Access violation in python_instances_of_class

[Tristan Croll]

The following bug report has been submitted:
Platform:        Windows-10-10.0.22631
ChimeraX Version: 1.8.dev202403220040 (2024-03-22 00:40:30 UTC)
Description
Trying to replicate this in a separate session, so far unsuccessfully. No idea what's going on here.

Log:
> isolde shorthand
    
    
    Initialising ISOLDE-specific command aliases:
    Alias	Equivalent full command
    -------------------------------------------------
    st	isolde step {arguments}
    aw	isolde add water {arguments}
    awsf	isolde add water {arguments} sim false
    al	isolde add ligand {arguments}
    aa	isolde add aa $1 sel {arguments}
    ht	isolde mod his sel {arguments}
    so	setattr sel atoms occupancy {arguments}
    ab	isolde adjust bfactors {arguments}
    ss	isolde sim start sel
    rt	isolde release torsions sel {arguments}
    rd	isolde release distances sel {arguments}
    ra	rd; rt
    pf	isolde pepflip sel
    cf	isolde cisflip sel
    cbb	color bfactor {arguments}
    cbo	color byattr occupancy {arguments}
    cbc	color {arguments} bychain; color {arguments} byhet
    cs	clipper set contourSensitivity {arguments}
    

  
UCSF ChimeraX version: 1.8.dev202403220040 (2024-03-22)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 6pa7

6pa7 title:  
The cryo-EM structure of the human DNMT3A2-DNMT3B3 complex bound to
nucleosome. [more info...]  
  
Chain information for 6pa7 #1  
---  
Chain | Description | UniProt  
A E | Histone H3.2 | H32_XENLA 1-135  
B F | Histone H4 | H4_XENLA 0-102  
C G | Histone H2A type 1 | H2A1_XENLA 1-129  
D H | Histone H2B 1.1 | H2B11_XENLA 1-122  
I | DNA (167-MER) |   
J | DNA (167-MER) |   
K P | DNA (cytosine-5)-methyltransferase 3A | DNM3A_HUMAN 224-912  
N S | DNA (cytosine-5)-methyltransferase 3B | DNM3B_HUMAN 1-770  
  
Non-standard residues in 6pa7 #1  
---  
CL — chloride ion  
SAH — S-adenosyl-L-homocysteine  
  

> cartoon /N,S,K,P

> hide /N,S,K,P

> coulombic /A,E,B,F,C,G,D,H

The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:  
/C ARG 11  
/C LYS 13  
/D LYS 28  
/E ARG 134  
/G LYS 118  
/G LYS 119  
/H LYS 28  

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for 6pa7_A SES surface #1.3: minimum, -16.45, mean 1.55,
maximum 14.23  
Coulombic values for 6pa7_B SES surface #1.4: minimum, -9.10, mean 2.86,
maximum 17.01  
Coulombic values for 6pa7_C SES surface #1.5: minimum, -19.64, mean 1.93,
maximum 13.99  
Coulombic values for 6pa7_D SES surface #1.6: minimum, -14.28, mean 1.30,
maximum 10.39  
Coulombic values for 6pa7_E SES surface #1.7: minimum, -15.63, mean 1.58,
maximum 17.56  
Coulombic values for 6pa7_F SES surface #1.8: minimum, -8.70, mean 2.90,
maximum 15.71  
Coulombic values for 6pa7_G SES surface #1.9: minimum, -18.27, mean 2.21,
maximum 15.33  
Coulombic values for 6pa7_H SES surface #1.10: minimum, -13.07, mean 1.60,
maximum 12.44  

> surface close

> addh

Summary of feedback from adding hydrogens to 6pa7 #1  
---  
warnings | Not adding hydrogens to /C ARG 11 CB because it is missing heavy-atom bond partners  
Not adding hydrogens to /C LYS 13 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /D LYS 28 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /E ARG 134 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /G LYS 118 CB because it is missing heavy-atom bond
partners  
4 messages similar to the above omitted  
notes | Termini for 6pa7 (#1) chain A determined from SEQRES records  
Termini for 6pa7 (#1) chain B determined from SEQRES records  
Termini for 6pa7 (#1) chain C determined from SEQRES records  
Termini for 6pa7 (#1) chain D determined from SEQRES records  
Termini for 6pa7 (#1) chain E determined from SEQRES records  
9 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /K SAH 1001, /P SAH 1001  
Chain-initial residues that are not actual N termini: /A LYS 37, /B LEU 22, /C
ARG 11, /D LYS 28, /E LYS 37, /F LYS 20, /G THR 10, /H ARG 27, /K HIS 613, /K
ASP 845, /N LYS 542, /N GLU 646, /P HIS 613, /P ASP 845, /S LYS 542, /S GLU
646  
Chain-final residues that are actual C termini: /A ALA 135, /B GLY 102, /F GLY
102, /H LYS 122, /K VAL 912, /P VAL 912, /K SAH 1001, /P SAH 1001  
Chain-final residues that are not actual C termini: /C LYS 118, /D ALA 121, /E
ARG 134, /G THR 120, /K THR 832, /N PRO 630, /N PHE 767, /P THR 832, /S PRO
630, /S PHE 767  
Chain-initial residues that are not actual 5' termini: /I DT 2  
Missing OXT added to C-terminal residue /K VAL 912  
Missing OXT added to C-terminal residue /P VAL 912  
1831 hydrogen bonds  
Adding 'H' to /A LYS 37  
Adding 'H' to /B LEU 22  
Adding 'H' to /C ARG 11  
Adding 'H' to /D LYS 28  
Adding 'H' to /E LYS 37  
11 messages similar to the above omitted  
/C LYS 118 is not terminus, removing H atom from 'C'  
/D ALA 121 is not terminus, removing H atom from 'C'  
/E ARG 134 is not terminus, removing H atom from 'C'  
/G THR 120 is not terminus, removing H atom from 'C'  
/N PHE 767 is not terminus, removing H atom from 'C'  
1 messages similar to the above omitted  
/J DA 166 is not terminus, removing H atom from O3'  
18209 hydrogens added  
  

