The following bug report has been submitted:
Platform: macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
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"size" : 15220686848,
"uuid" : "53b6853f-0bc3-33f5-be72-1aca3a188ff8"
},
"vmSummary" : "ReadOnly portion of Libraries: Total=1.5G resident=0K(0%) swapped_out_or_unallocated=1.5G(100%)\nWritable regions: Total=2.1G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=2.1G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 128K 1 \nActivity Tracing 256K 1 \nCG backing stores 2176K 4 \nCG image 188K 17 \nColorSync 228K 26 \nCoreAnimation 224K 17 \nCoreGraphics 12K 2 \nCoreUI image data 4404K 32 \nFoundation 16K 1 \nKernel Alloc Once 8K 1 \nMALLOC 1.2G 143 \nMALLOC guard page 192K 9 \nMALLOC_MEDIUM (reserved) 336.0M 5 reserved VM address space (unallocated)\nMach message 16K 4 \nOpenGL GLSL 384K 4 \nRosetta Arena 6144K 3 \nRosetta Generic 1436K 356 \nRosetta IndirectBranch 2048K 1 \nRosetta JIT 128.0M 1 \nRosetta Return Stack 740K 74 \nRosetta Thread Context 740K 74 \nSTACK GUARD 44K 11 \nStack 158.1M 30 \nStack Guard 56.1M 19 \nVM_ALLOCATE 160.5M 266 \nVM_ALLOCATE (reserved) 128.1M 13 reserved VM address space (unallocated)\n__CTF 756 1 \n__DATA 44.2M 663 \n__DATA_CONST 30.9M 339 \n__DATA_DIRTY 1644K 213 \n__FONT_DATA 4K 1 \n__GLSLBUILTINS 5176K 1 \n__LINKEDIT 736.2M 145 \n__OBJC_RO 82.7M 1 \n__OBJC_RW 3200K 2 \n__TEXT 794.8M 664 \n__UNICODE 592K 1 \ndyld private memory 1184K 3 \nmapped file 5.2G 1135 \nshared memory 3000K 23 \nunshared pmap 12.6M 8 \n=========== ======= ======= \nTOTAL 9.1G 4315 \nTOTAL, minus reserved VM space 8.6G 4315 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "6112dda2fc54bc3389840642",
"factorPackIds" : {
"SIRI_DICTATION_ASSETS" : "631730a28520965d1cba0681"
},
"deploymentId" : 240000145
},
{
"rolloutId" : "60186475825c62000ccf5450",
"factorPackIds" : {
},
"deploymentId" : 240000026
}
],
"experiments" : [
]
}
}
===== Log before crash start =====
UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/home/surfdrive/Documents_surfdrive/Talks_surfdrive/chains2022/movie-
> work/movies-andrea/uchl5/UCHL5_full-range.cxc
> delete all
> ~hbonds
> ~distance
> select clear
> stop
> view orient
> open 3a7s.pdb name uchl5-3a7s
uchl5-3a7s title:
Catalytic domain of UCH37 [more info...]
Chain information for uchl5-3a7s #1
---
Chain | Description | UniProt
A | ubiquitin carboxyl-terminal hydrolase isozyme L5 | UCHL5_HUMAN
Non-standard residues in uchl5-3a7s #1
---
CL — chloride ion
> open 3rii-a.pdb name uchl5-3rii
Chain information for uchl5-3rii #2
---
Chain | Description
A | No description available
> open 3ris-a.pdb name uchl5-3ris
Chain information for uchl5-3ris #3
---
Chain | Description
A | No description available
> open 3tb3-a.pdb name uchl5-3tb3
Chain information for uchl5-3tb3 #4
---
Chain | Description
A | No description available
> open 3ihr.pdb name uchl5-3ihr
uchl5-3ihr title:
Crystal structure of UCH37 [more info...]
Chain information for uchl5-3ihr #5
---
Chain | Description | UniProt
A | ubiquitin carboxyl-terminal hydrolase isozyme L5 | UCHL5_HUMAN
Non-standard residues in uchl5-3ihr #5
---
FMT — formic acid
NA — sodium ion
> open l5-4uem.pdb name apoL5_4uem
Chain information for apoL5_4uem #6
---
Chain | Description
A | No description available
> open l5-4uel.pdb name activeL5_4uel
Chain information for activeL5_4uel #7
---
Chain | Description
A | No description available
> open l5-4uf5.pdb name inactivel5_4uf5
Chain information for inactivel5_4uf5 #8
---
Chain | Description
A | No description available
> open rpn13-4uem.pdb name rpn13-4uem
Chain information for rpn13-4uem #9
---
Chain | Description
B | No description available
> open rpn13-4uel.pdb name rpn13-ub-4uel
Chain information for rpn13-ub-4uel #10
---
Chain | Description
C | No description available
> open ino80-4uf5.pdb name ino80-4uf5
Chain information for ino80-4uf5 #11
---
Chain | Description
B | No description available
> open ub-4uel.pdb name ub-4uel
Chain information for ub-4uel #12
---
Chain | Description
B | No description available
> open 4UEM.cif
4UEM.cif title:
UCH-L5 in complex with the RPN13 DEUBAD domain [more info...]
