Crash no Python or C stack traces, after running AlphaFold prediction

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-11.7.10-x86_64-i386-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Process:               ChimeraX [1645]
Path:                  /private/var/folders/*/ChimeraX-1.8.app/Contents/MacOS/ChimeraX
Identifier:            edu.ucsf.cgl.ChimeraX
Version:               ???
Code Type:             X86-64 (Native)
Parent Process:        ??? [1]
Responsible:           ChimeraX [1645]
User ID:               501

Date/Time:             2024-06-20 18:03:07.015 -0400
OS Version:            macOS 11.7.10 (20G1427)
Report Version:        12
Anonymous UUID:        FCDDA036-C5B4-36FE-D719-51D652E088E7


Time Awake Since Boot: 2400 seconds

System Integrity Protection: enabled

Crashed Thread:        Unknown

Exception Type:        EXC_BAD_ACCESS (SIGBUS)
Exception Codes:       KERN_MEMORY_ERROR at 0x000000010d010000
Exception Note:        EXC_CORPSE_NOTIFY

Termination Signal:    Bus error: 10
Termination Reason:    Namespace SIGNAL, Code 0xa
Terminating Process:   exc handler [1645]

VM Regions Near 0x10d010000:
--> mapped file                 10d010000-10d014000    [   16K] r-x/r-x SM=COW  Object_id=a59380ff
    mapped file                 10d014000-10d018000    [   16K] rw-/rw- SM=COW  Object_id=a59380ff

Backtrace not available

Unknown thread crashed with X86 Thread State (64-bit):
  rax: 0x0000000113535a90  rbx: 0x00007ffee2bef8f8  rcx: 0x000000000000000c  rdx: 0x00007ffee2bef8c8
  rdi: 0x000000010d010000  rsi: 0x00007ffee2bef918  rbp: 0x00007ffee2bef8b0  rsp: 0x00007ffee2bef870
   r8: 0x0000000000000073   r9: 0x0000000113497000  r10: 0x0000000000000010  r11: 0x0000000000000206
  r12: 0x00007ffee2bef8c8  r13: 0x000000010d010000  r14: 0x00007ffee2bef918  r15: 0x000000010d010000
  rip: 0x00000001134c7781  rfl: 0x0000000000010202  cr2: 0x000000010d010000
  
Logical CPU:     1
Error Code:      0x00000004 (no mapping for user data read)
Trap Number:     14

Unknown thread instruction stream:
  c3 55 48 89 e5 83 7f 0c-05 0f 94 c0 5d c3 90 55  .UH.........]..U
  48 89 e5 b9 08 00 00 00-48 8d 15 90 e5 06 00 48  H.......H......H
  8d 05 d2 2f 06 00 39 3c-11 74 0f 48 83 c1 10 48  .../..9 open "/Users/carloscordova/Downloads/prediction_SPAG17_PRM1 and
> PRM2/selected_prediction.pdb"

Chain information for selected_prediction.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> nucleotides atoms

> style nucleic stick

Changed 0 atom styles  

> sequence chain #1/A

Alignment identifier is 1/A  

> select add #1

38153 atoms, 38549 bonds, 2376 residues, 1 model selected  

> select subtract #1

Nothing selected  

> select add #1

38153 atoms, 38549 bonds, 2376 residues, 1 model selected  

> select subtract #1

Nothing selected  

> show target m

> color bychain

> mlp

Map values for surface "selected_prediction.pdb_A SES surface": minimum
-28.57, mean -3.834, maximum 26.88  
Map values for surface "selected_prediction.pdb_B SES surface": minimum
-23.46, mean -4.006, maximum 20.78  
Map values for surface "selected_prediction.pdb_C SES surface": minimum
-22.74, mean -4.66, maximum 22.28  
To also show corresponding color key, enter the above mlp command and add key
true  

> mlp

Map values for surface "selected_prediction.pdb_A SES surface": minimum
-28.57, mean -3.834, maximum 26.88  
Map values for surface "selected_prediction.pdb_B SES surface": minimum
-23.46, mean -4.006, maximum 20.78  
Map values for surface "selected_prediction.pdb_C SES surface": minimum
-22.74, mean -4.66, maximum 22.28  
To also show corresponding color key, enter the above mlp command and add key
true  

> undo

> redo

> select
> /A:34-40,65-69,221-226,246-252,316-322,369-373,521-524,784-788,806-810,818-823,831-839,1019-1023,1030-1038,1045-1053,1058-1066,1069-1076,1119-1125,1131-1134,1226-1228,1234-1241,1254-1261,1282-1287,1293-1297,1302-1305,1311-1314,1392-1396,1402-1406,1409-1411,1419-1423,1430-1434,1439-1442,1448-1451,1457-1468,1483-1494,1500-1504,1510-1513,1519-1522,1528-1531,1537-1540,1546-1549,1570-1573,1579-1584,1590-1594,1599-1602,1641-1645,1651-1655,1674-1679,1687-1694,1762-1770,2076-2079,2083-2089,2093-2102,2110-2112,2121-2125,2135-2143,2155-2166,2169-2180,2201-2203

5874 atoms, 5875 bonds, 352 residues, 1 model selected  

> hide target m

> show target m

> mlp sel

Map values for surface "selected_prediction.pdb_A SES surface": minimum
-28.57, mean -3.834, maximum 26.88  
To also show corresponding color key, enter the above mlp command and add key
true  

> select add #1

38153 atoms, 38549 bonds, 2376 residues, 2 models selected  

> select subtract #1

3 models selected  

> color bychain

> alphafold contacts /A toAtoms /B distance 8

Structure selected_prediction.pdb #1 does not have PAE data opened  

> open "/Users/carloscordova/Downloads/prediction_SPAG17_PRM1 and
> PRM2/predicted_aligned_error.json"

