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Opened 3 hours ago
#19851 new defect
ChimeraX bug report submission
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Unassigned | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | ||
| Project: |
Description
The following bug report has been submitted:
Platform: macOS-26.2-arm64-arm-64bit
ChimeraX Version: 1.11.1 (2026-01-23 05:51:34 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Bus error
Current thread 0x000000020c55ec40 (most recent call first):
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 248 in swap_buffers
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 561 in swap_buffers
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/statusbar.py", line 166 in status
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/statusbar.py", line 98 in _expose_event
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 122 in make_current
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 555 in make_current
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 584 in use_shared_context
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/sideview/tool.py", line 316 in render
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/sideview/tool.py", line 115 in _redraw
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 149 in invoke
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 248 in _activate
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 217 in activate
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 393 in activate_trigger
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 100 in draw_new_frame
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 169 in update_graphics_now
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/graphics.py", line 153 in resizeEvent
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/graphics.py", line 61 in event
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 414 in event_loop
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1064 in init
File "/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1229 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, chimerax.surface._surface, chimerax.pdb_lib._load_libs, psutil._psutil_osx, psutil._psutil_posix, lxml._elementpath, lxml.etree, PIL._imaging, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, pyKVFinder._pyKVFinder, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize (total: 60)
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"procLaunch" : "2026-02-09 13:26:38.4575 +0100",
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"procPath" : "\/Applications\/ChimeraX-1.11.1.app\/Contents\/MacOS\/ChimeraX",
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REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
MALLOC_LARGE 523400000-524688000 [ 18.5M] rw-\/rwx SM=PRV
GAP OF 0x3d7978000 BYTES
---> commpage (reserved) 8fc000000-bf1000000 [ 11.8G] ---\/--- SM=NUL reserved VM address space (unallocated)
MALLOC_SMALL bf1000000-bf1400000 [ 4096K] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000002, 0x0000000b00003a00","rawCodes":[2,47244655104],"type":"EXC_BAD_ACCESS","signal":"SIGBUS","subtype":"KERN_PROTECTION_FAILURE at 0x0000000b00003a00"},
"termination" : {"flags":0,"code":10,"namespace":"SIGNAL","indicator":"Bus error: 10","byProc":"ChimeraX","byPid":8016},
"vmregioninfo" : "0xb00003a00 is in 0x8fc000000-0xbf1000000; bytes after start: 8657058304 bytes before end: 4043294207
REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL
MALLOC_LARGE 523400000-524688000 [ 18.5M] rw-\/rwx SM=PRV
GAP OF 0x3d7978000 BYTES
---> commpage (reserved) 8fc000000-bf1000000 [ 11.8G] ---\/--- SM=NUL reserved VM address space (unallocated)
MALLOC_SMALL bf1000000-bf1400000 [ 4096K] rw-\/rwx SM=PRV ",
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===== Log before crash start =====
UCSF ChimeraX version: 1.11.1 (2026-01-23)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/paulminges/Library/CloudStorage/OneDrive-
> Personal/Documents/ResearchStuff/AG-Eder/2. Research/5. Endometriosis/1.
> Target
> Development/Structure_Analysis/MMP-10_01-476/AF-P09238-F1-model_v6.cif"
Chain information for AF-P09238-F1-model_v6.cif #1
---
Chain | Description | UniProt
A | Stromelysin-2 | MMP10_HUMAN 1-476
Color AF-P09238-F1-model_v6.cif by residue attribute pLDDT_score
> open "/Users/paulminges/Library/CloudStorage/OneDrive-
> Personal/Documents/ResearchStuff/AG-Eder/2. Research/5. Endometriosis/1.
> Target
> Development/Structure_Analysis/MMP-10_99-476/fold_2026_02_06_14_30_model_0.cif"
Chain information for fold_2026_02_06_14_30_model_0.cif #2
---
Chain | Description
A | .
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #2 to #1
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 AF-P09238-F1-model_v6.cif, chain A (#1) with
fold_2026_02_06_14_30_model_0.cif, chain A (#2), sequence alignment score =
1989.3
RMSD between 140 pruned atom pairs is 0.280 angstroms; (across all 378 pairs:
18.064)
> color #1 bfactor palette alphafold
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color byattribute bfactor palette alphafold
6887 atoms, 854 residues, atom bfactor range 20.2 to 98.9
> hide #1 models
> show #1 models
> hide #1 models
> show #1 models
> hide #2 models
> hide #1 models
> show #2 models
> show :167 atoms
> style :167 stick
Changed 17 atom styles
> style :169 stick
Changed 13 atom styles
> show :169 atoms
> undo
> show :69 atoms
> show :71 atoms
> show :83 atoms
> show :97 atoms
> show :119 atoms
> show :120 atoms
> show :123 atoms
> show :129 atoms
> show :191 atoms
> show :378 atoms
> ui tool show "Build Structure"
> ui tool show "Find Cavities"
pyKVFinder module not installed; fetching from PyPi repository...
Errors may have occurred when running pip:
pip standard error:
\---
ERROR: pip's dependency resolver does not currently take into account all the
packages that are installed. This behaviour is the source of the following
dependency conflicts.
nptyping 2.5.0 requires numpy=1.20.0; python_version >= "3.8", but you
have numpy 2.4.2 which is incompatible.
scipy 1.14.0 requires numpy=1.23.5, but you have numpy 2.4.2 which is
incompatible.
\---
pip standard output:
\---
\---
pyKVFinder module installed from PyPi repository.
> kvfinder #2
27 cavities found for fold_2026_02_06_14_30_model_0.cif #2
fold_2026_02_06_14_30_model_0.cif Cavities
---
ID | | Volume | Area | Points | Maximum
Depth | Average
Depth
2.1.19 | | 1202.04 | 900.1 | 5565 | 5.63 | 1.65
2.1.12 | | 119.23 | 120.41 | 552 | 6.03 | 2.71
2.1.1 | | 41.9 | 54.14 | 194 | 1.2 | 0.38
2.1.7 | | 37.15 | 57.87 | 172 | 2.24 | 0.72
2.1.24 | | 31.32 | 42.28 | 145 | 2.16 | 0.82
2.1.23 | | 31.1 | 35.48 | 144 | 1.8 | 0.41
2.1.8 | | 30.67 | 46.66 | 142 | 0 | 0
2.1.13 | | 30.67 | 42.97 | 142 | 1.9 | 0.47
2.1.18 | | 28.08 | 38.21 | 130 | 1.8 | 0.36
2.1.11 | | 25.7 | 37.58 | 119 | 3 | 1.39
2.1.20 | | 24.19 | 55.39 | 112 | 0 | 0
2.1.3 | | 22.9 | 41.28 | 106 | 0 | 0
2.1.10 | | 21.38 | 30.86 | 99 | 1.34 | 0.34
2.1.2 | | 16.63 | 31.73 | 77 | 2.24 | 1.34
2.1.16 | | 16.63 | 31.34 | 77 | 2.68 | 1.49
2.1.9 | | 15.12 | 30.2 | 70 | 1.9 | 0.72
2.1.4 | | 14.69 | 21.65 | 68 | 0.6 | 0.2
2.1.5 | | 12.31 | 29.54 | 57 | 0 | 0
2.1.14 | | 12.31 | 29.54 | 57 | 0 | 0
2.1.17 | | 12.31 | 29.54 | 57 | 0 | 0
2.1.26 | | 12.1 | 28.58 | 56 | 2.16 | 1.25
2.1.22 | | 11.66 | 21.35 | 54 | 0.85 | 0.25
2.1.6 | | 11.23 | 25.38 | 52 | 1.8 | 0.89
2.1.25 | | 10.8 | 21.69 | 50 | 1.34 | 0.52
2.1.15 | | 5.18 | 11.03 | 24 | 0.6 | 0.12
2.1.21 | | 5.18 | 10.41 | 24 | 0.85 | 0.24
2.1.27 | | 5.18 | 11.35 | 24 | 0.85 | 0.3
Populating font family aliases took 34 ms. Replace uses of missing font family
"Times" with one that exists to avoid this cost.