Chain information for 4UEM.cif #13
---
Chain | Description | UniProt
A | ubiquitin carboxyl-terminal hydrolase isozyme L5 | UCHL5_HUMAN
B | proteasomal ubiquitin receptor ADRM1 | ADRM1_HUMAN
> open 4UEL.cif
4UEL.cif title:
UCH-L5 in complex with ubiquitin-propargyl bound to the RPN13 DEUBAD domain
[more info...]
Chain information for 4UEL.cif #14
---
Chain | Description | UniProt
A | ubiquitin carboxyl-terminal hydrolase isozyme L5 | UCHL5_HUMAN
B | polyubiquitin-B | UBB_HUMAN
C | proteasomal ubiquitin receptor ADRM1 | ADRM1_HUMAN
Non-standard residues in 4UEL.cif #14
---
AYE — prop-2-en-1-amine (allylamine)
> open 4UF5.cif
4UF5.cif title:
Crystal structure of UCH-L5 in complex with inhibitory fragment of INO80G
[more info...]
Chain information for 4UF5.cif #15
---
Chain | Description | UniProt
A | ubiquitin carboxyl-terminal hydrolase isozyme L5 | UCHL5_HUMAN
B | nuclear factor related to κ-B-binding protein | NFRKB_HUMAN
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> set bgColor white
> graphics silhouettes false
> lighting simple
> name L5-1 #1/A
> name L5-2 #2/A
> name L5-3 #3/A
> name L5-4 #4/A
> name L5-5 #5/A
> name L5-apo #6
> name L5-active #7
> name L5-inactive #8
> name rpn13-apo #9
> name rpn13-active #10
> name ub #10
> name Uld #1-12/A:225-350
> name ULD-rpn13 #9/A:225-350
> name ULD-ino80 #11/A:225-350
> matchmaker #2-8/A to #1/A
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 uchl5-3a7s, chain A (#1) with uchl5-3rii, chain A (#2), sequence
alignment score = 981.8
RMSD between 199 pruned atom pairs is 0.515 angstroms; (across all 204 pairs:
0.699)
Matchmaker uchl5-3a7s, chain A (#1) with uchl5-3ris, chain A (#3), sequence
alignment score = 982.5
RMSD between 201 pruned atom pairs is 0.652 angstroms; (across all 204 pairs:
0.740)
Matchmaker uchl5-3a7s, chain A (#1) with uchl5-3tb3, chain A (#4), sequence
alignment score = 1009.7
RMSD between 200 pruned atom pairs is 0.621 angstroms; (across all 204 pairs:
0.805)
Matchmaker uchl5-3a7s, chain A (#1) with uchl5-3ihr, chain A (#5), sequence
alignment score = 1006
RMSD between 190 pruned atom pairs is 0.687 angstroms; (across all 203 pairs:
0.998)
Matchmaker uchl5-3a7s, chain A (#1) with apoL5_4uem, chain A (#6), sequence
alignment score = 935.5
RMSD between 179 pruned atom pairs is 0.801 angstroms; (across all 198 pairs:
2.497)
Matchmaker uchl5-3a7s, chain A (#1) with activeL5_4uel, chain A (#7), sequence
alignment score = 954.3
RMSD between 176 pruned atom pairs is 0.874 angstroms; (across all 204 pairs:
1.541)
Matchmaker uchl5-3a7s, chain A (#1) with inactivel5_4uf5, chain A (#8),
sequence alignment score = 984.9
RMSD between 191 pruned atom pairs is 0.822 angstroms; (across all 204 pairs:
1.111)
> matchmaker #13-15/A to #1/A
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 uchl5-3a7s, chain A (#1) with 4UEM.cif, chain A (#13), sequence
alignment score = 963.3
RMSD between 179 pruned atom pairs is 0.801 angstroms; (across all 196 pairs:
1.209)
Matchmaker uchl5-3a7s, chain A (#1) with 4UEL.cif, chain A (#14), sequence
alignment score = 948.3
RMSD between 176 pruned atom pairs is 0.874 angstroms; (across all 204 pairs:
1.541)
Matchmaker uchl5-3a7s, chain A (#1) with 4UF5.cif, chain A (#15), sequence
alignment score = 972.9
RMSD between 191 pruned atom pairs is 0.822 angstroms; (across all 204 pairs:
1.111)
> matchmaker #9/B to #13/B
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 4UEM.cif, chain B (#13) with rpn13-4uem, chain B (#9), sequence
alignment score = 499.5
RMSD between 98 pruned atom pairs is 0.000 angstroms; (across all 98 pairs:
0.000)
> matchmaker #10/C to #14/C
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 4UEL.cif, chain C (#14) with rpn13-ub-4uel, chain C (#10), sequence
alignment score = 498.9
RMSD between 98 pruned atom pairs is 0.000 angstroms; (across all 98 pairs:
0.000)
> matchmaker #11/B to #15/B
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 4UF5.cif, chain B (#15) with ino80-4uf5, chain B (#11), sequence