Opened AlphaFold PAE with values for 2376 residues and atoms  

> alphafold contacts /A toAtoms /B distance 8

Found 511 residue or atom pairs within distance 8  

> style ball

Changed 38153 atom styles  

> save "/Users/carloscordova/Downloads/prediction_SPAG17_PRM1 and
> PRM2/test1.cxs"

> select add #1

38153 atoms, 38549 bonds, 511 pseudobonds, 2376 residues, 2 models selected  

> select subtract #1

3 models selected  

> show target m

> color bychain

> select /A:181-270

1402 atoms, 1414 bonds, 90 residues, 1 model selected  

> select /A:181-405

3587 atoms, 3625 bonds, 225 residues, 1 model selected  

> undo

> redo

> undo

> select
> /A:13-16,18-23,44-58,70-87,104-114,122-152,154-157,159-162,206-208,231-239,256-270,275-304,311-314,324-326,334-367,427-433,438-440,443-458,464-466,478-490,495-505,508-511,528-535,544-554,556-561,571-585,592-605,639-667,768-774,790-802,846-853,858-891,942-945,948-951,1149-1155,1263-1267,1269-1272,1278-1280,1561-1567,1610-1612,1624-1629,1657-1669,1776-1802,1811-1825,1832-1854,1866-1872,1887-1902,1915-1917,1919-1922,2063-2065,2117-2119,2149-2151,2182-2187

9284 atoms, 9317 bonds, 559 residues, 1 model selected  

> save "/Users/carloscordova/Downloads/prediction_SPAG17_PRM1 and
> PRM2/Joint.cxs"

> show #!1 target m

> ui tool show "Show Sequence Viewer"

> sequence chain /B

Alignment identifier is 1/B  

> ui tool show "Show Sequence Viewer"

> sequence chain /C

Alignment identifier is 1/C  

> coulombic sel

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for selected_prediction.pdb_A SES surface #1.1: minimum,
-20.73, mean -1.75, maximum 23.10  
To also show corresponding color key, enter the above coulombic command and
add key true  

> undo

> show #!1 target m

> select /B:10-12,14-19

183 atoms, 183 bonds, 9 residues, 1 model selected  

> color sel bychain

> alphafold contacts /A toAtoms /B toAtoms C/ distance 8

Invalid "toAtoms" argument: only initial part "C" of atom specifier valid  

> select add #1

38153 atoms, 38549 bonds, 511 pseudobonds, 2376 residues, 3 models selected  

> select subtract #1

3 models selected  

> style ball

Changed 38153 atom styles  

Color zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic
models, 0 maps.  

Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 1 atomic models, 0 maps.  

> show atoms

> show cartoons

> show surfaces

> show target m

> select add #1

38153 atoms, 38549 bonds, 511 pseudobonds, 2376 residues, 2 models selected  

> select subtract #1

3 models selected  

> ui tool show Contacts

> contacts ignoreHiddenModels true

20334 contacts  

> ui tool show "Dock Prep"

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Summary of feedback from adding hydrogens to selected_prediction.pdb #1  
---  
notes | No usable SEQRES records for selected_prediction.pdb (#1) chain A; guessing termini instead  
No usable SEQRES records for selected_prediction.pdb (#1) chain B; guessing
termini instead  
No usable SEQRES records for selected_prediction.pdb (#1) chain C; guessing
termini instead  
Chain-initial residues that are actual N termini: /A MET 1, /B MET 1, /C MET 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A HIS 2223, /B HIS 51, /C HIS
102  
Chain-final residues that are not actual C termini:  
1613 hydrogen bonds  
0 hydrogens added  
  
Closest equivalent command: addcharge standardizeResidues none  
Using Amber 20 recommended default charges and atom types for standard
residues  
Dock prep finished  
Must select at least one chain from each list  

> interfaces select /C & ::polymer_type>0 contacting /A & ::polymer_type>0
> areaCutoff 0

18 contacting residues  

> sequence associate /A 1/B

Associated selected_prediction.pdb chain A to chain B with 49 mismatches
and/or gaps  

> sequence disassociate /B 1/B

Disassociated selected_prediction.pdb chain B from chain B  

> sequence associate /B 1/B

Associated selected_prediction.pdb chain B to chain B with 0 mismatches  

> save "/Users/carloscordova/Downloads/prediction_SPAG17_PRM1 and
> PRM2/SPAG17_prm1_2.cxs"

> select /B:9-51

821 atoms, 826 bonds, 506 pseudobonds, 43 residues, 2 models selected  

> select /A:2217,2219-2223/B:2,4-8

193 atoms, 192 bonds, 18 pseudobonds, 12 residues, 2 models selected  

> select /B:9-51

821 atoms, 826 bonds, 506 pseudobonds, 43 residues, 2 models selected  

> select /A:2217,2219-2223/B:2,4-8

193 atoms, 192 bonds, 18 pseudobonds, 12 residues, 2 models selected  

> ui tool show "AlphaFold Error Plot"

> alphafold pae #1 file "/Users/carloscordova/Downloads/prediction_SPAG17_PRM1
> and PRM2/predicted_aligned_error.json"

> color /A:1386-1823 lime

> color /A:1818-2063 lime

> save "/Users/carloscordova/Downloads/prediction_SPAG17_PRM1 and
> PRM2/SPAG17_prm1_2_2.cxs"