> color #2.1.19 #ff40ff
> color #2.1.12 #ff2600
> view #2.1.1 @ zoom 0.75
moved plane near -21.752435582755222 [ 0.59065753 -0.77190435 -0.23513262]
moved plane far -21.752435582755222 [ 0.59065753 -0.77190435 -0.23513262]
> surface #2.1.1-27 transparency 50
> ~surface #2.1
> surface #2.1.1
> show #!2/A:302,309,330-331,348,359,361,364
> view #!2.1.7 @ zoom 0.75
moved plane near -13.710346461062557 [-0.92443344 0.350093 0.15118761]
moved plane far -13.710346461062557 [-0.92443344 0.350093 0.15118761]
> ~surface #2.1
> surface #!2.1.7
> show #!2/A:245,247,250,254,256,261,273,275,279-280,312,314,317
> view #!2.1.7,24 @ zoom 0.75
moved plane near -71.73390792852253 [0.08976338 0.93453977 0.3443515 ]
moved plane far -71.73390792852253 [0.08976338 0.93453977 0.3443515 ]
> ~surface #2.1
> surface #!2.1.7,24
> show
> #!2/A:107-108,112,115,141-145,147,245,247,250,254,256,261,273,275,279-280,312,314,317
> view #!2.1.7,23-24 @ zoom 0.75
moved plane near -77.44345474660477 [0.08976338 0.93453977 0.3443515 ]
moved plane far -77.44345474660477 [0.08976338 0.93453977 0.3443515 ]
> ~surface #2.1
> surface #!2.1.7,23-24
> show
> #!2/A:41,44-45,107-108,112,114-115,141-145,147,150-152,245,247,250,254,256,261,273,275,279-280,312,314,317
> view #!2.1.1 @ zoom 0.75
moved plane near -25.69081191973434 [0.08976338 0.93453977 0.3443515 ]
moved plane far -25.69081191973434 [0.08976338 0.93453977 0.3443515 ]
> ~surface #2.1
> surface #!2.1.1
> show #!2/A:302,309,330-331,348,359,361,364
> view #!2.1.1,7 @ zoom 0.75
moved plane near -43.006016773335745 [0.08976338 0.93453977 0.3443515 ]
moved plane far -43.006016773335745 [0.08976338 0.93453977 0.3443515 ]
> ~surface #2.1
> surface #!2.1.1,7
> show
> #!2/A:245,247,250,254,256,261,273,275,279-280,302,309,312,314,317,330-331,348,359,361,364
> view #!2.1.1,7,24 @ zoom 0.75
moved plane near -89.17790178593533 [0.08976338 0.93453977 0.3443515 ]
moved plane far -89.17790178593533 [0.08976338 0.93453977 0.3443515 ]
> ~surface #2.1
> surface #!2.1.1,7,24
> show
> #!2/A:107-108,112,115,141-145,147,245,247,250,254,256,261,273,275,279-280,302,309,312,314,317,330-331,348,359,361,364
> view #!2.1.1,7,23-24 @ zoom 0.75
moved plane near -96.11064593109636 [0.08976338 0.93453977 0.3443515 ]
moved plane far -96.11064593109636 [0.08976338 0.93453977 0.3443515 ]
> ~surface #2.1
> surface #!2.1.1,7,23-24
> show
> #!2/A:41,44-45,107-108,112,114-115,141-145,147,150-152,245,247,250,254,256,261,273,275,279-280,302,309,312,314,317,330-331,348,359,361,364
> view #!2.1.1,7,13,23-24 @ zoom 0.75
moved plane near -96.38713809328924 [0.08976338 0.93453977 0.3443515 ]
moved plane far -96.38713809328924 [0.08976338 0.93453977 0.3443515 ]
> ~surface #2.1
> surface #!2.1.1,7,13,23-24
> show
> #!2/A:41,44-45,107-108,112,114-115,141-145,147,150-152,245-250,254,256,261,273,275,279-280,294-296,299-300,302,309,312,314,317,330-331,348,359,361,364
> view #!2.1.1,7-8,13,18,23-24 @ zoom 0.75
moved plane near -98.07428086281509 [0.08976338 0.93453977 0.3443515 ]
moved plane far -98.07428086281509 [0.08976338 0.93453977 0.3443515 ]
> ~surface #2.1
> surface #!2.1.1,7-8,13,18,23-24
> show
> #!2/A:41,44-45,107-108,112,114-115,141-145,147,150-152,199-200,207,218-220,222-223,243-250,254,256,261,273,275,279-280,291-292,294-296,299-300,302,309,312,314,317,330-331,339-341,348,359,361,364,377
> view #!2.1.1,7-8,11,13,18,20,23-24 @ zoom 0.75
moved plane near -98.07428086281509 [0.08976338 0.93453977 0.3443515 ]
moved plane far -98.07428086281509 [0.08976338 0.93453977 0.3443515 ]
> ~surface #2.1
> surface #!2.1.1,7-8,11,13,18,20,23-24
> show
> #!2/A:1-2,41,44-45,107-108,112,114-115,127-130,135,137,141-145,147,150-152,155-156,192-195,199-200,207,218-220,222-223,243-250,254,256,261,273,275,279-280,291-292,294-296,299-300,302,309,312,314,317,330-331,339-341,348,354,359,361,364,371-373,377
> view #!2.1.1,3,7-8,11,13,18,20,23-24 @ zoom 0.75
moved plane near -98.07428086281509 [0.08976338 0.93453977 0.3443515 ]
moved plane far -98.07428086281509 [0.08976338 0.93453977 0.3443515 ]
> ~surface #2.1
> surface #!2.1.1,3,7-8,11,13,18,20,23-24
> show
> #!2/A:1-2,41,44-45,107-108,112,114-115,127-130,135,137,141-145,147,150-152,155-156,192-195,199-200,207,218-220,222-223,243-250,254,256,261,273,275,279-280,291-292,294-296,299-300,302,309,312,314,317,330-331,334-335,337-341,348,350-352,354,357,359,361,364,371-373,377
> view #!2.1.1,3,7-8,10-11,13,16,18,20,23-24 @ zoom 0.75
moved plane near -98.07428086281509 [0.08976338 0.93453977 0.3443515 ]
moved plane far -98.07428086281509 [0.08976338 0.93453977 0.3443515 ]
> ~surface #2.1
> surface #!2.1.1,3,7-8,10-11,13,16,18,20,23-24
> show
> #!2/A:1-2,41,44-45,107-108,112,114-115,127-130,135,137,141-145,147,150-152,155-156,192-195,199-200,203-204,207,218-220,222-223,243-254,256,261,264-266,273,275,279-280,291-292,294-300,302,309,312,314,317,330-331,334-335,337-341,343,346,348,350-352,354,357,359,361,364,371-373,377
> view #!2.1.1-3,7-11,13,16,18,20,23-24 @ zoom 0.75
moved plane near -99.51619423592759 [0.08976338 0.93453977 0.3443515 ]
moved plane far -99.51619423592759 [0.08976338 0.93453977 0.3443515 ]
> ~surface #2.1
> surface #!2.1.1-3,7-11,13,16,18,20,23-24
> show
> #!2/A:1-2,41,44-45,107-108,112,114-115,127-130,135,137,141-145,147,150-152,155-156,192-195,199-200,203-204,207,218-220,222-223,243-254,256,261,264-266,273,275,279-280,290-292,294-300,302,304-306,309,312,314,317,327,330-331,334-341,343,346,348-352,354,356-359,361,364,368-373,377
> view #!2.1.1-5,7-11,13-14,16-18,20,23-24 @ zoom 0.75
moved plane near -99.56419069638942 [0.08976338 0.93453977 0.3443515 ]
moved plane far -99.56419069638942 [0.08976338 0.93453977 0.3443515 ]