alignment score = 582.8
RMSD between 110 pruned atom pairs is 0.000 angstroms; (across all 110 pairs:
0.000)
> matchmaker #12/B to #14/B
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 4UEL.cif, chain B (#14) with ub-4uel, chain B (#12), sequence
alignment score = 376.5
RMSD between 75 pruned atom pairs is 0.000 angstroms; (across all 75 pairs:
0.000)
> view
> view matrix camera
> 0.73046,0.077942,-0.67851,-121.86,0.43998,-0.81354,0.38022,86.379,-0.52235,-0.57627,-0.62854,-136.47
> view name view2
> view matrix camera
> 0.32874,0.87188,0.363,114.86,0.061267,-0.40325,0.91304,222.83,0.94243,-0.27791,-0.186,-31.174
> view name overview1
> view overview1
> colordef rpn13 lawn green
Color 'rpn13' is opaque: rgb(48.6%, 98.8%, 0%) hex: #7cfc00
> colordef ino80 orange red
Color 'ino80' is opaque: rgb(100%, 27.1%, 0%) hex: #ff4500
> colordef generic #e6e7e8
Color 'generic' is opaque: rgb(90.2%, 90.6%, 91%) hex: #e6e7e8
> colordef ub gold
Color 'ub' is opaque: rgb(100%, 84.3%, 0%) hex: #ffd700
> colordef l5active silver
Color 'l5active' is opaque: gray(75.3%) hex: #c0c0c0
> colordef l5inactive silver
Color 'l5inactive' is opaque: gray(75.3%) hex: #c0c0c0
> colordef uld light steel blue
Color 'uld' is opaque: rgb(69%, 76.9%, 87.1%) hex: #b0c4de
> colordef l5 royal blue
Color 'l5' is opaque: rgb(25.5%, 41.2%, 88.2%) hex: #4169e1
> color #12 ub
> color #1-8 l5
> color all byhetero
> color Uld uld
> color #9 rpn13
> color #11 ino80
> cofr 20.394, -3.2716, 33.906
> hide all
> hide cartoons
> movie record
> show #7 cartoons
> rock x 30 cycle 120
> rock y 30 cycle 120
> wait 60
> show #12 cartoons
> wait 60
> show #9 cartoons
> wait 120
> hide #9,12 cartoons
> morph #7,8 hideModels false frames 60
Computed 61 frame morph #16
> coordset #16 1,61
> color #16 uld
> hide cartoons
> stop
> cofr 39.217, 12.068, 15.496
> matchmaker #15/A:225-350 to #13/A:225-350
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 4UEM.cif, chain A (#13) with 4UF5.cif, chain A (#15), sequence
alignment score = 396.4
RMSD between 33 pruned atom pairs is 1.272 angstroms; (across all 81 pairs:
4.378)
> name ULD-ino80 #15/A:225-350
> name ULD-rpn13 #13/A:225-350
> name moved-ino80 #15/B
> name new-rpn13 #13/B
> color moved-ino80 orange red
> color new-rpn13 lawn green
> color ULD-rpn13 uld
> color ULD-ino80 uld
> cofr 39.217, 12.068, 15.496
> show ULD-rpn13 cartoons
> wait 20
> rock X 30 cycle 120
> show new-rpn13 cartoons
> wait 30
> show ULD-ino80 cartoons
> show moved-ino80 cartoons
> wait 120
> hide moved-ino80 cartoons
> hide new-rpn13 cartoons
> hide ULD-ino80 cartoons
> wait 30
> show #16 cartoons
> coordset #16 1,60 bounce true loop 2
> coordset #16 1,60
> show #7,8 models
> show #7 cartoons
> show #8 cartoons
> wait 180
> hide #7,16 cartoons
> show #11 cartoons
> wait 120
> show #12 cartoons
> wait 120
> hide #12 cartoons
> wait 120
> movie stop
> movie encode uchl5-test.mp4
Movie saved to uchl5-test.mp4
executed UCHL5_full-range.cxc
> stop
> open
> /Users/home/surfdrive/Documents_surfdrive/Talks_surfdrive/chains2022/movie-
> work/movies-andrea/uchl5/UCHL5_full-range.cxc
> delete all
> ~hbonds
> ~distance
> select clear
> stop
> view orient
> open 3a7s.pdb name uchl5-3a7s
uchl5-3a7s title:
Catalytic domain of UCH37 [more info...]
Chain information for uchl5-3a7s #1
---
Chain | Description | UniProt
A | ubiquitin carboxyl-terminal hydrolase isozyme L5 | UCHL5_HUMAN
Non-standard residues in uchl5-3a7s #1
---
CL — chloride ion
> open 3rii-a.pdb name uchl5-3rii
Chain information for uchl5-3rii #2
---
Chain | Description
A | No description available
> open 3ris-a.pdb name uchl5-3ris
Chain information for uchl5-3ris #3
---
Chain | Description
A | No description available
> open 3tb3-a.pdb name uchl5-3tb3
Chain information for uchl5-3tb3 #4
---
Chain | Description
A | No description available
> open 3ihr.pdb name uchl5-3ihr
uchl5-3ihr title:
Crystal structure of UCH37 [more info...]