> select /A,E,B,F,C,G,D,H

12490 atoms, 12567 bonds, 773 residues, 1 model selected  

> style sel stick

Changed 12490 atom styles  

> hide H

> coulombic sel

The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:  
/C ARG 11  
/C LYS 13  
/D LYS 28  
/E ARG 134  
/G LYS 118  
/G LYS 119  
/H LYS 28  

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for 6pa7_A SES surface #1.3: minimum, -15.87, mean 2.44,
maximum 14.42  
Coulombic values for 6pa7_B SES surface #1.4: minimum, -9.14, mean 3.81,
maximum 19.63  
Coulombic values for 6pa7_C SES surface #1.5: minimum, -18.86, mean 2.86,
maximum 18.61  
Coulombic values for 6pa7_D SES surface #1.6: minimum, -13.21, mean 2.13,
maximum 12.48  
Coulombic values for 6pa7_E SES surface #1.7: minimum, -15.70, mean 2.43,
maximum 15.27  
Coulombic values for 6pa7_F SES surface #1.8: minimum, -13.16, mean 3.82,
maximum 30.26  
Coulombic values for 6pa7_G SES surface #1.9: minimum, -17.38, mean 3.12,
maximum 19.59  
Coulombic values for 6pa7_H SES surface #1.10: minimum, -13.20, mean 2.47,
maximum 22.11  

> select clear

> lighting gentle multiShadow 255

> lighting soft multiShadow 255

> select /S:765

12 atoms, 11 bonds, 1 residue, 1 model selected  

> label sel text DNMT3B height 4

> select /P:741

10 atoms, 9 bonds, 1 residue, 1 model selected  

> label sel text DNMT3A height 4

> select clear

> lighting fillIntensity 0.5

> lighting fillIntensity 0.3

> close

> open 8qzz structureFactors true overSampling 2.5

Summary of feedback from opening 8qzz fetched from pdb  
---  
warning | WARNING: multiple experimental reflection datasets found:  
F_meas_au, F_meas_sigma_au,  
pdbx_F_plus, pdbx_F_plus_sigma, pdbx_F_minus, pdbx_F_minus_sigma,  
pdbx_anom_difference, pdbx_anom_difference_sigma,  
intensity_meas, intensity_sigma,  
pdbx_I_plus, pdbx_I_plus_sigma, pdbx_I_minus, pdbx_I_minus_sigma  
Automatically choosing "F_meas_au, F_meas_sigma_au".  
notes | Fetching compressed mmCIF 8qzz from http://files.rcsb.org/download/8qzz.cif  
Fetching compressed 8qzz structure factors from
http://files.rcsb.org/download/8qzz-sf.cif  
Resolution: 3.350277671680785  
Launching live xmap mgr took 1.3574819564819336 seconds.  
  
Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 38,38,38, pixel 0.67,0.67,0.659,
shown at level 0.0831, step 1, values float32  
Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 38,38,38, pixel 0.67,0.67,0.659,
shown at level -0.0636,0.0636, step 1, values float32  
Opened (LIVE) 2mFo-DFc_sharp_39 as #1.1.1.4, grid size 38,38,38, pixel
0.67,0.67,0.659, shown at level 0.268, step 1, values float32  
8qzz title:  
Crystal structure of human eIF2 alpha-gamma complexed with PPP1R15A_420-452
[more info...]  
  
Chain information for 8qzz  
---  
Chain | Description | UniProt  
1.2/A | Eukaryotic translation initiation factor 2 subunit 3 | IF2G_HUMAN 1-472  
1.2/B | Eukaryotic translation initiation factor 2 subunit 1 | IF2A_HUMAN 1-315  
1.2/C | Protein phosphatase 1 regulatory subunit 15A | PR15A_HUMAN 420-452  
  
Non-standard residues in 8qzz #1.2  
---  
GNP — phosphoaminophosphonic acid-guanylate ester  
  

> view :GNP

> addh

Summary of feedback from adding hydrogens to 8qzz #1.2  
---  
warnings | Not adding hydrogens to /A LYS 80 CB because it is missing heavy-atom bond partners  
Not adding hydrogens to /A ARG 98 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A ARG 103 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A MET 142 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A GLU 172 CB because it is missing heavy-atom bond
partners  
10 messages similar to the above omitted  
notes | Termini for 8qzz (#1.2) chain A determined from SEQRES records  
Termini for 8qzz (#1.2) chain B determined from SEQRES records  
Termini for 8qzz (#1.2) chain C determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini: /A LEU 10, /A LYS 80, /A
LEU 141, /A GLN 396, /B THR 185, /C SER 426  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A THR 66, /A PRO 136, /A
GLY 383, /A ASP 471, /B ASN 297, /C TYR 434  
502 hydrogen bonds  
Adding 'H' to /A LEU 10  
Adding 'H' to /A LYS 80  
Adding 'H' to /A LEU 141  
Adding 'H' to /A GLN 396  
Adding 'H' to /B THR 185  
1 messages similar to the above omitted  
/A ASP 471 is not terminus, removing H atom from 'C'  
/B ASN 297 is not terminus, removing H atom from 'C'  
/C TYR 434 is not terminus, removing H atom from 'C'  
4285 hydrogens added  
  