> ~surface #2.1
> surface #!2.1.1-5,7-11,13-14,16-18,20,23-24
> show
> #!2/A:1-2,41,44-45,107-108,112,114-115,127-130,135,137,141-145,147,150-152,155-156,192-195,198-200,203-204,207,210-214,218-220,222-223,230,234,240-254,256,261,264-266,273,275,279-280,288-300,302,304-306,309,312,314,317,327,330-331,334-341,343,346,348-352,354,356-359,361,364,368-373,377
> view #!2.1.1-5,7-11,13-14,16-18,20,22-24,26 @ zoom 0.75
moved plane near -103.20599891138795 [0.08976338 0.93453977 0.3443515 ]
moved plane far -103.20599891138795 [0.08976338 0.93453977 0.3443515 ]
> ~surface #2.1
> surface #!2.1.1-5,7-11,13-14,16-18,20,22-24,26
> show
> #!2/A:1-2,10,17,19,32,35-36,41,44-45,52,58-61,89,91,93,95,107-108,112,114-115,127-130,135,137,141-145,147,150-152,155-156,192-195,198-200,203-204,207,210-214,218-220,222-223,230,234,240-254,256,261,264-266,273,275,279-280,288-300,302,304-306,309,312,314,317,327,330-331,334-341,343,346,348-352,354,356-359,361,364,368-373,377
> view #!2.1.1-11,13-14,16-18,20,22-24,26 @ zoom 0.75
moved plane near -104.47141913339895 [0.08976338 0.93453977 0.3443515 ]
moved plane far -104.47141913339895 [0.08976338 0.93453977 0.3443515 ]
> ~surface #2.1
> surface #!2.1.1-11,13-14,16-18,20,22-24,26
> show
> #!2/A:1-2,10,17,19,32,35-36,41,44-45,52,58-61,89,91,93,95,107-108,112,114-115,127-130,135,137,141-145,147,150-152,155-156,192-200,203-204,207,210-214,218-220,222-223,230,234,240-254,256,261,264-266,273,275,279-280,288-300,302,304-306,309,312,314,317,327,330-331,334-341,343,346,348-354,356-359,361,364,368-373,377
> view #!2.1.1-11,13-14,16-18,20,22-26 @ zoom 0.75
moved plane near -104.47141913339895 [0.08976338 0.93453977 0.3443515 ]
moved plane far -104.47141913339895 [0.08976338 0.93453977 0.3443515 ]
> ~surface #2.1
> surface #!2.1.1-11,13-14,16-18,20,22-26
> show
> #!2/A:1-2,10,17,19,26,32,34-36,41,44-45,52,58-61,89,91,93,95,105-108,112-115,127-130,135,137,141-145,147,150-152,155-156,192-200,203-204,207,210-214,218-220,222-223,230,234,240-254,256,261,264-266,273,275,279-280,288-300,302,304-306,309,312,314,317,327,330-331,334-341,343,346,348-354,356-359,361,364,368-373,377
> view #!2.1.1-11,13-14,16-18,20-27 @ zoom 0.75
moved plane near -104.47141913339895 [0.08976338 0.93453977 0.3443515 ]
moved plane far -104.47141913339895 [0.08976338 0.93453977 0.3443515 ]
> ~surface #2.1
> surface #!2.1.1-11,13-14,16-18,20-27
> show
> #!2/A:1-2,10,17-19,26,32,34-36,41,44-45,52-54,58-61,68-74,89,91,93,95,105-108,112-115,127-130,135,137,141-145,147,150-152,155-156,192-200,203-204,207,210-214,218-220,222-223,230,234,240-254,256,261,264-266,273,275,279-280,288-300,302,304-306,309,312,314,317,327,330-331,334-341,343,346,348-354,356-359,361,364,368-373,377
> view #!2.1.1-11,13-18,20-27 @ zoom 0.75
moved plane near -104.96791811060478 [0.08976338 0.93453977 0.3443515 ]
moved plane far -104.96791811060478 [0.08976338 0.93453977 0.3443515 ]
> ~surface #2.1
> surface #!2.1.1-11,13-18,20-27
> show
> #!2/A:1-2,10,17-19,26,32,34-36,41,44-45,52-54,58-61,68-74,89,91,93,95,105-108,112-115,127-130,135,137,141-145,147,150-152,155-156,192-200,203-204,207,210-214,218-220,222-223,229-231,234,239-254,256,261,264-266,273,275,279-280,288-300,302,304-306,309,312,314,317,327,330-331,334-341,343,346,348-354,356-359,361,364,368-373,377
> color #2.1.12 #ffffff
> color #2.1.1 #ffffff
> color #2.1.7 #ffffff
> color #2.1.24 #ffffff
> color #2.1.23 #ffffff
> color #2.1.13 #ffffff
> hide
> #!2/A:1-2,10,17-19,26,32,34-36,41,44-45,52-54,58-61,68-74,89,91,93,95,105-108,112-115,127-130,135,137,141-145,147,150-152,155-156,192-200,203-204,207,210-214,218-220,222-223,229-231,234,239-254,256,261,264-266,273,275,279-280,288-300,302,304-306,309,312,314,317,327,330-331,334-341,343,346,348-354,356-359,361,364,368-373,377
> show
> #!2/A:1-2,10,17-19,26,32,34-36,41,44-45,52-54,58-61,68-74,89,91,93,95,105-108,112-115,127-130,135,137,141-145,147,150-152,155-156,192-200,203-204,207,210-214,218-220,222-223,229-231,234,239-254,256,261,264-266,273,275,279-280,288-300,302,304-306,309,312,314,317,327,330-331,334-341,343,346,348-354,356-359,361,364,368-373,377
> hide
> #!2/A:1-2,10,17-19,26,32,34-36,41,44-45,52-54,58-61,68-74,89,91,93,95,105-108,112-115,127-130,135,137,141-145,147,150-152,155-156,192-200,203-204,207,210-214,218-220,222-223,229-231,234,239-254,256,261,264-266,273,275,279-280,288-300,302,304-306,309,312,314,317,327,330-331,334-341,343,346,348-354,356-359,361,364,368-373,377
> view #!2.1.19 @ zoom 0.75
moved plane near -66.85196856802646 [-0.92746716 0.35202427 0.12603003]
moved plane far -66.85196856802646 [-0.92746716 0.35202427 0.12603003]
> ~surface #2.1
> surface #!2.1.19
> color #2.1.19 #941751
> view #!2.1.12 @ zoom 0.75
moved plane near -27.30401751900054 [ 0.41664711 -0.83415078 -0.36138295]
moved plane far -27.30401751900054 [ 0.41664711 -0.83415078 -0.36138295]
> ~surface #2.1
> surface #!2.1.12
> show #!2/A:200-202,244-246,248,292-294,296,341-343
> view #!2.1.19 @ zoom 0.75
moved plane near -77.08884382566059 [-0.78084395 0.53449146 0.32342169]
moved plane far -77.08884382566059 [-0.78084395 0.53449146 0.32342169]
> ~surface #2.1
> surface #!2.1.19
> show
> #!2/A:4-5,8,71-75,80-87,92-93,115-116,119-120,123,128-129,133-142,145,150-153,156,203-204,206,208,215,217-222,224-228,232-234,266-267
> view #!2.1.12 @ zoom 0.75
moved plane near -34.96102851020198 [-0.78084395 0.53449146 0.32342169]
moved plane far -34.96102851020198 [-0.78084395 0.53449146 0.32342169]
> ~surface #2.1
> surface #!2.1.12
> show #!2/A:200-202,244-246,248,292-294,296,341-343
> lighting full
> hide #!2.1.3 models
> hide #!2.1.4 models
> hide #!2.1.5 models
> hide #!2.1.6 models