Chain information for uchl5-3ihr #5
---
Chain | Description | UniProt
A | ubiquitin carboxyl-terminal hydrolase isozyme L5 | UCHL5_HUMAN
Non-standard residues in uchl5-3ihr #5
---
FMT — formic acid
NA — sodium ion
> open l5-4uem.pdb name apoL5_4uem
Chain information for apoL5_4uem #6
---
Chain | Description
A | No description available
> open l5-4uel.pdb name activeL5_4uel
Chain information for activeL5_4uel #7
---
Chain | Description
A | No description available
> open l5-4uf5.pdb name inactivel5_4uf5
Chain information for inactivel5_4uf5 #8
---
Chain | Description
A | No description available
> open rpn13-4uem.pdb name rpn13-4uem
Chain information for rpn13-4uem #9
---
Chain | Description
B | No description available
> open rpn13-4uel.pdb name rpn13-ub-4uel
Chain information for rpn13-ub-4uel #10
---
Chain | Description
C | No description available
> open ino80-4uf5.pdb name ino80-4uf5
Chain information for ino80-4uf5 #11
---
Chain | Description
B | No description available
> open ub-4uel.pdb name ub-4uel
Chain information for ub-4uel #12
---
Chain | Description
B | No description available
> open 4UEM.cif
4UEM.cif title:
UCH-L5 in complex with the RPN13 DEUBAD domain [more info...]
Chain information for 4UEM.cif #13
---
Chain | Description | UniProt
A | ubiquitin carboxyl-terminal hydrolase isozyme L5 | UCHL5_HUMAN
B | proteasomal ubiquitin receptor ADRM1 | ADRM1_HUMAN
> open 4UEL.cif
4UEL.cif title:
UCH-L5 in complex with ubiquitin-propargyl bound to the RPN13 DEUBAD domain
[more info...]
Chain information for 4UEL.cif #14
---
Chain | Description | UniProt
A | ubiquitin carboxyl-terminal hydrolase isozyme L5 | UCHL5_HUMAN
B | polyubiquitin-B | UBB_HUMAN
C | proteasomal ubiquitin receptor ADRM1 | ADRM1_HUMAN
Non-standard residues in 4UEL.cif #14
---
AYE — prop-2-en-1-amine (allylamine)
> open 4UF5.cif
4UF5.cif title:
Crystal structure of UCH-L5 in complex with inhibitory fragment of INO80G
[more info...]
Chain information for 4UF5.cif #15
---
Chain | Description | UniProt
A | ubiquitin carboxyl-terminal hydrolase isozyme L5 | UCHL5_HUMAN
B | nuclear factor related to κ-B-binding protein | NFRKB_HUMAN
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> set bgColor white
> graphics silhouettes false
> lighting simple
> name L5-1 #1/A
> name L5-2 #2/A
> name L5-3 #3/A
> name L5-4 #4/A
> name L5-5 #5/A
> name L5-apo #6
> name L5-active #7
> name L5-inactive #8
> name rpn13-apo #9
> name rpn13-active #10
> name ub #10
> name Uld #1-12/A:225-350
> name ULD-rpn13 #9/A:225-350
> name ULD-ino80 #11/A:225-350
> matchmaker #2-8/A to #1/A
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 uchl5-3a7s, chain A (#1) with uchl5-3rii, chain A (#2), sequence
alignment score = 981.8
RMSD between 199 pruned atom pairs is 0.515 angstroms; (across all 204 pairs:
0.699)
Matchmaker uchl5-3a7s, chain A (#1) with uchl5-3ris, chain A (#3), sequence
alignment score = 982.5
RMSD between 201 pruned atom pairs is 0.652 angstroms; (across all 204 pairs:
0.740)
Matchmaker uchl5-3a7s, chain A (#1) with uchl5-3tb3, chain A (#4), sequence
alignment score = 1009.7
RMSD between 200 pruned atom pairs is 0.621 angstroms; (across all 204 pairs:
0.805)
Matchmaker uchl5-3a7s, chain A (#1) with uchl5-3ihr, chain A (#5), sequence
alignment score = 1006
RMSD between 190 pruned atom pairs is 0.687 angstroms; (across all 203 pairs:
0.998)
Matchmaker uchl5-3a7s, chain A (#1) with apoL5_4uem, chain A (#6), sequence
alignment score = 935.5
RMSD between 179 pruned atom pairs is 0.801 angstroms; (across all 198 pairs:
2.497)
Matchmaker uchl5-3a7s, chain A (#1) with activeL5_4uel, chain A (#7), sequence
alignment score = 954.3
RMSD between 176 pruned atom pairs is 0.874 angstroms; (across all 204 pairs:
1.541)
Matchmaker uchl5-3a7s, chain A (#1) with inactivel5_4uf5, chain A (#8),
sequence alignment score = 984.9
RMSD between 191 pruned atom pairs is 0.822 angstroms; (across all 204 pairs:
1.111)
> matchmaker #13-15/A to #1/A
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 uchl5-3a7s, chain A (#1) with 4UEM.cif, chain A (#13), sequence
alignment score = 963.3
RMSD between 179 pruned atom pairs is 0.801 angstroms; (across all 196 pairs:
1.209)
Matchmaker uchl5-3a7s, chain A (#1) with 4UEL.cif, chain A (#14), sequence