> alphafold match #1 trim false

Fetching AlphaFold database settings from
https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database3.json  
Fetching compressed AlphaFold O75807 from
https://alphafold.ebi.ac.uk/files/AF-O75807-F1-model_v4.cif  
3 AlphaFold models found using UniProt identifiers: P41091 (chain A), P05198
(chain B), O75807 (chain C)  
AlphaFold prediction matching 8qzz  
---  
Chain| UniProt Id| UniProt Name| RMSD| Length| Seen| % Id  
C | O75807 | PR15A_HUMAN | 1.81 | 674 | 9 | 100   
B | P05198 | IF2A_HUMAN | 0.79 | 315 | 113 | 100   
A | P41091 | IF2G_HUMAN | 1.74 | 472 | 433 | 100   
  
Opened 3 AlphaFold models  

> isolde start

> set selectionWidth 4

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
Opened (LIVE) MDFF potential as #1.1.1.5, grid size 38,38,38, pixel
0.67,0.67,0.659, shown at level 0.238, step 1, values float32  
Done loading forcefield  

> isolde set simFidelityMode Highest/Slowest

ISOLDE: setting sim fidelity mode to Highest/Slowest  
nonbonded_cutoff_distance = 1.700000  
use_gbsa = True  
gbsa_cutoff = 2.000000  

> matchmaker #2.1 to #1.2

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 8qzz, chain A (#1.2) with AlphaFold IF2G_HUMAN chain A, chain A
(#2.1), sequence alignment score = 2269.1  
RMSD between 351 pruned atom pairs is 1.199 angstroms; (across all 433 pairs:
1.741)  
  

> color #2.1 bychain

> color #2.1 byhetero

> color modify #2.1 hue + 50

ISOLDE: attempting to load PAE matrix for model #2.1 from the AlphaFold-EBI
database. If this fails or you wish to use a different PAE matrix, use the
"Load PAE matrix" button in ISOLDE's reference model restraints widget.  

> alphafold pae #2.1 uniprotId P41091 plot false

s1:
MAGGEAGVTLGQPHLSRQDLTTLDVTKLTPLSHEVISRQATINIGTIGHVAHGKSTVVKAISGVHTVRFKNELERNITIKLGYANAKIYKLDDPSCPRPECYRSCGSSTPDEFPTDIPGTKGNFKLVRHVSFVDCPGHDILMATMLNGAAVMDAALLLIAGNESCPQPQTSEHLAAIEIMKLKHILILQNKIDLVKESQAKEQYEQILAFVQGTVAEGAPIIPISAQLKYNIEVVCEYIVKKIPVPPRDFTSEPRLIVIRSFDVNKPGCEVDDLKGGVAGGSILKGVLKVGQEIEVRPGIVSKDSEGKLMCKPIFSKIVSLFAEHNDLQYAAPGGLIGVGTKIDPTLCRADRMVGQVLGAVGALPEIFTELEISYFLLRRLLGVRTEGDKKAAKVQKLSKNEVLMVNIGSLSTGGRVSAVKADLGKIVLTNPVCTEVGEKIALSRRVEKHWRLIGWGQIRRGVTIKPTVDDD  
s2:
MAGGEAGVTLGQPHLSRQDLTTLDVTKLTPLSHEVISRQATINIGTIGHVAHGKSTVVKAISGVHTVRFKNELERNITIKLGYANAKIYKLDDPSCPRPECYRSCGSSTPDEFPTDIPGTKGNFKLVRHVSFVDCPGHDILMATMLNGAAVMDAALLLIAGNESCPQPQTSEHLAAIEIMKLKHILILQNKIDLVKESQAKEQYEQILAFVQGTVAEGAPIIPISAQLKYNIEVVCEYIVKKIPVPPRDFTSEPRLIVIRSFDVNKPGCEVDDLKGGVAGGSILKGVLKVGQEIEVRPGIVSKDSEGKLMCKPIFSKIVSLFAEHNDLQYAAPGGLIGVGTKIDPTLCRADRMVGQVLGAVGALPEIFTELEISYFLLRRLLGVRTEGDKKAAKVQKLSKNEVLMVNIGSLSTGGRVSAVKADLGKIVLTNPVCTEVGEKIALSRRVEKHWRLIGWGQIRRGVTIKPTVDDD  
s1:
MPGLSCRFYQHKFPEVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSINKLIRIGRNECVVVIRVDKEKGYIDLSKRRVSPEEAIKCEDKFTKSKTVYSILRHVAEVLEYTKDEQLESLFQRTAWVFDDKYKRPGYGAYDAFKHAVSDPSILDSLDLNEDEREVLINNINRRLTPQAVKIRADIEVACYGYEGIDAVKEALRAGLNCSTENMPIKINLIAPPRYVMTTTTLERTEGLSVLSQAMAVIKEKIEEKRGVFNVQMEPK..VVTDTDETELARQMERLERENAEVDGDDDAEEMEAKAED...........................................................................................................................................................................................................................................................................................................................................................................................  
s2:
...........................................................................................................................................................................................................................MAGGEAGVTLGQPHLSRQDLTTLDVTK.LTPLS..HEVISRQATINIGTIGHVAHGKSTVVKAISGVHTVRFKNELERNITIKLGYANAKIYKL..DDPSCPRPECYRSCGSSTPDEFPTDIPGTKGNFKLVRHVSFVDCPGHDILMATMLNGAAVMDAALLLIAGNESCPQPQTSEHLAAIEIMKLKHILILQNKIDLVKESQAKEQYEQILAFVQGTVAEGAPIIPISAQLKYNIEVVCEYIVKKIPVPPRDFTSEPRLIVIRSFDVNKPGCEVDDLKGGVAGGSILKGVLKVGQEIEVRPGIVSKDSEGKLMCKPIFSKIVSLFAEHNDLQYAAPGGLIGVGTKIDPTLCRADRMVGQVLGAVGALPEIFTELEISYFLLRRLLGVRTEGDKKAAKVQKLSKNEVLMVNIGSLSTGGRVSAVKADLGKIVLTNPVCTEVGEKIALSRRVEKHWRLIGWGQIRRGVTIKPTVDDD  
s1:
..................................................................................................................................................................................................................................................................................ASTPPASAFLKAWVYRPGEDTEEEED.EDVDSED.....................................................................................................................................................................  
s2:
MAGGEAGVTLGQPHLSRQDLTTLDVTKLTPLSHEVISRQATINIGTIGHVAHGKSTVVKAISGVHTVRFKNELERNITIKLGYANAKIYKLDDPSCPRPECYRSCGSSTPDEFPTDIPGTKGNFKLVRHVSFVDCPGHDILMATMLNGAAVMDAALLLIAGNESCPQPQTSEHLAAIEIMKLKHILILQNKIDLVKESQAKEQYEQILAFVQGTVAEGAPIIPISAQLKYNIEVVCEYIVKKIPVPPRDFTSEPRLIVIRSFDVNKPGCEVDDLKGGVAGGSILKG.VLKVGQEIEVRPGIVSKDSEGKLMCKPIFSKIVSLFAEHNDLQYAAPGGLIGVGTKIDPTLCRADRMVGQVLGAVGALPEIFTELEISYFLLRRLLGVRTEGDKKAAKVQKLSKNEVLMVNIGSLSTGGRVSAVKADLGKIVLTNPVCTEVGEKIALSRRVEKHWRLIGWGQIRRGVTIKPTVDDD  