> hide #!2.1.9 models
> hide #!2.1.10 models
> hide #!2.1.11 models
> hide #!2.1.12 models
> hide #!2.1.13 models
> hide #!2.1.14 models
> hide #!2.1.15 models
> hide #!2.1.16 models
> hide #!2.1.17 models
> hide #!2.1.19 models
> hide #!2.1.20 models
> hide #!2.1.21 models
> hide #!2.1.22 models
> hide #!2.1.23 models
> hide #!2.1.26 models
> hide #!2.1.25 models
> hide #!2.1.24 models
> hide #!2.1.27 models
> hide #!2.1.18 models
> hide #!2.1.7 models
> hide #!2.1.8 models
> ui favorite true "Model Panel"
> select add #2.1
8369 atoms, 27 residues, 28 models selected
> select subtract #2.1
27 models selected
> select add #2.1
8369 atoms, 27 residues, 28 models selected
> select subtract #2.1
27 models selected
> lighting full
> show #!2#!2.1.1-2 atoms
> hide #!2#!2.1.1-2 atoms
> undo
> show sel & #!2.1.1-2 cartoons
> rename #2 MMP10-Maturaed
> show #!2.1.12 models
> hide #!2.1.12 models
> show #!2.1.11 models
> hide #!2.1.11 models
> show #!2.1.10 models
> hide #!2.1.10 models
> show #!2.1.22 models
> hide #!2.1.22 models
> show #!2.1.23 models
> hide #!2.1.23 models
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> color byattribute a:kvfinder_depth #!2.1.1-2,4,6-7,9-13,15-16,18-19,21-27
7838 atoms, 21 residues, 21 surfaces, atom kvfinder_depth range 0 to 6.03
> toolshed show
> preset "overall look" "publication 2 (depth-cued)"
Using preset: Overall Look / Publication 2 (Depth-Cued)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes f
lighting depthCue t
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> ui tool show "Side View"
> lighting full
> view orient
> view #!2.1.16 @ zoom 0.75
moved plane near -23.8754916114606 [-0.85362759 -0.41623138 -0.31316351]
moved plane far -23.8754916114606 [-0.85362759 -0.41623138 -0.31316351]
> ~surface #2.1
> surface #!2.1.16
> show #!2/A:203-204,251-253,264-266
> ui tool show "Side View"
> view #!2.1.19 @ zoom 0.75
moved plane near -71.46288334640842 [-0.85362759 -0.41623138 -0.31316351]
moved plane far -71.46288334640842 [-0.85362759 -0.41623138 -0.31316351]
> ~surface #2.1
> surface #!2.1.19
> show
> #!2/A:4-5,8,71-75,80-87,92-93,115-116,119-120,123,128-129,133-142,145,150-153,156,203-204,206,208,215,217-222,224-228,232-234,266-267
> color #2.1.19 #941751
> show #!2.1.19 models
> hide #!2.1.2 models
> hide #!2.1.1 models
> color #2.1.19 #941751fe
> color #2.1.19 #941751fd
> color #2.1.19 #941751f7
> color #2.1.19 #941751f5
> color #2.1.19 #941751ed
> color #2.1.19 #941751e8
> color #2.1.19 #941751e1
> color #2.1.19 #941751db
> color #2.1.19 #941751d6
> color #2.1.19 #941751d5
> color #2.1.19 #941751d4
> color #2.1.19 #941751d3
> color #2.1.19 #941751d1
> color #2.1.19 #941751d0
> color #2.1.19 #941751cf
> color #2.1.19 #941751cd
> color #2.1.19 #941751cc
> color #2.1.19 #941751cb
> color #2.1.19 #941751c5
> color #2.1.19 #941751c1
> color #2.1.19 #941751bb
> color #2.1.19 #941751b3
> color #2.1.19 #941751b0
> color #2.1.19 #941751ae
> color #2.1.19 #941751ad
> color #2.1.19 #941751ac
> color #2.1.19 #941751ab
> color #2.1.19 #941751aa
> color #2.1.19 #941751a9
> color #2.1.19 #941751a6
> color #2.1.19 #941751a5
> color #2.1.19 #941751a3
> color #2.1.19 #941751a2
> color #2.1.19 #941751a0
> color #2.1.19 #9417519f
> color #2.1.19 #9417519d
> color #2.1.19 #9417519c
> color #2.1.19 #9417519b
> color #2.1.19 #9417519a
> color #2.1.19 #94175199
> color #2.1.19 #94175198
> color #2.1.19 #94175196
> color #2.1.19 #94175195
> color #2.1.19 #94175194
> color #2.1.19 #94175193
> color #2.1.19 #94175192
> color #2.1.19 #94175191
> color #2.1.19 #94175190
> color #2.1.19 #9417518f
> color #2.1.19 #9417518d
> color #2.1.19 #9417518c
> color #2.1.19 #9417518a
> color #2.1.19 #94175189
> color #2.1.19 #94175188
> color #2.1.19 #94175187
> color #2.1.19 #94175186
> color #2.1.19 #94175185
> color #2.1.19 #94175184
> color #2.1.19 #94175183
> color #2.1.19 #94175182
> color #2.1.19 #94175181
> color #2.1.19 #94175180
> show #1 models
> hide #1 models
> show sel & #!2.1.19 surfaces
> surface (#!2.1.19 & sel)
> open /Users/paulminges/Downloads/conservation.defattr
Summary of feedback from opening
/Users/paulminges/Downloads/conservation.defattr
---
note | Assigned attribute 'conservation' to 783 residues using match mode: any
> close #1
> open "/Users/paulminges/Library/CloudStorage/OneDrive-
> Personal/Documents/ResearchStuff/AG-Eder/2. Research/5. Endometriosis/1.
> Target
> Development/Structure_Analysis/MMP-10_99-476/fold_2026_02_06_14_30_model_0.cif"
Chain information for fold_2026_02_06_14_30_model_0.cif #1
---
Chain | Description
A | .
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #!2 to #1
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 fold_2026_02_06_14_30_model_0.cif, chain A (#1) with
MMP10-Maturaed, chain A (#2), sequence alignment score = 1989.3
RMSD between 378 pruned atom pairs is 0.000 angstroms; (across all 378 pairs:
0.000)
> select add #2
11423 atoms, 3163 bonds, 405 residues, 57 models selected
> select subtract #2
27 models selected
> select add #2
11423 atoms, 3163 bonds, 405 residues, 30 models selected
> select subtract #2
27 models selected
> move x 50 models #2
> move x 10 models #2
> rename #2 MMP10-Maturaed_pLDDT
> rename #2 MMP10-Maturated_pLDDT
> rename #1 MMP10-Maturated_Cons
> open conservation.defattr
No such file/path: conservation.defattr
> color #1 byattribute conservation palette red-white-blue
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> open conservation.defattr
No such file/path: conservation.defattr
> open "/Users/paulminges/Library/CloudStorage/OneDrive-
> Personal/Documents/ResearchStuff/AG-Eder/2. Research/5. Endometriosis/1.