alignment score = 948.3
RMSD between 176 pruned atom pairs is 0.874 angstroms; (across all 204 pairs:
1.541)
Matchmaker uchl5-3a7s, chain A (#1) with 4UF5.cif, chain A (#15), sequence
alignment score = 972.9
RMSD between 191 pruned atom pairs is 0.822 angstroms; (across all 204 pairs:
1.111)
> matchmaker #9/B to #13/B
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 4UEM.cif, chain B (#13) with rpn13-4uem, chain B (#9), sequence
alignment score = 499.5
RMSD between 98 pruned atom pairs is 0.000 angstroms; (across all 98 pairs:
0.000)
> matchmaker #10/C to #14/C
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 4UEL.cif, chain C (#14) with rpn13-ub-4uel, chain C (#10), sequence
alignment score = 498.9
RMSD between 98 pruned atom pairs is 0.000 angstroms; (across all 98 pairs:
0.000)
> matchmaker #11/B to #15/B
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 4UF5.cif, chain B (#15) with ino80-4uf5, chain B (#11), sequence
alignment score = 582.8
RMSD between 110 pruned atom pairs is 0.000 angstroms; (across all 110 pairs:
0.000)
> matchmaker #12/B to #14/B
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 4UEL.cif, chain B (#14) with ub-4uel, chain B (#12), sequence
alignment score = 376.5
RMSD between 75 pruned atom pairs is 0.000 angstroms; (across all 75 pairs:
0.000)
> view
> view matrix camera
> 0.73046,0.077942,-0.67851,-121.86,0.43998,-0.81354,0.38022,86.379,-0.52235,-0.57627,-0.62854,-136.47
> view name view2
> view matrix camera
> 0.32874,0.87188,0.363,114.86,0.061267,-0.40325,0.91304,222.83,0.94243,-0.27791,-0.186,-31.174
> view name overview1
> view overview1
> colordef rpn13 lawn green
Color 'rpn13' is opaque: rgb(48.6%, 98.8%, 0%) hex: #7cfc00
> colordef ino80 orange red
Color 'ino80' is opaque: rgb(100%, 27.1%, 0%) hex: #ff4500
> colordef generic #e6e7e8
Color 'generic' is opaque: rgb(90.2%, 90.6%, 91%) hex: #e6e7e8
> colordef ub gold
Color 'ub' is opaque: rgb(100%, 84.3%, 0%) hex: #ffd700
> colordef l5active silver
Color 'l5active' is opaque: gray(75.3%) hex: #c0c0c0
> colordef l5inactive silver
Color 'l5inactive' is opaque: gray(75.3%) hex: #c0c0c0
> colordef uld light steel blue
Color 'uld' is opaque: rgb(69%, 76.9%, 87.1%) hex: #b0c4de
> colordef l5 royal blue
Color 'l5' is opaque: rgb(25.5%, 41.2%, 88.2%) hex: #4169e1
> color #12 ub
> color #1-8 l5
> color all byhetero
> color Uld uld
> color #9 rpn13
> color #11 ino80
> cofr 20.394, -3.2716, 33.906
> hide all
> hide cartoons
> movie record
> show #7 cartoons
> rock x 30 cycle 120
> rock y 30 cycle 120
> wait 60
> show #12 cartoons
> wait 60
> show #9 cartoons
> wait 120
> hide #9,12 cartoons
> morph #7,8 hideModels false frames 60
Computed 61 frame morph #16
> coordset #16 1,61
> color #16 uld
> hide cartoons
> stop
> cofr 39.217, 12.068, 15.496
> matchmaker #15/A:225-350 to #13/A:225-350
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 4UEM.cif, chain A (#13) with 4UF5.cif, chain A (#15), sequence
alignment score = 396.4
RMSD between 33 pruned atom pairs is 1.272 angstroms; (across all 81 pairs:
4.378)
> name ULD-ino80 #15/A:225-350
> name ULD-rpn13 #13/A:225-350
> name moved-ino80 #15/B
> name new-rpn13 #13/B
> color moved-ino80 orange red
> color new-rpn13 lawn green
> color ULD-rpn13 uld
> color ULD-ino80 uld
> cofr 39.217, 12.068, 15.496
> show ULD-rpn13 cartoons
> wait 20
> rock X 30 cycle 120
> show new-rpn13 cartoons
> wait 30
> show ULD-ino80 cartoons
> show moved-ino80 cartoons
> wait 120
> hide moved-ino80 cartoons
> hide new-rpn13 cartoons
> hide ULD-ino80 cartoons
> wait 30
> show #16 cartoons
> coordset #16 1,60 bounce true loop 2
> show #7,8 models
> show #7 cartoons
> show #8 cartoons
> wait 90
> show #9 cartoons
> wait 30
> hide #9 cartoons
> coordset #16 1,60
> hide #7,16 cartoons
> show #11 cartoons
> wait 120
> show #12 cartoons
> wait 120
> hide #12 cartoons
> wait 120
> movie stop
> movie encode uchl5-test.mp4
Movie saved to uchl5-test.mp4
executed UCHL5_full-range.cxc
> stop
> open
> /Users/home/surfdrive/Documents_surfdrive/Talks_surfdrive/chains2022/movie-
> work/movies-andrea/uchl5/UCHL5_full-range.cxc
> delete all
> ~hbonds
> ~distance
> select clear
> stop
> view orient
> open 3a7s.pdb name uchl5-3a7s
uchl5-3a7s title:
Catalytic domain of UCH37 [more info...]