> close session

> ui tool show AlphaFold

> toolshed show

> alphafold predict
> MAPKKEKGGTVNTSSKIWEPSLIAAQFNQNDWQASIAFVVGNQIEDDLLIQALTVAVQVPQRKLFSMVSWQDILQQINEINTLVGSASSKKAKKPVGGNAPLYYEVLTAAKAIMDSGEKLTLPLIGKLLKFQLLQIKFKDQQRRENEKKVIEDKPKLEKDKGKAKSPKEKKAPSAKPAKGKGKDQPEANAPVKKTTQLKRRGEDDHTNRYIDDEPDDGAQHYIIVVGFNNPQLLAIMAELGIPITSVIKISSENYEPLQTHLAAVNQQQEVLLQSEDLEAEKLKKENAIKELKTFWKYLEPVLNNEKPETNLFDVARLEYMVKAADFPSDWSDGEMMLKLGTDIFENIACLMYDILDWKRQHQHYLESMQLINVPQVVNEKPVLEAMPTSEAPQPAVPAPGKKKAQYEEPQAPPPVTSVITTEVDMRYYNYLLNPIREEFISVPLILHCMLEQVVATEEDLVPPSLREPSPRADGLDHRIAAHIVSLLPSLCLSEREKKNLHDIFLSEEENESKAVPKGPLLLNYHDAHAHKKYALQDQKNFDPVQIEQEMQSKLPLWEFLQFPLPPPWNNTKRLATIHELMHFCTSDVLSWNEVERAFKVFTFESLKLSEVDEKGKLKPSGMMCGSDSEMFNIPWDNPARFAKQIRQQYVMKMNTQEAKQKADIKIKDRTLFVDQNLSMSVQDNESNREPSDPSQCDANNMKHSDLNNLKLSVPDNRQLLEQESIMKAQPQHESLEQTTNNEIKDDAVTKADSHEKKPKKMMVEADLEDIKKTQQRSLMDWSFTEHFKPKVLLQVLQEAHKQYRCVDSYYHTQDNSLLLVFHNPMNRQRLHCEYWNIALHSNVGFRNYLELVAKSIQDWITKEEAIYQESKMNEKIIRTRAELELKSSANAKLTSASKIFSIKESKSNKGISKTEISDQEKEKEKEKIPFILEGSLKAWKEEQHRLAEEERLREEKKAEKKGKEAGKKKGKDNAEKEDSRSLKKKSPYKEKSKEEQVKIQEVTEESPHQPEPKITYPFHGYNMGNIPTQISGSNYYLYPSDGGQIEVEKTMFEKGPTFIKVRVVKDNHNFMIHLNDPKEIVKKEEKGDYYLEEEEEGDEEQSLETEVSDAKNKAFSKFGSFSATLENGICLSISYYGSNGMAPEDKDPDLETILNIPSALTPTVVPVIVTVPQSKAKGKIKGKEKPKESLKEEEHPKEEEKKEEEVEPEPVLQETLDVPTFQSLNVSCPSGLLLTFIGQESTGQYVIDEEPTWDIMVRQSYPQRVKHYEFYKTVMPPAEQEASRVITSQGTVVKYMLDGSTQILFADGAVSRSPNSGLICPPSEMPATPHSGDLMDSISQQKSETIPSEITNTKKGKSHKSQSSMAHKGEIHDPPPEAVQTVTPVEVHIGTWFTTTPEGNRIGTKGLERIADLTPLLSFQATDPVNGTVMTTREDKVVIVERKDGTRIVDHADGTRITTFYQVYEDQIILPDDQETTEGPRTVTRQVKCMRVESSRYATVIANCEDSSCCATFGDGTTIIAKPQGTYQVLPPNTGSLYIDKDCSAVYCHESSSNIYYPFQKREQLRAGRYIMRHTSEVICEVLDPEGNTFQVMADGSISTILPEKKLEDDLNEKTEGYDSLSSMHLEKNHQQIYGEHVPRFFVMYADGSGMELLRDSDIEEYLSLAYKESNTVVLQEPVQEQPGTLTITVLRPFHEASPWQVKKEDTIVPPNLRSRSWETFPSVEKKTPGPPFGTQIWKGLCIESKQLVSAPGAILKSPSVLQMRQFIQHEVIKNEVKLRLQVSLKDYINYILKKEDELQEMMVKDSRTEEERGNAADLLKLVMSFPKMEETTKSHVTEVAAHLTDLFKQSLATPPKCPPDTFGKDFFEKTWRHTASSKRWKEKIDKTRKEIETTQNYLMDIKNRIIPPFFKSELNQLYQSQYNHLDSLSKKLPSFTKKNEDANETAVQDTSDLNLDFKPHKVSEQKSSSVPSLPKPEISADKKDFTAQNQTENLTKSPEEAESYEPVKIPTQSLLQDVAGQTRKEKVKLPHYLLSSKPKSQPLAKVQDSVGGKVNTSSVASAAINNAKSSLFGFHLLPSSVKFGVLKEGHTYATVVKLKNVGVDFCRFKVKQPPPSTGLKVTYKPGPVAAGMQTELNIELFATAVGEDGAKGSAHISHNIEIMTEHEVLFLPVEATVLTSSNYDKRPKDFPQGKENPMVQRTSTIYSSTLGVFMSRKVSPH:MADNEKLDNQRLKNFKNKGRDLETMRRQRNEVVVELRKNKRDEHLLKRRNVPHEDICEDSDIDGDYRVQNTSLEAIVQNASSDNQGIQLSAVQAARKLLSSDRNPPIDDLIKSGILPILVHCLERDDNPSLQFEAAWALTNIASGTSEQTQAVVQSNAVPLFLRLLHSPHQNVCEQAVWALGNIIGDGPQCRDYVISLGVVKPLLSFISPSIPITFLRNVTWVMVNLCRHKDPPPPMETIQEILPALCVLIHHTDVNILVDTVWALSYLTDAGNEQIQMVIDSGIVPHLVPLLSHQEVKVQTAALRAVGNIVTGTDEQTQVVLNCDALSHFPALLTHPKEKINKEAVWFLSNITAGNQQQVQAVIDANLVPMIIHLLDKGDFGTQKEAAWAISNLTISGRKDQVAYLIQQNVIPPFCNLLTVKDAQVVQVVLDGLSNILKMAEDEAETIGNLIEECGGLEKIEQLQNHENEDIYKLAYEIIDQFFSSDDIDEDPSLVPEAIQGGTFGFNSSANVPTEGFQF