> isolde restrain distances "#1.2/A" templateAtoms "#2.1/A" perChain false
> adjustForConfidence true useCoordinateAlignment false kappa 4.40 fallOff
> 2.50 groupName "Reference Distance Restraints"

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
[Repeated 1 time(s)]ISOLDE: Corrected atom nomenclature of 56 residues in
model #2.1 to IUPAC-IUB standards.  

> isolde restrain torsions #1.2/A templateResidues #2.1/A adjustForConfidence
> true sidechains true springConstant 250.00 alpha 0.20

The "isolde restrain torsions" command only applies to protein chains. Other
residues have been ignored.  

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
[Repeated 1 time(s)]

> matchmaker #2.2 to #1.2

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 8qzz, chain B (#1.2) with AlphaFold IF2A_HUMAN chain B, chain B
(#2.2), sequence alignment score = 1283.3  
RMSD between 113 pruned atom pairs is 0.785 angstroms; (across all 113 pairs:
0.785)  
  

> color #2.2 bychain

> color #2.2 byhetero

> color modify #2.2 hue + 50

ISOLDE: attempting to load PAE matrix for model #2.2 from the AlphaFold-EBI
database. If this fails or you wish to use a different PAE matrix, use the
"Load PAE matrix" button in ISOLDE's reference model restraints widget.  