Chain information for uchl5-3a7s #1
---
Chain | Description | UniProt
A | ubiquitin carboxyl-terminal hydrolase isozyme L5 | UCHL5_HUMAN
Non-standard residues in uchl5-3a7s #1
---
CL — chloride ion
> open 3rii-a.pdb name uchl5-3rii
Chain information for uchl5-3rii #2
---
Chain | Description
A | No description available
> open 3ris-a.pdb name uchl5-3ris
Chain information for uchl5-3ris #3
---
Chain | Description
A | No description available
> open 3tb3-a.pdb name uchl5-3tb3
Chain information for uchl5-3tb3 #4
---
Chain | Description
A | No description available
> open 3ihr.pdb name uchl5-3ihr
uchl5-3ihr title:
Crystal structure of UCH37 [more info...]
Chain information for uchl5-3ihr #5
---
Chain | Description | UniProt
A | ubiquitin carboxyl-terminal hydrolase isozyme L5 | UCHL5_HUMAN
Non-standard residues in uchl5-3ihr #5
---
FMT — formic acid
NA — sodium ion
> open l5-4uem.pdb name apoL5_4uem
Chain information for apoL5_4uem #6
---
Chain | Description
A | No description available
> open l5-4uel.pdb name activeL5_4uel
Chain information for activeL5_4uel #7
---
Chain | Description
A | No description available
> open l5-4uf5.pdb name inactivel5_4uf5
Chain information for inactivel5_4uf5 #8
---
Chain | Description
A | No description available
> open rpn13-4uem.pdb name rpn13-4uem
Chain information for rpn13-4uem #9
---
Chain | Description
B | No description available
> open rpn13-4uel.pdb name rpn13-ub-4uel
Chain information for rpn13-ub-4uel #10
---
Chain | Description
C | No description available
> open ino80-4uf5.pdb name ino80-4uf5
Chain information for ino80-4uf5 #11
---
Chain | Description
B | No description available
> open ub-4uel.pdb name ub-4uel
Chain information for ub-4uel #12
---
Chain | Description
B | No description available
> open 4UEM.cif
4UEM.cif title:
UCH-L5 in complex with the RPN13 DEUBAD domain [more info...]
Chain information for 4UEM.cif #13
---
Chain | Description | UniProt
A | ubiquitin carboxyl-terminal hydrolase isozyme L5 | UCHL5_HUMAN
B | proteasomal ubiquitin receptor ADRM1 | ADRM1_HUMAN
> open 4UEL.cif
4UEL.cif title:
UCH-L5 in complex with ubiquitin-propargyl bound to the RPN13 DEUBAD domain
[more info...]
Chain information for 4UEL.cif #14
---
Chain | Description | UniProt
A | ubiquitin carboxyl-terminal hydrolase isozyme L5 | UCHL5_HUMAN
B | polyubiquitin-B | UBB_HUMAN
C | proteasomal ubiquitin receptor ADRM1 | ADRM1_HUMAN
Non-standard residues in 4UEL.cif #14
---
AYE — prop-2-en-1-amine (allylamine)
> open 4UF5.cif
4UF5.cif title:
Crystal structure of UCH-L5 in complex with inhibitory fragment of INO80G
[more info...]