Missing or invalid "sequences" argument: Sequences argument
"MAPKKEKGGTVNTSSKIWEPSLIAAQFNQNDWQASIAFVVGNQIEDDLLIQALTVAVQVPQRKLFSMVSWQDILQQINEINTLVGSASSKKAKKPVGGNAPLYYEVLTAAKAIMDSGEKLTLPLIGKLLKFQLLQIKFKDQQRRENEKKVIEDKPKLEKDKGKAKSPKEKKAPSAKPAKGKGKDQPEANAPVKKTTQLKRRGEDDHTNRYIDDEPDDGAQHYIIVVGFNNPQLLAIMAELGIPITSVIKISSENYEPLQTHLAAVNQQQEVLLQSEDLEAEKLKKENAIKELKTFWKYLEPVLNNEKPETNLFDVARLEYMVKAADFPSDWSDGEMMLKLGTDIFENIACLMYDILDWKRQHQHYLESMQLINVPQVVNEKPVLEAMPTSEAPQPAVPAPGKKKAQYEEPQAPPPVTSVITTEVDMRYYNYLLNPIREEFISVPLILHCMLEQVVATEEDLVPPSLREPSPRADGLDHRIAAHIVSLLPSLCLSEREKKNLHDIFLSEEENESKAVPKGPLLLNYHDAHAHKKYALQDQKNFDPVQIEQEMQSKLPLWEFLQFPLPPPWNNTKRLATIHELMHFCTSDVLSWNEVERAFKVFTFESLKLSEVDEKGKLKPSGMMCGSDSEMFNIPWDNPARFAKQIRQQYVMKMNTQEAKQKADIKIKDRTLFVDQNLSMSVQDNESNREPSDPSQCDANNMKHSDLNNLKLSVPDNRQLLEQESIMKAQPQHESLEQTTNNEIKDDAVTKADSHEKKPKKMMVEADLEDIKKTQQRSLMDWSFTEHFKPKVLLQVLQEAHKQYRCVDSYYHTQDNSLLLVFHNPMNRQRLHCEYWNIALHSNVGFRNYLELVAKSIQDWITKEEAIYQESKMNEKIIRTRAELELKSSANAKLTSASKIFSIKESKSNKGISKTEISDQEKEKEKEKIPFILEGSLKAWKEEQHRLAEEERLREEKKAEKKGKEAGKKKGKDNAEKEDSRSLKKKSPYKEKSKEEQVKIQEVTEESPHQPEPKITYPFHGYNMGNIPTQISGSNYYLYPSDGGQIEVEKTMFEKGPTFIKVRVVKDNHNFMIHLNDPKEIVKKEEKGDYYLEEEEEGDEEQSLETEVSDAKNKAFSKFGSFSATLENGICLSISYYGSNGMAPEDKDPDLETILNIPSALTPTVVPVIVTVPQSKAKGKIKGKEKPKESLKEEEHPKEEEKKEEEVEPEPVLQETLDVPTFQSLNVSCPSGLLLTFIGQESTGQYVIDEEPTWDIMVRQSYPQRVKHYEFYKTVMPPAEQEASRVITSQGTVVKYMLDGSTQILFADGAVSRSPNSGLICPPSEMPATPHSGDLMDSISQQKSETIPSEITNTKKGKSHKSQSSMAHKGEIHDPPPEAVQTVTPVEVHIGTWFTTTPEGNRIGTKGLERIADLTPLLSFQATDPVNGTVMTTREDKVVIVERKDGTRIVDHADGTRITTFYQVYEDQIILPDDQETTEGPRTVTRQVKCMRVESSRYATVIANCEDSSCCATFGDGTTIIAKPQGTYQVLPPNTGSLYIDKDCSAVYCHESSSNIYYPFQKREQLRAGRYIMRHTSEVICEVLDPEGNTFQVMADGSISTILPEKKLEDDLNEKTEGYDSLSSMHLEKNHQQIYGEHVPRFFVMYADGSGMELLRDSDIEEYLSLAYKESNTVVLQEPVQEQPGTLTITVLRPFHEASPWQVKKEDTIVPPNLRSRSWETFPSVEKKTPGPPFGTQIWKGLCIESKQLVSAPGAILKSPSVLQMRQFIQHEVIKNEVKLRLQVSLKDYINYILKKEDELQEMMVKDSRTEEERGNAADLLKLVMSFPKMEETTKSHVTEVAAHLTDLFKQSLATPPKCPPDTFGKDFFEKTWRHTASSKRWKEKIDKTRKEIETTQNYLMDIKNRIIPPFFKSELNQLYQSQYNHLDSLSKKLPSFTKKNEDANETAVQDTSDLNLDFKPHKVSEQKSSSVPSLPKPEISADKKDFTAQNQTENLTKSPEEAESYEPVKIPTQSLLQDVAGQTRKEKVKLPHYLLSSKPKSQPLAKVQDSVGGKVNTSSVASAAINNAKSSLFGFHLLPSSVKFGVLKEGHTYATVVKLKNVGVDFCRFKVKQPPPSTGLKVTYKPGPVAAGMQTELNIELFATAVGEDGAKGSAHISHNIEIMTEHEVLFLPVEATVLTSSNYDKRPKDFPQGKENPMVQRTSTIYSSTLGVFMSRKVSPH:MADNEKLDNQRLKNFKNKGRDLETMRRQRNEVVVELRKNKRDEHLLKRRNVPHEDICEDSDIDGDYRVQNTSLEAIVQNASSDNQGIQLSAVQAARKLLSSDRNPPIDDLIKSGILPILVHCLERDDNPSLQFEAAWALTNIASGTSEQTQAVVQSNAVPLFLRLLHSPHQNVCEQAVWALGNIIGDGPQCRDYVISLGVVKPLLSFISPSIPITFLRNVTWVMVNLCRHKDPPPPMETIQEILPALCVLIHHTDVNILVDTVWALSYLTDAGNEQIQMVIDSGIVPHLVPLLSHQEVKVQTAALRAVGNIVTGTDEQTQVVLNCDALSHFPALLTHPKEKINKEAVWFLSNITAGNQQQVQAVIDANLVPMIIHLLDKGDFGTQKEAAWAISNLTISGRKDQVAYLIQQNVIPPFCNLLTVKDAQVVQVVLDGLSNILKMAEDEAETIGNLIEECGGLEKIEQLQNHENEDIYKLAYEIIDQFFSSDDIDEDPSLVPEAIQGGTFGFNSSANVPTEGFQF"
is not a chain specifier, alignment id, UniProt id, or sequence characters  

