 10 atoms, 10 bonds, 1 residue, 1 model selected > select #1/A:498-808 2448 atoms, 2496 bonds, 311 residues, 1 model selected > color (#!1 & sel) red > select #1/A 6589 atoms, 6721 bonds, 824 residues, 1 model selected > interfaces select & ~solvent Missing or invalid ""atoms"" argument: invalid atoms specifier > select #1/A:3-4 10 atoms, 9 bonds, 2 residues, 1 model selected > select #1/A:3-4 10 atoms, 9 bonds, 2 residues, 1 model selected > select #1/A 6589 atoms, 6721 bonds, 824 residues, 1 model selected > select #1/A:309 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/A:309 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/A 6589 atoms, 6721 bonds, 824 residues, 1 model selected > select #1/A:309 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/A:309-311 25 atoms, 25 bonds, 3 residues, 1 model selected > select #1/A:309 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/A:309 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/A:311 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/A:311 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/A:309 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/A:309 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/A:311 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/A:311-312 18 atoms, 17 bonds, 2 residues, 1 model selected > select #1/A 6589 atoms, 6721 bonds, 824 residues, 1 model selected > select #1/A:311 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/A:311 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/A:309 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/A:309 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/A:311 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/A:311 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/A:309 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/A:309-311 25 atoms, 25 bonds, 3 residues, 1 model selected > select #1/A 6589 atoms, 6721 bonds, 824 residues, 1 model selected > select #1/A:824 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/A:824 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/A 6589 atoms, 6721 bonds, 824 residues, 1 model selected > select #1/A:823-824 20 atoms, 20 bonds, 2 residues, 1 model selected > select #1/A:823-824 20 atoms, 20 bonds, 2 residues, 1 model selected > show target m > log metadata #1 Metadata for AF-P90786-F1-model_v4.pdb #1 --- Title | Alphafold monomer V2.0 prediction for piwi-like protein (P90786) Source (natural) | Caenorhabditis elegans > log chains #1 Chain information for AF-P90786-F1-model_v4.pdb #1 --- Chain | Description | UniProt A | piwi-like protein | P90786_CAEEL 1-824 > log metadata #2 The model has no metadata > log chains #2 Chain information for Undefined.pdb #2 --- Chain | Description ? | No description available > log metadata #1 Metadata for AF-P90786-F1-model_v4.pdb #1 --- Title | Alphafold monomer V2.0 prediction for piwi-like protein (P90786) Source (natural) | Caenorhabditis elegans > log chains #1 Chain information for AF-P90786-F1-model_v4.pdb #1 --- Chain | Description | UniProt A | piwi-like protein | P90786_CAEEL 1-824 > log metadata #2 The model has no metadata > log chains #2 Chain information for Undefined.pdb #2 --- Chain | Description ? | No description available > nucleotides sel atoms > style nucleic & sel stick Changed 0 atom styles > nucleotides sel fill > style nucleic & sel stick Changed 0 atom styles > select #1/A 6589 atoms, 6721 bonds, 824 residues, 1 model selected Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps, got 2 atomic models, 0 maps. > surface (#!1 & sel) > surface hidePatches (#!1 & sel) > hide #2 models > select #1/A:97 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/A:97-98 17 atoms, 16 bonds, 2 residues, 1 model selected > select #1/A 6589 atoms, 6721 bonds, 824 residues, 1 model selected > select #1/A:48 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/A:48-49 16 atoms, 16 bonds, 2 residues, 1 model selected > surface (#!1 & sel) > select #1/A 6589 atoms, 6721 bonds, 824 residues, 1 model selected > surface (#!1 & sel) ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 83 OpenGL renderer: Apple M2 OpenGL vendor: Apple Python: 3.9.11 Locale: UTF-8 Qt version: PyQt6 6.4.2, Qt 6.4.2 Qt runtime version: 6.4.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac14,7 Model Number: Z16R0005YLL/A Chip: Apple M2 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 24 GB System Firmware Version: 8419.60.44 OS Loader Version: 8419.60.44 Software: System Software Overview: System Version: macOS 13.1 (22C65) Kernel Version: Darwin 22.2.0 Time since boot: 44 days, 7 hours, 34 minutes Graphics/Displays: Apple M2: Chipset Model: Apple M2 Type: GPU Bus: Built-In Total Number of Cores: 10 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 DELL SE2722HX: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 75.00Hz Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.2.1 Babel: 2.12.1 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 build: 0.10.0 certifi: 2021.10.8 cftime: 1.6.2 charset-normalizer: 3.1.0 ChimeraX-AddCharge: 1.5.9.1 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.3.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.9.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.43.10 ChimeraX-AtomicLibrary: 10.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.1 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.8 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 ChimeraX-ChangeChains: 1.0.2 ChimeraX-CheckWaters: 1.3.1 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.3 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.6.1 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.4.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.4 ChimeraX-DockPrep: 1.1.1 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: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-Label: 1.1.7 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.2 ChimeraX-Map: 1.1.4 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.0.12 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.9 ChimeraX-ModelPanel: 1.3.7 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.0 ChimeraX-NRRD: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.10.1 ChimeraX-PDB: 2.7.2 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 3.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.1 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.8.3 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.1 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.10.3 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Topography: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.28.4 ChimeraX-uniprot: 2.2.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.1 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.1.3 contourpy: 1.0.7 cxservices: 1.2.2 cycler: 0.11.0 Cython: 0.29.33 debugpy: 1.6.7 decorator: 5.1.1 docutils: 0.19 executing: 1.2.0 filelock: 3.9.0 fonttools: 4.39.3 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.8.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.35 imagecodecs: 2022.2.22 imagesize: 1.4.1 importlib-metadata: 6.6.0 ipykernel: 6.21.1 ipython: 8.10.0 ipython-genutils: 0.2.0 ipywidgets: 8.0.6 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.0.2 jupyter-core: 5.3.0 jupyterlab-widgets: 3.0.7 kiwisolver: 1.4.4 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.2 matplotlib: 3.6.3 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.2 networkx: 2.8.8 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.4 numpy: 1.23.5 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.3.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 3.5.0 prompt-toolkit: 3.0.38 psutil: 5.9.4 ptyprocess: 0.7.0 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.14.0 pynrrd: 1.0.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.4.2 PyQt6-Qt6: 6.4.3 PyQt6-sip: 13.4.1 PyQt6-WebEngine-commercial: 6.4.0 PyQt6-WebEngine-Qt6: 6.4.3 python-dateutil: 2.8.2 pytz: 2023.3 pyzmq: 25.0.2 qtconsole: 5.4.0 QtPy: 2.3.1 RandomWords: 0.4.0 requests: 2.28.2 scipy: 1.9.3 setuptools: 67.4.0 setuptools-scm: 7.0.5 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.4.1 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.4 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.1 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 stack-data: 0.6.2 tables: 3.7.0 tcia-utils: 1.2.0 tifffile: 2022.10.10 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.3.1 traitlets: 5.9.0 typing-extensions: 4.5.0 tzdata: 2023.3 urllib3: 1.26.15 wcwidth: 0.2.6 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.7 zipp: 3.15.0 }}} " defect closed normal Surface can't reproduce Eric Pettersen all ChimeraX