Chain information for 4UF5.cif #15
---
Chain | Description | UniProt
A | ubiquitin carboxyl-terminal hydrolase isozyme L5 | UCHL5_HUMAN
B | nuclear factor related to κ-B-binding protein | NFRKB_HUMAN
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> set bgColor white
> graphics silhouettes false
> lighting simple
> name L5-1 #1/A
> name L5-2 #2/A
> name L5-3 #3/A
> name L5-4 #4/A
> name L5-5 #5/A
> name L5-apo #6
> name L5-active #7
> name L5-inactive #8
> name rpn13-apo #9
> name rpn13-active #10
> name ub #10
> name Uld #1-12/A:225-350
> name ULD-rpn13 #9/A:225-350
> name ULD-ino80 #11/A:225-350
> matchmaker #2-8/A to #1/A
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 uchl5-3a7s, chain A (#1) with uchl5-3rii, chain A (#2), sequence
alignment score = 981.8
RMSD between 199 pruned atom pairs is 0.515 angstroms; (across all 204 pairs:
0.699)
Matchmaker uchl5-3a7s, chain A (#1) with uchl5-3ris, chain A (#3), sequence
alignment score = 982.5
RMSD between 201 pruned atom pairs is 0.652 angstroms; (across all 204 pairs:
0.740)
Matchmaker uchl5-3a7s, chain A (#1) with uchl5-3tb3, chain A (#4), sequence
alignment score = 1009.7
RMSD between 200 pruned atom pairs is 0.621 angstroms; (across all 204 pairs:
0.805)
Matchmaker uchl5-3a7s, chain A (#1) with uchl5-3ihr, chain A (#5), sequence
alignment score = 1006
RMSD between 190 pruned atom pairs is 0.687 angstroms; (across all 203 pairs:
0.998)
Matchmaker uchl5-3a7s, chain A (#1) with apoL5_4uem, chain A (#6), sequence
alignment score = 935.5
RMSD between 179 pruned atom pairs is 0.801 angstroms; (across all 198 pairs:
2.497)
Matchmaker uchl5-3a7s, chain A (#1) with activeL5_4uel, chain A (#7), sequence
alignment score = 954.3
RMSD between 176 pruned atom pairs is 0.874 angstroms; (across all 204 pairs:
1.541)
Matchmaker uchl5-3a7s, chain A (#1) with inactivel5_4uf5, chain A (#8),
sequence alignment score = 984.9
RMSD between 191 pruned atom pairs is 0.822 angstroms; (across all 204 pairs:
1.111)
> matchmaker #13-15/A to #1/A
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 uchl5-3a7s, chain A (#1) with 4UEM.cif, chain A (#13), sequence
alignment score = 963.3
RMSD between 179 pruned atom pairs is 0.801 angstroms; (across all 196 pairs:
1.209)
Matchmaker uchl5-3a7s, chain A (#1) with 4UEL.cif, chain A (#14), sequence
alignment score = 948.3
RMSD between 176 pruned atom pairs is 0.874 angstroms; (across all 204 pairs:
1.541)
Matchmaker uchl5-3a7s, chain A (#1) with 4UF5.cif, chain A (#15), sequence
alignment score = 972.9
RMSD between 191 pruned atom pairs is 0.822 angstroms; (across all 204 pairs:
1.111)
> matchmaker #9/B to #13/B
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 4UEM.cif, chain B (#13) with rpn13-4uem, chain B (#9), sequence
alignment score = 499.5
RMSD between 98 pruned atom pairs is 0.000 angstroms; (across all 98 pairs:
0.000)
> matchmaker #10/C to #14/C
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 4UEL.cif, chain C (#14) with rpn13-ub-4uel, chain C (#10), sequence
alignment score = 498.9
RMSD between 98 pruned atom pairs is 0.000 angstroms; (across all 98 pairs:
0.000)
> matchmaker #11/B to #15/B
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 4UF5.cif, chain B (#15) with ino80-4uf5, chain B (#11), sequence
alignment score = 582.8
RMSD between 110 pruned atom pairs is 0.000 angstroms; (across all 110 pairs:
0.000)
> matchmaker #12/B to #14/B
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 4UEL.cif, chain B (#14) with ub-4uel, chain B (#12), sequence
alignment score = 376.5
RMSD between 75 pruned atom pairs is 0.000 angstroms; (across all 75 pairs:
0.000)
> view
> view matrix camera
> 0.73046,0.077942,-0.67851,-121.86,0.43998,-0.81354,0.38022,86.379,-0.52235,-0.57627,-0.62854,-136.47
> view name view2
> view matrix camera
> 0.32874,0.87188,0.363,114.86,0.061267,-0.40325,0.91304,222.83,0.94243,-0.27791,-0.186,-31.174
> view name overview1
> view overview1
> colordef rpn13 lawn green
Color 'rpn13' is opaque: rgb(48.6%, 98.8%, 0%) hex: #7cfc00
> colordef ino80 orange red
Color 'ino80' is opaque: rgb(100%, 27.1%, 0%) hex: #ff4500
> colordef generic #e6e7e8
Color 'generic' is opaque: rgb(90.2%, 90.6%, 91%) hex: #e6e7e8
> colordef ub gold
Color 'ub' is opaque: rgb(100%, 84.3%, 0%) hex: #ffd700
> colordef l5active silver
Color 'l5active' is opaque: gray(75.3%) hex: #c0c0c0
> colordef l5inactive silver
Color 'l5inactive' is opaque: gray(75.3%) hex: #c0c0c0
> colordef uld light steel blue
Color 'uld' is opaque: rgb(69%, 76.9%, 87.1%) hex: #b0c4de
> colordef l5 royal blue
Color 'l5' is opaque: rgb(25.5%, 41.2%, 88.2%) hex: #4169e1
> color #12 ub
> color #1-8 l5
> color all byhetero
> color Uld uld
> color #9 rpn13
> color #11 ino80
> cofr 20.394, -3.2716, 33.906
> hide all
> hide cartoons
> movie record
> show #7 cartoons
> rock x 30 cycle 120
> rock y 30 cycle 120
> wait 60
> show #12 cartoons
> wait 60
> show #9 cartoons