> open "/Users/carloscordova/Downloads/prediction_SPAG17_PRM1 and
> PRM2/SPAG17_prm1_2_2.cxs" format session

opened ChimeraX session  

> alphafold contacts /A toAtoms C/ distance 8

Invalid "toAtoms" argument: only initial part "C" of atom specifier valid  

> alphafold contacts to C/ distance 8

Missing or invalid "atoms" argument: invalid atoms specifier  

> alphafold contacts A/ to C/ distance 8

Missing or invalid "atoms" argument: invalid atoms specifier  

> interfaces select & ~solvent

Missing or invalid "atoms" argument: invalid atoms specifier  

> alphafold contacts A/ to B/ to C/ distance 8

Missing or invalid "atoms" argument: invalid atoms specifier  

> interfaces select & ~solvent

Missing or invalid "atoms" argument: invalid atoms specifier  

> select /A

35362 atoms, 35734 bonds, 17853 pseudobonds, 2223 residues, 2 models selected  

> alphafold contacts A/ to B/ to C/ distance 8

Missing or invalid "atoms" argument: invalid atoms specifier  

> alphafold contacts A/ to C/ distance 8

Missing or invalid "atoms" argument: invalid atoms specifier  

> alphafold contacts /A toAtoms /C distance 8

Structure selected_prediction.pdb #1 does not have PAE data opened  

Color zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic
models, 0 maps.  

Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 1 atomic models, 0 maps.  

> interfaces select & ~solvent

Missing or invalid "atoms" argument: invalid atoms specifier  

> close

> ui tool show AlphaFold

> open "/Users/carloscordova/Downloads/prediction_SPAG17_PRM1 and
> PRM2/SPAG17_prm1_2_2.cxs" format session

opened ChimeraX session  

> ui tool show "AlphaFold Error Plot"

> alphafold pae #1 file "/Users/carloscordova/Downloads/prediction_SPAG17_PRM1
> and PRM2/predicted_aligned_error.json"

> conects /A to /C distance 6

Unknown command: alphafold conects /A to /C distance 6  

> conects /A to /C distance 8

Unknown command: alphafold conects /A to /C distance 8  

> alphafold contacts /A toAtoms /C distance 8

Found 358 residue or atom pairs within distance 8  
Destroying pre-existing alignment with identifier 1/A  
Alignment identifier is 1/A  
Destroying pre-existing alignment with identifier 1/B  
Alignment identifier is 1/B  

> show target m

> interfaces select & ~solvent

Missing or invalid "atoms" argument: invalid atoms specifier  

> show sel atoms

> hbonds sel reveal true

9 hydrogen bonds found  

> interfaces select & ~solvent

Missing or invalid "atoms" argument: invalid atoms specifier  

> label (#!1 & sel) attribute label_specifier

> interfaces select & ~solvent

Missing or invalid "atoms" argument: invalid atoms specifier  

> label (#!1 & sel) text "/{0.chain_id} {0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> save "/Users/carloscordova/Downloads/prediction_SPAG17_PRM1 and
> PRM2/SPAG17_prm1_2_3.cxs"

> select down

193 atoms, 192 bonds, 18 pseudobonds, 12 residues, 2 models selected  

> ~hbonds

> style sel ball

Changed 193 atom styles  

> view /A:747

> label (#!1 & sel) text "/{0.chain_id} {0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> label (#!1 & sel) attribute label_specifier

Destroying pre-existing alignment with identifier 1/A  
Alignment identifier is 1/A  
Destroying pre-existing alignment with identifier 1/B  
Alignment identifier is 1/B  

> undo

> show sel atoms

> ui tool show "Show Sequence Viewer"