> Target Development/Structure_Analysis/MMP-10_99-476/conservation.defattr"
Summary of feedback from opening
/Users/paulminges/Library/CloudStorage/OneDrive-
Personal/Documents/ResearchStuff/AG-Eder/2. Research/5. Endometriosis/1.
Target Development/Structure_Analysis/MMP-10_99-476/conservation.defattr
---
note | Assigned attribute 'conservation' to 783 residues using match mode: any
> color #2 byattribute conservation palette red-white-blue
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> select add #1
3054 atoms, 3163 bonds, 378 residues, 1 model selected
> ui tool show "Render/Select by Attribute"
> info residues #1 attribute conservation
residue id #1/A:1 conservation 0.2609 index 0
residue id #1/A:2 conservation 0.2174 index 1
residue id #1/A:3 conservation 0.1304 index 2
residue id #1/A:4 conservation 0.3043 index 3
residue id #1/A:5 conservation 0.4783 index 4
residue id #1/A:6 conservation 0.3478 index 5
residue id #1/A:7 conservation 0.0435 index 6
residue id #1/A:8 conservation 0.3913 index 7
residue id #1/A:9 conservation 0.6522 index 8
residue id #1/A:10 conservation 0.9565 index 9
residue id #1/A:11 conservation 0.2609 index 10
residue id #1/A:12 conservation 0.6087 index 11
residue id #1/A:13 conservation 0.2174 index 12
residue id #1/A:14 conservation 0.3478 index 13
residue id #1/A:15 conservation 0.6957 index 14
residue id #1/A:16 conservation 0.8696 index 15
residue id #1/A:17 conservation 0.7391 index 16
residue id #1/A:18 conservation 0.7826 index 17
residue id #1/A:19 conservation 0.8261 index 18
residue id #1/A:20 conservation 0.2174 index 19
residue id #1/A:21 conservation 0.6522 index 20
residue id #1/A:22 conservation 0.6522 index 21
residue id #1/A:23 conservation 0.6087 index 22
residue id #1/A:24 conservation 0.5217 index 23
residue id #1/A:25 conservation 0.4348 index 24
residue id #1/A:26 conservation 0.6522 index 25
residue id #1/A:27 conservation 0.3043 index 26
residue id #1/A:28 conservation 0.2174 index 27
residue id #1/A:29 conservation 0.1304 index 28
residue id #1/A:30 conservation 0.2609 index 29
residue id #1/A:31 conservation 0.6522 index 30
residue id #1/A:32 conservation 0.3913 index 31
residue id #1/A:33 conservation 0.087 index 32
residue id #1/A:34 conservation 0.7391 index 33
residue id #1/A:35 conservation 0.3913 index 34
residue id #1/A:36 conservation 0.1739 index 35
residue id #1/A:37 conservation 0.3043 index 36
residue id #1/A:38 conservation 0.9565 index 37
residue id #1/A:39 conservation 0.3478 index 38
residue id #1/A:40 conservation 0.2174 index 39
residue id #1/A:41 conservation 0.5217 index 40
residue id #1/A:42 conservation 1.0 index 41
residue id #1/A:43 conservation 0.1739 index 42
residue id #1/A:44 conservation 0.1304 index 43
residue id #1/A:45 conservation 0.6957 index 44
residue id #1/A:46 conservation 0.6522 index 45
residue id #1/A:47 conservation 0.913 index 46
residue id #1/A:48 conservation 0.9565 index 47
residue id #1/A:49 conservation 0.3913 index 48
residue id #1/A:50 conservation 1.0 index 49
residue id #1/A:51 conservation 0.1739 index 50
residue id #1/A:52 conservation 0.3043 index 51
residue id #1/A:53 conservation 0.1304 index 52
residue id #1/A:54 conservation 0.1304 index 53
residue id #1/A:55 conservation 0.2609 index 54
residue id #1/A:56 conservation 0.6087 index 55
residue id #1/A:57 conservation 0.3478 index 56
residue id #1/A:58 conservation 0.8261 index 57
residue id #1/A:59 conservation 1.0 index 58
residue id #1/A:60 conservation 0.9565 index 59
residue id #1/A:61 conservation 0.5217 index 60
residue id #1/A:62 conservation 0.7391 index 61
residue id #1/A:63 conservation 0.3043 index 62
residue id #1/A:64 conservation 1.0 index 63
residue id #1/A:65 conservation 0.4348 index 64
residue id #1/A:66 conservation 0.1304 index 65
residue id #1/A:67 conservation 0.087 index 66
residue id #1/A:68 conservation 0.2174 index 67
residue id #1/A:69 conservation 0.9565 index 68
residue id #1/A:70 conservation 0.6522 index 69
residue id #1/A:71 conservation 0.8696 index 70
residue id #1/A:72 conservation 0.1739 index 71
residue id #1/A:73 conservation 0.3913 index 72
residue id #1/A:74 conservation 0.0435 index 73
residue id #1/A:75 conservation 1.0 index 74
residue id #1/A:76 conservation 1.0 index 75
residue id #1/A:77 conservation 1.0 index 76
residue id #1/A:78 conservation 0.6087 index 77
residue id #1/A:79 conservation 0.6957 index 78
residue id #1/A:80 conservation 0.0435 index 79
residue id #1/A:81 conservation 0.0435 index 80
residue id #1/A:82 conservation 0.913 index 81
residue id #1/A:83 conservation 0.913 index 82
residue id #1/A:84 conservation 1.0 index 83
residue id #1/A:85 conservation 1.0 index 84
residue id #1/A:86 conservation 0.2609 index 85
residue id #1/A:87 conservation 0.1739 index 86
residue id #1/A:88 conservation 0.9565 index 87
residue id #1/A:89 conservation 0.7391 index 88
residue id #1/A:90 conservation 0.4348 index 89
residue id #1/A:91 conservation 0.6087 index 90
residue id #1/A:92 conservation 0.2174 index 91
residue id #1/A:93 conservation 0.0435 index 92
residue id #1/A:94 conservation 1.0 index 93
residue id #1/A:95 conservation 0.8261 index 94
residue id #1/A:96 conservation 0.1304 index 95
residue id #1/A:97 conservation 1.0 index 96
residue id #1/A:98 conservation 1.0 index 97
residue id #1/A:99 conservation 1.0 index 98
residue id #1/A:100 conservation 0.3913 index 99
residue id #1/A:101 conservation 0.7391 index 100
residue id #1/A:102 conservation 1.0 index 101
residue id #1/A:103 conservation 0.087 index 102
residue id #1/A:104 conservation 0.9565 index 103
residue id #1/A:105 conservation 0.8261 index 104
residue id #1/A:106 conservation 0.087 index 105
residue id #1/A:107 conservation 0.1304 index 106
residue id #1/A:108 conservation 0.0435 index 107
residue id #1/A:109 conservation 0.0435 index 108
residue id #1/A:110 conservation 0.8696 index 109
residue id #1/A:111 conservation 0.2609 index 110
residue id #1/A:112 conservation 0.5652 index 111
residue id #1/A:113 conservation 0.913 index 112
residue id #1/A:114 conservation 0.7391 index 113
residue id #1/A:115 conservation 0.5652 index 114
residue id #1/A:116 conservation 0.8696 index 115
residue id #1/A:117 conservation 0.9565 index 116
residue id #1/A:118 conservation 0.5652 index 117
residue id #1/A:119 conservation 1.0 index 118
residue id #1/A:120 conservation 1.0 index 119
residue id #1/A:121 conservation 0.3043 index 120
residue id #1/A:122 conservation 1.0 index 121
residue id #1/A:123 conservation 1.0 index 122
residue id #1/A:124 conservation 0.3478 index 123
residue id #1/A:125 conservation 0.913 index 124
residue id #1/A:126 conservation 1.0 index 125