> alphafold pae #2.2 uniprotId P05198 plot false

s1:
MAGGEAGVTLGQPHLSRQDLTTLDVTKLTPLSHEVISRQATINIGTIGHVAHGKSTVVKAISGVHTVRFKNELERNITIKLGYANAKIYKLDDPSCPRPECYRSCGSSTPDEFPTDIPGTKGNFKLVRHVSFVDCPGHDILMATMLNGAAVMDAALLLIAGNESCPQPQTSEHLAAIEIMKLKHILILQNKIDLVKESQAKEQYEQILAFVQGTVAEGAPIIPISAQLKYNIEVVCEYIVKKIPVPPRDFTSEPRLIVI.....RSFD..VNKPGC.EVDDLKGGVAGGSILKGVLKVGQEIEVRPGIVSKDSEGKLMCKPIFSKIVSLFAEHNDL.QYAAPGGL....IGVGTKID........PTLCRADRMVG.QVLGAVGALPEIFTELEISYFLLRRLLGVRTEGDKK..AAKVQKLSKNEVLMVNIGSLSTGGRVSAVKADLGKIVLTNPVCTEVGEKIALSRRVEKHWRLIGWGQIRRGVTIKPTVDDD  
s2:
....................................................................................................................MPGLSCRF..YQH.KFPEV..EDVVMVNVRSIAE.MGAYVSLLEYNNIEGMILLSE.LSRRRIRSINKLIRIGRNECVVVIRVDKEK.....GYIDLSKRRVSPEEAIKCEDKFTKSKTVYSILRHVAEV.LEYTKDEQLESLFQRTAWVFDDKYKRPGYGAYDAFKHAVSDPSILDSLDLNEDEREVLINNINRRLTPQAVKIRADIEVACYGYEGIDAVKEALRAGLNCSTENMPIKINLIAPPRYVMTTTTLERTEGLSVLSQAMAVIKEKIEEKRGVFNVQMEPKVVTDTDETELARQMERLERENA...EVDGDDDAEEMEAKAED.................................................  
s1:
MPGLSCRFYQHKFPEVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSINKLIRIGRNECVVVIRVDKEKGYIDLSKRRVSPEEAIKCEDKFTKSKTVYSILRHVAEVLEYTKDEQLESLFQRTAWVFDDKYKRPGYGAYDAFKHAVSDPSILDSLDLNEDEREVLINNINRRLTPQAVKIRADIEVACYGYEGIDAVKEALRAGLNCSTENMPIKINLIAPPRYVMTTTTLERTEGLSVLSQAMAVIKEKIEEKRGVFNVQMEPKVVTDTDETELARQMERLERENAEVDGDDDAEEMEAKAED  
s2:
MPGLSCRFYQHKFPEVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSINKLIRIGRNECVVVIRVDKEKGYIDLSKRRVSPEEAIKCEDKFTKSKTVYSILRHVAEVLEYTKDEQLESLFQRTAWVFDDKYKRPGYGAYDAFKHAVSDPSILDSLDLNEDEREVLINNINRRLTPQAVKIRADIEVACYGYEGIDAVKEALRAGLNCSTENMPIKINLIAPPRYVMTTTTLERTEGLSVLSQAMAVIKEKIEEKRGVFNVQMEPKVVTDTDETELARQMERLERENAEVDGDDDAEEMEAKAED  
s1:
.....................................................................................................................................................................................................................................................................................ASTPPASAFLKAWVYRPGEDTEEEEDEDVDSED.....  
s2:
MPGLSCRFYQHKFPEVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSINKLIRIGRNECVVVIRVDKEKGYIDLSKRRVSPEEAIKCEDKFTKSKTVYSILRHVAEVLEYTKDEQLESLFQRTAWVFDDKYKRPGYGAYDAFKHAVSDPSILDSLDLNEDEREVLINNINRRLTPQAVKIRADIEVACYGYEGIDAVKEALRAGLNCSTENMPIKINLIAPPRYVMTTTTLERTEGLSVLSQAMAVIKEKIEEKRGVFNVQMEPKVVTDTDETELARQMERLERENAEVDGDDDAEEMEAKAED  

> isolde restrain distances "#1.2/B" templateAtoms "#2.2/B" perChain false
> adjustForConfidence true useCoordinateAlignment false kappa 4.40 fallOff
> 2.50 groupName "Reference Distance Restraints"

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
[Repeated 1 time(s)]ISOLDE: Corrected atom nomenclature of 68 residues in
model #2.2 to IUPAC-IUB standards.  

> isolde restrain torsions #1.2/B templateResidues #2.2/B adjustForConfidence
> true sidechains true springConstant 250.00 alpha 0.20

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
[Repeated 1 time(s)]

> matchmaker #2.3 to #1.2

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 8qzz, chain C (#1.2) with AlphaFold PR15A_HUMAN chain C, chain C
(#2.3), sequence alignment score = 131  
RMSD between 8 pruned atom pairs is 0.588 angstroms; (across all 9 pairs:
1.812)  
  

> color #2.3 bychain

> color #2.3 byhetero

> color modify #2.3 hue + 50

ISOLDE: attempting to load PAE matrix for model #2.3 from the AlphaFold-EBI
database. If this fails or you wish to use a different PAE matrix, use the
"Load PAE matrix" button in ISOLDE's reference model restraints widget.  