> ui tool show ViewDockX

No suitable models found for ViewDockX  

> toolshed show

> view /A:749

> show (#!1 & sel) target ab

> style (#!1 & sel) stick

Changed 193 atom styles  

> show (#!1 & sel-residues & sidechain) target ab

> view sel

> undo

> select
> /A:13-16,18-23,44-58,70-87,104-114,122-152,154-157,159-162,206-208,231-239,256-270,275-304,311-314,324-326,334-367,427-433,438-440,443-458,464-466,478-490,495-505,508-511,528-535,544-554,556-561,571-585,592-605,639-667,768-774,790-802,846-853,858-891,942-945,948-951,1149-1155,1263-1267,1269-1272,1278-1280,1561-1567,1610-1612,1624-1629,1657-1669,1776-1802,1811-1825,1832-1854,1866-1872,1887-1902,1915-1917,1919-1922,2063-2065,2117-2119,2149-2151,2182-2187

9284 atoms, 9317 bonds, 4116 pseudobonds, 559 residues, 2 models selected  

> select
> /A:13-16,18-23,44-58,70-87,104-114,122-152,154-157,159-162,206-208,231-239,256-270,275-304,311-314,324-326,334-367,427-433,438-440,443-458,464-466,478-490,495-505,508-511,528-535,544-554,556-561,571-585,592-605,639-667,768-774,790-802,846-853,858-891,942-945,948-951,1149-1155,1263-1267,1269-1272,1278-1280,1561-1567,1610-1612,1624-1629,1657-1669,1776-1802,1811-1825,1832-1854,1866-1872,1887-1902,1915-1917,1919-1922,2063-2065,2117-2119,2149-2151,2182-2187

9284 atoms, 9317 bonds, 4116 pseudobonds, 559 residues, 2 models selected  

> undo

> hide #* target a

> show (#!1 & sel) target ab

> undo

Drag select of selected_prediction.pdb_A SES surface, 73163 of 3586690
triangles, selected_prediction.pdb_C SES surface, 63322 of 269958 triangles,
59 residues, 89 pseudobonds  

> show (#!1 & sel) target ab

> view sel

> undo

> show (#!1 & sel) target ab

> label (#!1 & sel) text "/{0.chain_id} {0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> style sel ball

Changed 990 atom styles  

> style sel ball

Changed 990 atom styles  

> style (#!1 & sel) ball

Changed 990 atom styles  

> select clear

Drag select of selected_prediction.pdb_A SES surface, 304181 of 3586690
triangles, selected_prediction.pdb_C SES surface, 32262 of 269958 triangles,
223 residues, 842 pseudobonds  

> label (#!1 & sel) text "/{0.chain_id} {0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> undo

> redo

> ~label (#!1 & sel) residues

> undo

Drag select of selected_prediction.pdb_A SES surface, 21800 of 3586690
triangles, selected_prediction.pdb_C SES surface, 3846 of 269958 triangles, 25
residues, 87 pseudobonds  
Drag select of selected_prediction.pdb_A SES surface, 54367 of 3586690
triangles, selected_prediction.pdb_C SES surface, 9787 of 269958 triangles, 45
residues, 236 pseudobonds  

> undo

Drag select of selected_prediction.pdb_A SES surface, 351675 of 3586690
triangles, selected_prediction.pdb_C SES surface, 32324 of 269958 triangles,
272 residues, 988 pseudobonds  

> show (#!1 & sel-residues & sidechain) target ab

> show (#!1 & sel) target ab

> view sel

> undo

> show (#!1 & sel) target ab

> save "/Users/carloscordova/Downloads/prediction_SPAG17_PRM1 and
> PRM2/SPAG17_prm1_2_4.cxs"

> close session

> open "/Users/carloscordova/Downloads/prediction_SPAG17_PRM1 and
> PRM2/selected_prediction.pdb" format pdb

Chain information for selected_prediction.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> color bychain

Drag select of 211 residues  

> style sel ball

Changed 3517 atom styles  

> sequence chain #1/A

Alignment identifier is 1/A  

> select /B:1-51

965 atoms, 971 bonds, 51 residues, 1 model selected  

> select /A:1-2223

35362 atoms, 35734 bonds, 2223 residues, 1 model selected  

> select /B:1-51

965 atoms, 971 bonds, 51 residues, 1 model selected  

> undo

> alphafold contacts /A toAtoms /C distance 8

Structure selected_prediction.pdb #1 does not have PAE data opened  

> ui tool show "AlphaFold Error Plot"

> alphafold pae #1 file "/Users/carloscordova/Downloads/prediction_SPAG17_PRM1
> and PRM2/predicted_aligned_error.json"

> alphafold contacts /A toAtoms /C distance 8

Found 358 residue or atom pairs within distance 8  
Drag select of 17 residues, 19 pseudobonds  

> ui tool show "Show Sequence Viewer"

> sequence chain /B

Alignment identifier is 1/B  

> ui tool show "Show Sequence Viewer"

> sequence chain /C

Alignment identifier is 1/C  

> show (#!1 & sel) target ab

> label (#!1 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> undo

> redo

> label (#!1 & sel) text "/{0.chain_id} {0.label_one_letter_code}
> {0.number}{0.insertion_code}"

Drag select of 26 residues, 42 pseudobonds  

> show (#!1 & sel) target ab

> label (#!1 & sel) text "/{0.chain_id} {0.label_one_letter_code}
> {0.number}{0.insertion_code}"

Drag select of 275 residues, 274 pseudobonds  

> show (#!1 & sel) target ab

> undo

Drag select of 1 residues  

> undo

Drag select of 306 residues, 296 pseudobonds  

> select subtract /A:2139

5605 atoms, 357 pseudobonds, 348 residues, 2 models selected  

> select subtract /A:2097

5589 atoms, 357 pseudobonds, 347 residues, 2 models selected  

> undo

Drag select of 35 residues, 114 pseudobonds  
Drag select of 50 residues, 111 pseudobonds  
Drag select of 31 residues, 11 pseudobonds  