residue id #1/A:127 conservation 0.9565 index 126
residue id #1/A:128 conservation 0.087 index 127
residue id #1/A:129 conservation 1.0 index 128
residue id #1/A:130 conservation 0.8696 index 129
residue id #1/A:131 conservation 0.1304 index 130
residue id #1/A:132 conservation 0.1739 index 131
residue id #1/A:133 conservation 0.1304 index 132
residue id #1/A:134 conservation 0.1304 index 133
residue id #1/A:135 conservation 0.8261 index 134
residue id #1/A:136 conservation 0.5652 index 135
residue id #1/A:137 conservation 1.0 index 136
residue id #1/A:138 conservation 0.3478 index 137
residue id #1/A:139 conservation 0.913 index 138
residue id #1/A:140 conservation 0.087 index 139
residue id #1/A:141 conservation 0.9565 index 140
residue id #1/A:142 conservation 0.0435 index 141
residue id #1/A:143 conservation 0.087 index 142
residue id #1/A:144 conservation 0.1739 index 143
residue id #1/A:145 conservation 0.2174 index 144
residue id #1/A:146 conservation 0.1739 index 145
residue id #1/A:147 conservation 0.087 index 146
residue id #1/A:148 conservation 0.0435 index 147
residue id #1/A:149 conservation 0.0435 index 148
residue id #1/A:150 conservation 0.6087 index 149
residue id #1/A:151 conservation 0.2174 index 150
residue id #1/A:152 conservation 1.0 index 151
residue id #1/A:153 conservation 0.4783 index 152
residue id #1/A:154 conservation 0.4348 index 153
residue id #1/A:155 conservation 0.913 index 154
residue id #1/A:156 conservation 0.9565 index 155
residue id #1/A:157 conservation 0.2609 index 156
residue id #1/A:158 conservation 0.1739 index 157
residue id #1/A:159 conservation 0.8261 index 158
residue id #1/A:160 conservation 0.7826 index 159
residue id #1/A:161 conservation 0.8696 index 160
residue id #1/A:162 conservation 0.2609 index 161
residue id #1/A:163 conservation 0.7826 index 162
residue id #1/A:164 conservation 1.0 index 163
residue id #1/A:165 conservation 1.0 index 164
residue id #1/A:166 conservation 0.3043 index 165
residue id #1/A:167 conservation 0.3478 index 166
residue id #1/A:168 conservation 0.2609 index 167
residue id #1/A:169 conservation 0.0435 index 168
residue id #1/A:170 conservation 0.2174 index 169
residue id #1/A:171 conservation 0.0435 index 170
residue id #1/A:172 conservation 0.1304 index 171
residue id #1/A:173 conservation 0.0435 index 172
residue id #1/A:174 conservation 0.1739 index 173
residue id #1/A:175 conservation 0.087 index 174
residue id #1/A:176 conservation 0.087 index 175
residue id #1/A:177 conservation 0.1739 index 176
residue id #1/A:178 conservation 0.2609 index 177
residue id #1/A:179 conservation 0.087 index 178
residue id #1/A:180 conservation 0.0435 index 179
residue id #1/A:181 conservation 0.087 index 180
residue id #1/A:182 conservation 0.6522 index 181
residue id #1/A:183 conservation 0.0435 index 182
residue id #1/A:184 conservation 0.2174 index 183
residue id #1/A:185 conservation 0.1304 index 184
residue id #1/A:186 conservation 0.087 index 185
residue id #1/A:187 conservation 0.0435 index 186
residue id #1/A:188 conservation 0.7391 index 187
residue id #1/A:189 conservation 0.1304 index 188
residue id #1/A:190 conservation 0.087 index 189
residue id #1/A:191 conservation 0.8696 index 190
residue id #1/A:192 conservation 0.5217 index 191
residue id #1/A:193 conservation 0.2609 index 192
residue id #1/A:194 conservation 0.087 index 193
residue id #1/A:195 conservation 0.3478 index 194
residue id #1/A:196 conservation 0.3043 index 195
residue id #1/A:197 conservation 0.7391 index 196
residue id #1/A:198 conservation 0.6957 index 197
residue id #1/A:199 conservation 0.5652 index 198
residue id #1/A:200 conservation 0.4348 index 199
residue id #1/A:201 conservation 0.1304 index 200
residue id #1/A:202 conservation 0.3043 index 201
residue id #1/A:203 conservation 0.3478 index 202
residue id #1/A:204 conservation 0.7391 index 203
residue id #1/A:205 conservation 0.6087 index 204
residue id #1/A:206 conservation 0.6522 index 205
residue id #1/A:207 conservation 0.0435 index 206
residue id #1/A:208 conservation 0.1739 index 207
residue id #1/A:209 conservation 0.4348 index 208
residue id #1/A:210 conservation 0.8696 index 209
residue id #1/A:211 conservation 0.8696 index 210
residue id #1/A:212 conservation 0.5217 index 211
residue id #1/A:213 conservation 0.5217 index 212
residue id #1/A:214 conservation 0.1739 index 213
residue id #1/A:215 conservation 0.5652 index 214
residue id #1/A:216 conservation 0.8261 index 215
residue id #1/A:217 conservation 0.6957 index 216
residue id #1/A:218 conservation 0.1304 index 217
residue id #1/A:219 conservation 0.2174 index 218
residue id #1/A:220 conservation 0.087 index 219
residue id #1/A:221 conservation 0.0435 index 220
residue id #1/A:222 conservation 0.087 index 221
residue id #1/A:223 conservation 0.1304 index 222
residue id #1/A:224 conservation 0.1739 index 223
residue id #1/A:225 conservation 0.1304 index 224
residue id #1/A:226 conservation 0.3043 index 225
residue id #1/A:227 conservation 0.087 index 226
residue id #1/A:228 conservation 0.087 index 227
residue id #1/A:229 conservation 0.3478 index 228
residue id #1/A:230 conservation 0.5652 index 229
residue id #1/A:231 conservation 0.3043 index 230
residue id #1/A:232 conservation 0.087 index 231
residue id #1/A:233 conservation 0.5652 index 232
residue id #1/A:234 conservation 0.8261 index 233
residue id #1/A:235 conservation 0.4783 index 234
residue id #1/A:236 conservation 0.2174 index 235
residue id #1/A:237 conservation 0.8261 index 236
residue id #1/A:238 conservation 0.8261 index 237
residue id #1/A:239 conservation 0.2174 index 238
residue id #1/A:240 conservation 0.0435 index 239
residue id #1/A:241 conservation 0.2609 index 240
residue id #1/A:242 conservation 0.5217 index 241
residue id #1/A:243 conservation 0.7391 index 242
residue id #1/A:244 conservation 0.6522 index 243
residue id #1/A:245 conservation 0.6522 index 244
residue id #1/A:246 conservation 0.6957 index 245
residue id #1/A:247 conservation 0.1304 index 246
residue id #1/A:248 conservation 0.0435 index 247
residue id #1/A:249 conservation 0.1739 index 248
residue id #1/A:250 conservation 0.3043 index 249
residue id #1/A:251 conservation 0.3043 index 250
residue id #1/A:252 conservation 0.1304 index 251
residue id #1/A:253 conservation 0.1739 index 252
residue id #1/A:254 conservation 0.2609 index 253
residue id #1/A:255 conservation 0.1304 index 254
residue id #1/A:256 conservation 0.8696 index 255
residue id #1/A:257 conservation 0.6087 index 256
residue id #1/A:258 conservation 0.7826 index 257
residue id #1/A:259 conservation 0.3043 index 258
residue id #1/A:260 conservation 0.087 index 259