> wait 120
> hide #9,12 cartoons
> morph #7,8 hideModels false frames 60
Computed 61 frame morph #16
> coordset #16 1,61
> color #16 uld
> hide cartoons
> stop
> cofr 39.217, 12.068, 15.496
> matchmaker #15/A:225-350 to #13/A:225-350
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 4UEM.cif, chain A (#13) with 4UF5.cif, chain A (#15), sequence
alignment score = 396.4
RMSD between 33 pruned atom pairs is 1.272 angstroms; (across all 81 pairs:
4.378)
> name ULD-ino80 #15/A:225-350
> name ULD-rpn13 #13/A:225-350
> name moved-ino80 #15/B
> name new-rpn13 #13/B
> color moved-ino80 orange red
> color new-rpn13 lawn green
> color ULD-rpn13 uld
> color ULD-ino80 uld
> cofr 39.217, 12.068, 15.496
> show ULD-rpn13 cartoons
> wait 20
> rock X 30 cycle 120
> show new-rpn13 cartoons
> wait 30
> show ULD-ino80 cartoons
> show moved-ino80 cartoons
> wait 120
> hide moved-ino80 cartoons
> hide new-rpn13 cartoons
> hide ULD-ino80 cartoons
> wait 30
> show #16 cartoons
> coordset #16 1,60 bounce true loop 2
> show #7,8 models
> show #7 cartoons
> show #8 cartoons
> wait 120
> show #9 cartoons
> wait 30
> hide #9 cartoons
> coordset #16 1,60
> hide #7,16 cartoons
> wait 60
> show #11 cartoons
> wait 90
> show #12 cartoons
> wait 60
> hide #12 cartoons
> wait 120
> movie stop
> movie encode uchl5-test.mp4
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M1
OpenGL vendor: Apple
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: MacBookAir10,1
Processor Name: Unknown
Processor Speed: 2.4 GHz
Number of Processors: 1
Total Number of Cores: 8
L2 Cache: 8 MB
Memory: 8 GB
Software:
System Software Overview:
System Version: macOS 12.4 (21F79)
Kernel Version: Darwin 21.5.0
Time since boot: 3 days 17:19
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Family: Supported, Metal GPUFamily Apple 7
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.3
Babel: 2.10.1
backcall: 0.2.0
blockdiag: 3.0.0
certifi: 2021.10.8
cftime: 1.6.0
charset-normalizer: 2.0.12
ChimeraX-AddCharge: 1.2.3
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.4.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.39.1
ChimeraX-AtomicLibrary: 7.0
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.1
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.7
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.1
ChimeraX-CommandLine: 1.2.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.4
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.1.5
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.1.2
ChimeraX-Help: 1.2
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
ChimeraX-Label: 1.1.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.6
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.7
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.5.5
ChimeraX-ModelPanel: 1.3.2
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.2
ChimeraX-OpenCommand: 1.9
ChimeraX-PDB: 2.6.6
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
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
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.6
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.8
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.0.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.1
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.18.3
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.26
debugpy: 1.6.0
decorator: 5.1.1
docutils: 0.17.1
entrypoints: 0.4
filelock: 3.4.2
fonttools: 4.33.3
funcparserlib: 1.0.0
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.27
imagecodecs: 2021.11.20
imagesize: 1.3.0
ipykernel: 6.6.1
ipython: 7.31.1
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.0.3
jupyter-client: 7.1.0
jupyter-core: 4.10.0
kiwisolver: 1.4.2
line-profiler: 3.4.0
lxml: 4.7.1
lz4: 3.1.10
MarkupSafe: 2.1.1
matplotlib: 3.5.1
matplotlib-inline: 0.1.3
msgpack: 1.0.3
nest-asyncio: 1.5.5
netCDF4: 1.5.8
networkx: 2.6.3
numexpr: 2.8.1
numpy: 1.22.1
openvr: 1.16.802
packaging: 21.0
ParmEd: 3.4.3
parso: 0.8.3
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.0.1
pip: 21.3.1
pkginfo: 1.8.2
prompt-toolkit: 3.0.29
psutil: 5.9.0
ptyprocess: 0.7.0
pycollada: 0.7.2
pydicom: 2.2.2
Pygments: 2.11.2
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.0
PyQt6-Qt6: 6.3.0
PyQt6-sip: 13.3.1
PyQt6-WebEngine-commercial: 6.3.0
PyQt6-WebEngine-Qt6: 6.3.0
python-dateutil: 2.8.2
pytz: 2022.1
pyzmq: 23.1.0
qtconsole: 5.3.0
QtPy: 2.1.0
RandomWords: 0.3.0
requests: 2.27.1
scipy: 1.7.3
setuptools: 59.8.0
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.3.2
sphinx-autodoc-typehints: 1.15.2
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
suds-community: 1.0.0
tables: 3.7.0
tifffile: 2021.11.2
tinyarray: 1.2.4
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.9
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.1
wheel-filename: 1.3.0
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Hi Titia,
--Eric