> select add /A:1651

2570 atoms, 6 bonds, 283 pseudobonds, 160 residues, 2 models selected  

> select add /A:787

2587 atoms, 23 bonds, 283 pseudobonds, 161 residues, 2 models selected  

> select add /A:1652

2604 atoms, 39 bonds, 283 pseudobonds, 162 residues, 2 models selected  

> select add /A:1643

2624 atoms, 59 bonds, 283 pseudobonds, 163 residues, 2 models selected  

> select add /A:1644

2640 atoms, 74 bonds, 284 pseudobonds, 164 residues, 2 models selected  

> show (#!1 & sel) target ab

> label (#!1 & sel) text "/{0.chain_id} {0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> view sel

> save "/Users/carloscordova/Downloads/prediction_SPAG17_PRM1 and
> PRM2/SPAG17_prm1_2_5.cxs"

> view /C:1

> select /A

35362 atoms, 35734 bonds, 2223 residues, 1 model selected  

> style sel sphere

Changed 35362 atom styles  

> undo

> style sel ball

Changed 35362 atom styles  

> undo

> rainbow sel

> undo

> color bfactor sel

2640 atoms, 164 residues, atom bfactor range 12.6 to 95.4  

> undo

> color sel bypolymer

> undo

> mlp sel

Map values for surface "selected_prediction.pdb_A SES surface": minimum
-28.57, mean -3.834, maximum 26.88  
Map values for surface "selected_prediction.pdb_C SES surface": minimum
-22.74, mean -4.66, maximum 22.28  
To also show corresponding color key, enter the above mlp command and add key
true  

> undo

> close session

> ui tool show AlphaFold

> alphafold predict
> MAPKKEKPTGSANYKIWEPSLIAAHLNQNDWKASIAFVVGNRVEDDLLIHALDLAVRLPQRKLFSIVSWEDILQQMDEIQSLAESASAKKGKKPTSVNLPLHYEVFLAAKIIMESGEKLTLPLIGKLLKCQLLHIKSKDQQRRENEKKMVEERTKSEKDKGKGKSPKEKKVASAKPGKGKSKDQPEATVTVRKTTQLKRRGEDDEAKSYIDDEPDDGAQYYIIVVGFNNPQLLAIMTELGIPITSVIKISSENYEPLQTHLAAVRQQQEAVLQPEDIEAEKLKRKNSIKELEVFWKYLEPILNNEKLEIHLFDVARLQYMVKATYFPSDWSDNEQMLALGTEIFENIACLMYDSLDWKRQHHHYLQSMQLINVPQVVSEKTVLEAITIPEPPPSTAPAPTGKKKAQYEESHAPPTVAFIITTEVDMRYYNDLLNPIPEEFISVSLILHCMVEQVVATEEDLIPPSLVEPAPRADGLDYRIAAHIVSILPSLCLSEKEKKNLREIFLTEGESESKALPKGPLLLNYHDAHAHKKYALKDQKNFDPVQVEQEMQSKLPLWEFLQFPLPPPWNSTKRLATIHELMHFCTNEVLSWNEVERAFKVFTFESLKLSEVDEEGRLKPTETTSDTDVENFNIPWDNPARFAKLIRQRYIHRMSMQKAPPVVVEIENTERTLFVNKNFAKAEQDAQGDENSPNSDEPDAISVTGSTSNSTKPWNSSNRQFSEKETSGSMWPQPESMDQTMDTEIKDDAATKDDSPEKKPKKMVVEADIEDIKKTQQRSLMDWSFTEYFQPKVLLQVLQEAHQQYRCVDSYYHTQDNSLLLVFHNPMNLQRLQCEHWNIALHSNVGFRNYLELVAKSIEDWVTQEEAKYQEAKMAEELNRIRIELELKATVKTSASKIPGPKRSKTNKVSSKTELSDQEKDKEKEKDKIPFVLEGSLKAWKEEQERLAEEERLKEEKKAEKKGKDTGKKKGKDKADKDDAKALKKKSSSKEKPKEEPAKTLEVIEETAPLPVPEVVYPFRGYNMGDIPIQISGTNYYLYPSDGGQIEVEKTRFERGSTFIKVKVKKDKHNFIIHLKDPKEIVKKEKEEKNSEEEEEEEEEKEEVEEKKPKEGEEEKVKQKVEMKRAQIEKEAVSKFGSFSATLENGICLSISYYGSNGMAPEVINSELEAMMNIPSAMTATVVPAVVTVPQGKGKAKPKGKEKHKDSIKEEELPKEEEKKNHIQEEVEPEIVIQESPPYVPTFQNLNVSCPSGLLLTFIGQESTDYSIVDEEPTRNLMIRQSYPQRLKHYEFYKAVMPPLEQEASRVVTSQGTVIKYMLDGSTQILFADGAVSSSPDSGPVYTSPELPTSPHNGDLVDSASQPKSETGPEIIITKKGKGHKNQTVANKSETHDIIPEVPPPTPVESHIGTWFTTTPDGRRIGTKGLEKIEDLKPYLFFQATDPINGTVMTTREDKVIIVEKKDGTRVVDHADGTRITTFYQVYEDHITPSNDEETTEGPRTVTRQVKCMRIESSHYATIITNCEDSSCCATFGDGTSIIAKPQGSYQVLPPNTGCLYIDKDCSATYCHESSNNLYHPFQKREQLRASRYIMKHTSEVICEVQDPEGNTFQVMADGSVSTTLPKKKLEDDFNVQMEGYESLSSLHLEKNHMQIYGEHVPRFFVVYTDGSGVELLRDSDIEEYLSLAYGESTTVVLQEPVQEYPGALSITVLRPFHEASQWIMKKELDTIVPPNLQSRSWERFPSVEKKTPGPPFGTQIWKGLSIGSKQLTNIPAPILEGPKVLQMRQFIQHEVIKNEVKLKLQISLKDYINHILKKEDELQEMTVKDSRTEEERGNAADLLKLVMSFPKMEETTKSHMTKVAAHLTVLFKQSMASAPKCSPDSYSKEFLEKKWRSLSQGTSWKEKLEQQRNNIKKTQSYLMQIKTKEVTPYFKSELSSLFKSKYDYLEKFSKSLPPFVKKNEAKLMTAVPDLYSDSTLTVDTEKEASNTHPLLNQEVAENIQESPREKETEYVNKSLQTSSSQNQYENVTISPKESVYQSQTEIETKDTKESAIQNFTEKFKKYTKKSASQNEIEDLIKSTKESVSQRQTENVTRPPTEEPDIYMPIKIPTQSLLQDVTGQARKEKVRLPYYMMSSKPKSQPYAKVEDPVGGRVNTSSIASAAMYNPNASPFGFHLLPPSVKFGVLKEGHTYATIVKLKNVGVDFCRFRVKQPPPSTGLKVTYKPGPVAAGLQAELKVELFAMAVGEDGAKGSAHISHNIEIMTEHDVLFLPVEATVLTSSNYDNRPKNLPQGKENPMVFRTSTISSSSLGVVMSQKATHH,MADNEKLDNQRLKNFKNKGRDLETMRRQRNEVVVELRKNKRDEHLLKRRNVPQEDICEDSDIDGDYRVQNTSLEAIVQNASSDNQGIQLSAVQAARKLLSSDRNPPIDDLIKSGILPILVHCLERDDNPSLQFEAAWALTNIASGTSEQTQAVVQSNAVPLFLRLLHSPHQNVCEQAVWALGNIIGDGPQCRDYVISLGVVKPLLSFISPSIPITFLRNVTWVMVNLCRHKDPPPPMETIQEILPALCVLIHHTDVNILVDTVWALSYLTDAGNEQIQMVIDSGIVPHLVPLLSHQEVKVQTAALRAVGNIVTGTDEQTQVVLNCDALSHFPALLTHPKEKINKEAVWFLSNITAGNQQQVQAVIDANLVPMIIHLLDKGDFGTQKEAAWAISNLTISGRKDQVAYLIQQNVIPPFCNLLTVKDAQVVQVVLDGLSNILKMAEDQAETIANLIEECGGLEKIEQLQNHENEDIYKLAYEIIDQFFSSDDIDEDPSLVPESVQGGTFGFNSSTNVPTEGFQF