residue id #1/A:261 conservation 0.2174 index 260
residue id #1/A:262 conservation 0.8696 index 261
residue id #1/A:263 conservation 0.2174 index 262
residue id #1/A:264 conservation 0.1739 index 263
residue id #1/A:265 conservation 0.2609 index 264
residue id #1/A:266 conservation 0.4348 index 265
residue id #1/A:267 conservation 0.1304 index 266
residue id #1/A:268 conservation 0.087 index 267
residue id #1/A:269 conservation 0.3043 index 268
residue id #1/A:270 conservation 0.087 index 269
residue id #1/A:271 conservation 0.087 index 270
residue id #1/A:272 conservation 0.6957 index 271
residue id #1/A:273 conservation 0.6087 index 272
residue id #1/A:274 conservation 0.8261 index 273
residue id #1/A:275 conservation 0.2609 index 274
residue id #1/A:276 conservation 0.087 index 275
residue id #1/A:277 conservation 0.4348 index 276
residue id #1/A:278 conservation 0.1739 index 277
residue id #1/A:279 conservation 0.1739 index 278
residue id #1/A:280 conservation 0.4783 index 279
residue id #1/A:281 conservation 0.7826 index 280
residue id #1/A:282 conservation 0.3478 index 281
residue id #1/A:283 conservation 0.5652 index 282
residue id #1/A:284 conservation 0.2174 index 283
residue id #1/A:285 conservation 0.1304 index 284
residue id #1/A:286 conservation 0.0435 index 285
residue id #1/A:287 conservation 0.1304 index 286
residue id #1/A:288 conservation 0.2609 index 287
residue id #1/A:289 conservation 0.5652 index 288
residue id #1/A:290 conservation 0.7391 index 289
residue id #1/A:291 conservation 0.6522 index 290
residue id #1/A:292 conservation 0.8261 index 291
residue id #1/A:293 conservation 0.2609 index 292
residue id #1/A:294 conservation 0.2609 index 293
residue id #1/A:295 conservation 0.1739 index 294
residue id #1/A:296 conservation 0.1304 index 295
residue id #1/A:297 conservation 0.1739 index 296
residue id #1/A:298 conservation 0.1304 index 297
residue id #1/A:299 conservation 0.1304 index 298
residue id #1/A:300 conservation 0.6522 index 299
residue id #1/A:301 conservation 0.6522 index 300
residue id #1/A:302 conservation 0.6087 index 301
residue id #1/A:303 conservation 0.6087 index 302
residue id #1/A:304 conservation 0.8261 index 303
residue id #1/A:305 conservation 0.087 index 304
residue id #1/A:306 conservation 0.087 index 305
residue id #1/A:307 conservation 0.3043 index 306
residue id #1/A:308 conservation 0.2174 index 307
residue id #1/A:309 conservation 0.6087 index 308
residue id #1/A:310 conservation 0.6957 index 309
residue id #1/A:311 conservation 0.7391 index 310
residue id #1/A:312 conservation 0.3478 index 311
residue id #1/A:313 conservation 0.5652 index 312
residue id #1/A:314 conservation 0.5652 index 313
residue id #1/A:315 conservation 0.087 index 314
residue id #1/A:316 conservation 0.0435 index 315
residue id #1/A:317 conservation 0.2609 index 316
residue id #1/A:318 conservation 0.1304 index 317
residue id #1/A:319 conservation 0.4783 index 318
residue id #1/A:320 conservation 0.2174 index 319
residue id #1/A:321 conservation 0.0435 index 320
residue id #1/A:322 conservation 0.5217 index 321
residue id #1/A:323 conservation 0.1739 index 322
residue id #1/A:324 conservation 0.8261 index 323
residue id #1/A:325 conservation 0.2174 index 324
residue id #1/A:326 conservation 0.1739 index 325
residue id #1/A:327 conservation 0.5652 index 326
residue id #1/A:328 conservation 0.1739 index 327
residue id #1/A:329 conservation 0.087 index 328
residue id #1/A:330 conservation 0.2609 index 329
residue id #1/A:331 conservation 0.4783 index 330
residue id #1/A:332 conservation 0.3478 index 331
residue id #1/A:333 conservation 0.7826 index 332
residue id #1/A:334 conservation 0.3043 index 333
residue id #1/A:335 conservation 0.087 index 334
residue id #1/A:336 conservation 0.1739 index 335
residue id #1/A:337 conservation 0.2609 index 336
residue id #1/A:338 conservation 0.2609 index 337
residue id #1/A:339 conservation 0.5217 index 338
residue id #1/A:340 conservation 0.4783 index 339
residue id #1/A:341 conservation 0.3913 index 340
residue id #1/A:342 conservation 0.087 index 341
residue id #1/A:343 conservation 0.2174 index 342
residue id #1/A:344 conservation 0.0435 index 343
residue id #1/A:345 conservation 0.087 index 344
residue id #1/A:346 conservation 0.5217 index 345
residue id #1/A:347 conservation 0.3043 index 346
residue id #1/A:348 conservation 0.2174 index 347
residue id #1/A:349 conservation 0.6957 index 348
residue id #1/A:350 conservation 0.8261 index 349
residue id #1/A:351 conservation 0.5652 index 350
residue id #1/A:352 conservation 0.1304 index 351
residue id #1/A:353 conservation 0.7826 index 352
residue id #1/A:354 conservation 0.1739 index 353
residue id #1/A:355 conservation 0.087 index 354
residue id #1/A:356 conservation 0.2609 index 355
residue id #1/A:357 conservation 0.1739 index 356
residue id #1/A:358 conservation 0.2174 index 357
residue id #1/A:359 conservation 0.4348 index 358
residue id #1/A:360 conservation 0.4783 index 359
residue id #1/A:361 conservation 0.1739 index 360
residue id #1/A:362 conservation 0.1304 index 361
residue id #1/A:363 conservation 0.1304 index 362
residue id #1/A:364 conservation 0.087 index 363
residue id #1/A:365 conservation 0.0435 index 364
residue id #1/A:366 conservation 0.2174 index 365
residue id #1/A:367 conservation 0.2174 index 366
residue id #1/A:368 conservation 0.087 index 367
residue id #1/A:369 conservation 0.087 index 368
residue id #1/A:370 conservation 0.1739 index 369
residue id #1/A:371 conservation 0.2174 index 370
residue id #1/A:372 conservation 0.2609 index 371
residue id #1/A:373 conservation 0.3043 index 372
residue id #1/A:374 conservation 0.2609 index 373
residue id #1/A:375 conservation 0.6522 index 374
residue id #1/A:376 conservation 0.3478 index 375
residue id #1/A:377 conservation 0.087 index 376
residue id #1/A:378 conservation 0.8261 index 377
> open /Users/paulminges/Downloads/conservation.defattr
Summary of feedback from opening
/Users/paulminges/Downloads/conservation.defattr
---
note | Assigned attribute 'conservation' to 783 residues using match mode: any
> open /Users/paulminges/Downloads/conservation.defattr
Summary of feedback from opening
/Users/paulminges/Downloads/conservation.defattr
---
note | Assigned attribute 'conservation' to 783 residues using match mode: any
> info residues #1 attribute conservation
residue id #1/A:1 conservation 0.261 index 0
residue id #1/A:2 conservation 0.217 index 1
residue id #1/A:3 conservation 0.13 index 2
residue id #1/A:4 conservation 0.304 index 3
residue id #1/A:5 conservation 0.478 index 4
residue id #1/A:6 conservation 0.348 index 5