> alphafold pae #2.3 uniprotId O75807 plot false

Fetching compressed AlphaFold PAE O75807 from
https://alphafold.ebi.ac.uk/files/AF-O75807-F1-predicted_aligned_error_v4.json  
s1:
MAGGEAGVTLGQPHLSRQDLTTLDVTKLTPLSHEVISRQATINIGTIGHVAHGKSTVVKAISGVHTVRFKNELERNITIKL...GYANAKIYKLDDPSCP...RPECYRSCGSSTPDEFPT..DIPGTKGNFKLVRHVSFVDCPGHDILMATMLNGAAVMDAALLLIAGNESCPQPQTSEHLAAIEIMKLKHILILQNKIDLVKESQAKEQYEQILAFVQGT....VAEGA.PIIPISA......QLKYNIEVVCEYIVKKIPVPPRDFTSEPRLIVIRSFDVNKPGCE...VDDLKGGVAGGSILKGVLKVGQ............EIEVRP.GIVSKDSEGK.LMCKPIFSKIVSLFA........EHNDLQYAAPGGLIGVGTKIDPTLCRADRMVGQVLGAVGALPEIFTELEISYFLLRRLLGVRTEGDKKAAKVQKLSKNEVLMVNIGSLSTGGRVSAVKADLGKIVLTNPVCTEVGEKIALSRRVEK.HWRLIGWGQIRRGVTIKPTVDDD....................................................................................................................................................................................  
s2:
MAPGQA......PHQATPWRDAHPFFLLSP.VMGLLSRAWSRLRG.LGPL...EPWLVEAVKGAALVEAGLEGEARTPLAIPHTPWGRRPEEEAEDSGGPGEDRETLGLKTSSSLPEAWGLLDDDDGMYGE....REATSVP.RGQGSQFADGQRAPLSPSLLIRTLQGSDKNPGEEKAEEEGVAEEEGVNKFSYPPSHRECCPAVEEEDDEEAVKKEAHRTSTSALSPGSKPSTWVSCPGEEENQATEDKRTERSKGARKTSVSPRSSGSDPRSWEYRSGEASEEKEEKAHKETGKGEAAPGPQSSAPAQRPQLKSWWCQPSDEEEGEVKALGAAEKDGEAECPPCIPPPSAFLKAWVYWPGEDTEEEEDEEEDEDSDSGSDEEEGEAEASSSTPATGVFLKSWVYQPGEDTEEEEDEDSDTGSAEDEREAETSASTPPASAFLKAWVYRPGEDTEEEEDEDVDSE.DKEDDSEAALGEAESDPHPSHPDQRAHFR..GWG.YRPG...KETEEEEAAEDWGEAEPCPFRVAIYVPGEKPPPPWAPPRLPLRLQRRLKRPETPTHDPDPETPLKARKVRFSEKVTVHFLAVWAGPAQAARQGPWEQLARDRSRFARRITQAQEELSPCLTPAARARAWARLRNPPLAPIPALTQTLPSSSVPSSPVQTTPLSQAVATPSRSSAAAAAALDLSGRRG  
s1:
MPGLSCRFYQHKFPEVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSINKLIRIGRNECVVVIRVDKEKGYIDLSKRRVSPEEAIKCEDKFTKSKTVYSILRHVAEVLEYTKDEQLESLFQRTAWVFDDKYKRPGYGAYDAFKHAVSDPSILDSLDLNEDEREVLINNINRRLTPQAVKIRADIEVACYGYEGIDAVKEALRAGLNCSTENMPIKINLIAPPRYVMTTTTLERTEGLSVLSQAMAVIKEKIEEKRGVFNVQMEPKVV.TDTDETELARQMERLERENAEVDGDDDAEEMEAKAED.............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................  
s2:
.....................................................................................................................................................................................................................................MAPGQAPHQATPWRDAHPFFLLSPVMGLLSRAWSRLRGL..GPLEPWLVEAVKGAALVEAGLEGEARTPLAIPHTPWGRRPEEEAEDSGGPGEDRETLGLKTSSSLPEAWGLLDDDDGMYGEREATSVPRGQGSQFADGQRAPLSPSLLIRTLQGSDKNPGEEKAEEEGVAEEEGVNKFSYPPSHRECCPAVEEEDDEEAVKKEAHRTSTSALSPGSKPSTWVSCPGEEENQATEDKRTERSKGARKTSVSPRSSGSDPRSWEYRSGEASEEKEEKAHKETGKGEAAPGPQSSAPAQRPQLKSWWCQPSDEEEGEVKALGAAEKDGEAECPPCIPPPSAFLKAWVYWPGEDTEEEEDEEEDEDSDSGSDEEEGEAEASSSTPATGVFLKSWVYQPGEDTEEEEDEDSDTGSAEDEREAETSASTPPASAFLKAWVYRPGEDTEEEEDEDVDSEDKEDDSEAALGEAESDPHPSHPDQRAHFRGWGYRPGKETEEEEAAEDWGEAEPCPFRVAIYVPGEKPPPPWAPPRLPLRLQRRLKRPETPTHDPDPETPLKARKVRFSEKVTVHFLAVWAGPAQAARQGPWEQLARDRSRFARRITQAQEELSPCLTPAARARAWARLRNPPLAPIPALTQTLPSSSVPSSPVQTTPLSQAVATPSRSSAAAAAALDLSGRRG  
s1:
...................................................................................................................................................................................................................................................................................................................................................................................................................................ASTPPASAFLKAWVYRPGEDTEEEEDEDVDSED..............................................................................................................................................................................................................................  
s2:
MAPGQAPHQATPWRDAHPFFLLSPVMGLLSRAWSRLRGLGPLEPWLVEAVKGAALVEAGLEGEARTPLAIPHTPWGRRPEEEAEDSGGPGEDRETLGLKTSSSLPEAWGLLDDDDGMYGEREATSVPRGQGSQFADGQRAPLSPSLLIRTLQGSDKNPGEEKAEEEGVAEEEGVNKFSYPPSHRECCPAVEEEDDEEAVKKEAHRTSTSALSPGSKPSTWVSCPGEEENQATEDKRTERSKGARKTSVSPRSSGSDPRSWEYRSGEASEEKEEKAHKETGKGEAAPGPQSSAPAQRPQLKSWWCQPSDEEEGEVKALGAAEKDGEAECPPCIPPPSAFLKAWVYWPGEDTEEEEDEEEDEDSDSGSDEEEGEAEASSSTPATGVFLKSWVYQPGEDTEEEEDEDSDTGSAEDEREAETSASTPPASAFLKAWVYRPGEDTEEEEDEDVDSEDKEDDSEAALGEAESDPHPSHPDQRAHFRGWGYRPGKETEEEEAAEDWGEAEPCPFRVAIYVPGEKPPPPWAPPRLPLRLQRRLKRPETPTHDPDPETPLKARKVRFSEKVTVHFLAVWAGPAQAARQGPWEQLARDRSRFARRITQAQEELSPCLTPAARARAWARLRNPPLAPIPALTQTLPSSSVPSSPVQTTPLSQAVATPSRSSAAAAAALDLSGRRG  

> isolde restrain distances "#1.2/C" templateAtoms "#2.3/C" perChain false
> adjustForConfidence true useCoordinateAlignment false kappa 4.40 fallOff
> 2.50 groupName "Reference Distance Restraints"

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
[Repeated 1 time(s)]ISOLDE: Corrected atom nomenclature of 156 residues in
model #2.3 to IUPAC-IUB standards.  