Please cite ColabFold: Making protein folding accessible to all. Nature
Methods (2022) if you use these predictions.  
Running AlphaFold prediction  


===== Log before crash end =====

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 INTEL-16.5.14
OpenGL renderer: Intel Iris OpenGL Engine
OpenGL vendor: Intel Inc.

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro11,1
      Processor Name: Dual-Core Intel Core i5
      Processor Speed: 2.8 GHz
      Number of Processors: 1
      Total Number of Cores: 2
      L2 Cache (per Core): 256 KB
      L3 Cache: 3 MB
      Hyper-Threading Technology: Enabled
      Memory: 8 GB
      System Firmware Version: 478.0.0.0.0
      SMC Version (system): 2.16f68

Software:

    System Software Overview:

      System Version: macOS 11.7.10 (20G1427)
      Kernel Version: Darwin 20.6.0
      Time since boot: 5 minutes

Graphics/Displays:

    Intel Iris:

      Chipset Model: Intel Iris
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x0a2e
      Revision ID: 0x0009
      Metal Family: Supported, Metal GPUFamily macOS 1
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 2.4.1
    Babel: 2.15.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.17
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.7
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.57.1
    ChimeraX-AtomicLibrary: 14.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.6
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.7
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.8
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.4
    ChimeraX-DiffPlot: 1.0
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    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: 1.2.2
    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-IUPAC: 1.0
    ChimeraX-Label: 1.1.10
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.2
    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: 2.1.3
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.1
    ChimeraX-MedicalToolbar: 1.0.3
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.17
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.5
    ChimeraX-PDB: 2.7.5
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.4.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.0.15
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.16.5
    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
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.39.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.3
    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: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.2.1
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.1
    decorator: 5.1.1
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.4
    fonttools: 4.53.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.11.0
    html2text: 2024.2.26
    idna: 3.7
    ihm: 1.0
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.3
    jedi: 0.19.1
    jinja2: 3.1.4
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.11
    kiwisolver: 1.4.5
    line-profiler: 4.1.2
    lxml: 5.2.1
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.8.4
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.0
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.3.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.2
    prompt-toolkit: 3.0.47
    psutil: 5.9.8
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pygments: 2.17.2
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.1.2
    pyproject-hooks: 1.1.0
    PyQt6-commercial: 6.6.1
    PyQt6-Qt6: 6.6.3
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine-commercial: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.3
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pyzmq: 26.0.3
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.13.0
    setuptools: 69.5.1
    setuptools-scm: 8.0.4
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 7.2.6
    sphinx-autodoc-typehints: 2.0.1
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
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    superqt: 0.6.3
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    tornado: 6.4.1
    traitlets: 5.14.2
    typing-extensions: 4.12.2
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.11