> isolde restrain torsions #1.2/C templateResidues #2.3/C adjustForConfidence
> true sidechains true springConstant 250.00 alpha 0.20

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
[Repeated 1 time(s)]

> hide #!2 models

> select #1

8498 atoms, 8564 bonds, 3 pseudobonds, 556 residues, 30 models selected  

> isolde sim start #1.2/A-C

Loading residue template for GNP from internal database  
ISOLDE: started sim  

> select clear

> isolde sim pause

> select #1/A:1-200

2585 atoms, 2607 bonds, 2 pseudobonds, 174 residues, 2 models selected  

> rd to /A:250-500

> isolde sim resume

> isolde sim pause

> show #!2 models

> hide #!2 models

> isolde sim stop discardTo start

Sim termination reason: None  
reverting to start  
Updating bulk solvent parameters...  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> select #1/A:1-200

2585 atoms, 2607 bonds, 2 pseudobonds, 174 residues, 2 models selected  

> rd to /A:250-500

> show #!2 models

> hide #!2 models

> select #1/A

6590 atoms, 6645 bonds, 3 pseudobonds, 434 residues, 2 models selected  

> rd

> select #1

8498 atoms, 8564 bonds, 3 pseudobonds, 556 residues, 34 models selected  

> isolde sim start #1.2/A-C

ISOLDE: started sim  

> select clear

> isolde sim pause

> isolde sim resume

> isolde sim pause

> open CZF fromDatabase ccd

CZF title:  
[[(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(oxidanylidene)-3~{H}-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-
oxidanyl-phosphoryl] phosphono hydrogen phosphate  
  
Opened CCD CZF  

> select #3

47 atoms, 49 bonds, 1 residue, 1 model selected  

> ui mousemode right "translate selected atoms"

> select clear

> ui mousemode right "isolde tug atom"

> hide #3 models

> hide HC

> cbb

19838 atoms, 2018 residues, atom bfactor range 0 to 404  

> ab 10

> cbb

19838 atoms, 2018 residues, atom bfactor range 0 to 404  

> ab 10

[Repeated 1 time(s)]

> cbc

> label sel

> select up

45 atoms, 47 bonds, 1 residue, 1 model selected  

> color sel orange

> color byhetero

> isolde sim stop

Sim termination reason: None  
Updating bulk solvent parameters...  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 7 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> color sel orange

> color byhetero

> select up

45 atoms, 47 bonds, 1 residue, 1 model selected  

> color sel orange

> color byhetero

> select clear

> cofr showPivot false

> show #3 models

> hide #3 models

> show #3 models

> hide #3 models

> show #3 models

> hide #3 models

> select #1

8498 atoms, 8564 bonds, 3 pseudobonds, 556 residues, 35 models selected  

> rt

> select clear

> show #3 models

> hide #3 models

> show #3 models

> color #3 brown

> color byhetero

> hide #3 models

> label sel text GTP

> label #3 text XTP

> show #!3 models

> hide #!3 models

> select clear

> cd "C:/Users/Tristan Croll/Documents/Structures/anti-
> isrib/8qzz_eif2_gamma_gtp"

Current working directory is: C:\Users\Tristan
Croll\Documents\Structures\anti-isrib\8qzz_eif2_gamma_gtp  

> movie record size 1920,1080 supersample 3

> rock y 30 180 cycle 90

> movie crossfade 30

> hide :GNP

> show #!3 models

> rock y 30 180 cycle 90

> movie stop

> movie encode 8qzz_GTP_vs_XTP.mp4

Movie saved to 8qzz_GTP_vs_XTP.mp4  
  

> save working.cxs

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX-daily\bin\Lib\site-
packages\chimerax\core\session.py", line 917, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX-daily\bin\Lib\site-
packages\chimerax\core\session.py", line 641, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX-daily\bin\Lib\site-
packages\chimerax\core\session.py", line 260, in discovery  
if hasattr(sm, 'include_state') and not sm.include_state(value):  
^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX-daily\bin\Lib\site-
packages\chimerax\core\attributes.py", line 256, in include_state  
self._python_instances = [[inst for inst in inst_func(self.session)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX-daily\bin\Lib\site-
packages\chimerax\core\attributes.py", line 256, in <listcomp>  
self._python_instances = [[inst for inst in inst_func(self.session)  
^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX-daily\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 2636, in <lambda>  
register_class(reg_class, lambda *args, cls=reg_class:
python_instances_of_class(cls),  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX-daily\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 44, in python_instances_of_class  
instances = f(inst_class)  
^^^^^^^^^^^^^  
OSError: exception: access violation reading 0x000000000000002B  
  
OSError: exception: access violation reading 0x000000000000002B  
  
File "C:\Program Files\ChimeraX-daily\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 44, in python_instances_of_class  
instances = f(inst_class)  
^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Cannot save 'working.cxs': exception: access violation reading
0x000000000000002B  

> save working.cxs

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX-daily\bin\Lib\site-
packages\chimerax\core\session.py", line 917, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX-daily\bin\Lib\site-
packages\chimerax\core\session.py", line 641, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX-daily\bin\Lib\site-
packages\chimerax\core\session.py", line 260, in discovery  
if hasattr(sm, 'include_state') and not sm.include_state(value):  
^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX-daily\bin\Lib\site-
packages\chimerax\core\attributes.py", line 256, in include_state  
self._python_instances = [[inst for inst in inst_func(self.session)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX-daily\bin\Lib\site-
packages\chimerax\core\attributes.py", line 256, in <listcomp>  
self._python_instances = [[inst for inst in inst_func(self.session)  
^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX-daily\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 2636, in <lambda>  
register_class(reg_class, lambda *args, cls=reg_class:
python_instances_of_class(cls),  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX-daily\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 44, in python_instances_of_class  
instances = f(inst_class)  
^^^^^^^^^^^^^  
OSError: exception: access violation reading 0x000000000000002B  
  
OSError: exception: access violation reading 0x000000000000002B  
  
File "C:\Program Files\ChimeraX-daily\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 44, in python_instances_of_class  
instances = f(inst_class)  
^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Cannot save 'working.cxs': exception: access violation reading
0x000000000000002B  

> cd "C:\Users\Tristan Croll/Desktop"

Current working directory is: C:\Users\Tristan Croll\Desktop  

> save test.cxs

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX-daily\bin\Lib\site-
packages\chimerax\core\session.py", line 917, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX-daily\bin\Lib\site-
packages\chimerax\core\session.py", line 641, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX-daily\bin\Lib\site-
packages\chimerax\core\session.py", line 260, in discovery  
if hasattr(sm, 'include_state') and not sm.include_state(value):  
^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX-daily\bin\Lib\site-
packages\chimerax\core\attributes.py", line 256, in include_state  
self._python_instances = [[inst for inst in inst_func(self.session)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX-daily\bin\Lib\site-
packages\chimerax\core\attributes.py", line 256, in <listcomp>  
self._python_instances = [[inst for inst in inst_func(self.session)  
^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX-daily\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 2636, in <lambda>  
register_class(reg_class, lambda *args, cls=reg_class:
python_instances_of_class(cls),  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX-daily\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 44, in python_instances_of_class  
instances = f(inst_class)  
^^^^^^^^^^^^^  
OSError: exception: access violation reading 0x000000000000002B  
  
OSError: exception: access violation reading 0x000000000000002B  
  
File "C:\Program Files\ChimeraX-daily\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 44, in python_instances_of_class  
instances = f(inst_class)  
^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Cannot save 'test.cxs': exception: access violation reading 0x000000000000002B  




OpenGL version: 3.3.0 NVIDIA 529.19
OpenGL renderer: NVIDIA GeForce RTX 3070 Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: en_GB.cp1252
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.2
Qt platform: windows

Manufacturer: HP
Model: HP ZBook Studio 15.6 inch G8 Mobile Workstation PC
OS: Microsoft Windows 11 Pro (Build 22631)
Memory: 34,007,068,672
MaxProcessMemory: 137,438,953,344
CPU: 16 11th Gen Intel(R) Core(TM) i7-11800H @ 2.30GHz
OSLanguage: en-GB

Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    asttokens: 2.4.1
    Babel: 2.14.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.5.1
    build: 1.1.1
    certifi: 2024.2.2
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.16
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.3
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.5
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.56
    ChimeraX-AtomicLibrary: 14.0.2
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
    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: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.23.0
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.8.dev202403220040
    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
    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-ISOLDE: 1.8.dev0
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.9
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    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: 2.1.3
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.15
    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: 1.1
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.3
    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: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.3
    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: 1.0
    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: 1.16.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2
    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: 1.37.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.2
    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: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    comtypes: 1.3.1
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.9
    debugpy: 1.8.1
    decorator: 5.1.1
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.1
    fonttools: 4.50.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2024.2.26
    idna: 3.6
    ihm: 0.43
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.2
    jedi: 0.19.1
    Jinja2: 3.1.3
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.10
    kiwisolver: 1.4.5
    line-profiler: 4.1.2
    lxml: 5.1.0
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.8.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.8
    ndindex: 1.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.2.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.9.0
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 24.0
    ParmEd: 4.2.2
    parso: 0.8.3
    pep517: 0.13.1
    pillow: 10.2.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.0
    prompt-toolkit: 3.0.43
    psutil: 5.9.8
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.3.0
    pygments: 2.17.2
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3302
    pyparsing: 3.1.2
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.6.1
    PyQt6-Qt6: 6.6.2
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine-commercial: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.2
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pywin32: 306
    pyzmq: 25.1.2
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.12.0
    setuptools: 69.2.0
    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: 2.0.0
    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
    stack-data: 0.6.3
    superqt: 0.6.1
    tables: 3.9.2
    tcia-utils: 1.5.1
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    tornado: 6.4
    traitlets: 5.14.1
    typing-extensions: 4.10.0
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.10
    WMI: 1.5.1

[Eric Pettersen]

Adding Tristan to ticket we already have open for this.