residue id #1/A:7 conservation 0.043 index 6
residue id #1/A:8 conservation 0.391 index 7
residue id #1/A:9 conservation 0.652 index 8
residue id #1/A:10 conservation 0.957 index 9
residue id #1/A:11 conservation 0.261 index 10
residue id #1/A:12 conservation 0.609 index 11
residue id #1/A:13 conservation 0.217 index 12
residue id #1/A:14 conservation 0.348 index 13
residue id #1/A:15 conservation 0.696 index 14
residue id #1/A:16 conservation 0.87 index 15
residue id #1/A:17 conservation 0.739 index 16
residue id #1/A:18 conservation 0.783 index 17
residue id #1/A:19 conservation 0.826 index 18
residue id #1/A:20 conservation 0.217 index 19
residue id #1/A:21 conservation 0.652 index 20
residue id #1/A:22 conservation 0.652 index 21
residue id #1/A:23 conservation 0.609 index 22
residue id #1/A:24 conservation 0.522 index 23
residue id #1/A:25 conservation 0.435 index 24
residue id #1/A:26 conservation 0.652 index 25
residue id #1/A:27 conservation 0.304 index 26
residue id #1/A:28 conservation 0.217 index 27
residue id #1/A:29 conservation 0.13 index 28
residue id #1/A:30 conservation 0.261 index 29
residue id #1/A:31 conservation 0.652 index 30
residue id #1/A:32 conservation 0.391 index 31
residue id #1/A:33 conservation 0.087 index 32
residue id #1/A:34 conservation 0.739 index 33
residue id #1/A:35 conservation 0.391 index 34
residue id #1/A:36 conservation 0.174 index 35
residue id #1/A:37 conservation 0.304 index 36
residue id #1/A:38 conservation 0.957 index 37
residue id #1/A:39 conservation 0.348 index 38
residue id #1/A:40 conservation 0.217 index 39
residue id #1/A:41 conservation 0.522 index 40
residue id #1/A:42 conservation 1.0 index 41
residue id #1/A:43 conservation 0.174 index 42
residue id #1/A:44 conservation 0.13 index 43
residue id #1/A:45 conservation 0.696 index 44
residue id #1/A:46 conservation 0.652 index 45
residue id #1/A:47 conservation 0.913 index 46
residue id #1/A:48 conservation 0.957 index 47
residue id #1/A:49 conservation 0.391 index 48
residue id #1/A:50 conservation 1.0 index 49
residue id #1/A:51 conservation 0.174 index 50
residue id #1/A:52 conservation 0.304 index 51
residue id #1/A:53 conservation 0.13 index 52
residue id #1/A:54 conservation 0.13 index 53
residue id #1/A:55 conservation 0.261 index 54
residue id #1/A:56 conservation 0.609 index 55
residue id #1/A:57 conservation 0.348 index 56
residue id #1/A:58 conservation 0.826 index 57
residue id #1/A:59 conservation 1.0 index 58
residue id #1/A:60 conservation 0.957 index 59
residue id #1/A:61 conservation 0.522 index 60
residue id #1/A:62 conservation 0.739 index 61
residue id #1/A:63 conservation 0.304 index 62
residue id #1/A:64 conservation 1.0 index 63
residue id #1/A:65 conservation 0.435 index 64
residue id #1/A:66 conservation 0.13 index 65
residue id #1/A:67 conservation 0.087 index 66
residue id #1/A:68 conservation 0.217 index 67
residue id #1/A:69 conservation 0.957 index 68
residue id #1/A:70 conservation 0.652 index 69
residue id #1/A:71 conservation 0.87 index 70
residue id #1/A:72 conservation 0.174 index 71
residue id #1/A:73 conservation 0.391 index 72
residue id #1/A:74 conservation 0.043 index 73
residue id #1/A:75 conservation 1.0 index 74
residue id #1/A:76 conservation 1.0 index 75
residue id #1/A:77 conservation 1.0 index 76
residue id #1/A:78 conservation 0.609 index 77
residue id #1/A:79 conservation 0.696 index 78
residue id #1/A:80 conservation 0.043 index 79
residue id #1/A:81 conservation 0.043 index 80
residue id #1/A:82 conservation 0.913 index 81
residue id #1/A:83 conservation 0.913 index 82
residue id #1/A:84 conservation 1.0 index 83
residue id #1/A:85 conservation 1.0 index 84
residue id #1/A:86 conservation 0.261 index 85
residue id #1/A:87 conservation 0.174 index 86
residue id #1/A:88 conservation 0.957 index 87
residue id #1/A:89 conservation 0.739 index 88
residue id #1/A:90 conservation 0.435 index 89
residue id #1/A:91 conservation 0.609 index 90
residue id #1/A:92 conservation 0.217 index 91
residue id #1/A:93 conservation 0.043 index 92
residue id #1/A:94 conservation 1.0 index 93
residue id #1/A:95 conservation 0.826 index 94
residue id #1/A:96 conservation 0.13 index 95
residue id #1/A:97 conservation 1.0 index 96
residue id #1/A:98 conservation 1.0 index 97
residue id #1/A:99 conservation 1.0 index 98
residue id #1/A:100 conservation 0.391 index 99
residue id #1/A:101 conservation 0.739 index 100
residue id #1/A:102 conservation 1.0 index 101
residue id #1/A:103 conservation 0.087 index 102
residue id #1/A:104 conservation 0.957 index 103
residue id #1/A:105 conservation 0.826 index 104
residue id #1/A:106 conservation 0.087 index 105
residue id #1/A:107 conservation 0.13 index 106
residue id #1/A:108 conservation 0.043 index 107
residue id #1/A:109 conservation 0.043 index 108
residue id #1/A:110 conservation 0.87 index 109
residue id #1/A:111 conservation 0.261 index 110
residue id #1/A:112 conservation 0.565 index 111
residue id #1/A:113 conservation 0.913 index 112
residue id #1/A:114 conservation 0.739 index 113
residue id #1/A:115 conservation 0.565 index 114
residue id #1/A:116 conservation 0.87 index 115
residue id #1/A:117 conservation 0.957 index 116
residue id #1/A:118 conservation 0.565 index 117
residue id #1/A:119 conservation 1.0 index 118
residue id #1/A:120 conservation 1.0 index 119
residue id #1/A:121 conservation 0.304 index 120
residue id #1/A:122 conservation 1.0 index 121
residue id #1/A:123 conservation 1.0 index 122
residue id #1/A:124 conservation 0.348 index 123
residue id #1/A:125 conservation 0.913 index 124
residue id #1/A:126 conservation 1.0 index 125
residue id #1/A:127 conservation 0.957 index 126
residue id #1/A:128 conservation 0.087 index 127
residue id #1/A:129 conservation 1.0 index 128
residue id #1/A:130 conservation 0.87 index 129
residue id #1/A:131 conservation 0.13 index 130
residue id #1/A:132 conservation 0.174 index 131
residue id #1/A:133 conservation 0.13 index 132
residue id #1/A:134 conservation 0.13 index 133
residue id #1/A:135 conservation 0.826 index 134
residue id #1/A:136 conservation 0.565 index 135
residue id #1/A:137 conservation 1.0 index 136
residue id #1/A:138 conservation 0.348 index 137
residue id #1/A:139 conservation 0.913 index 138
residue id #1/A:140 conservation 0.087 index 139
residue id #1/A:141 conservation 0.957 index 140
residue id #1/A:142 conservation 0.043 index 141
residue id #1/A:143 conservation 0.087 index 142
residue id #1/A:144 conservation 0.174 index 143
residue id #1/A:145 conservation 0.217 index 144
residue id #1/A:146 conservation 0.174 index 145
residue id #1/A:147 conservation 0.087 index 146
residue id #1/A:148 conservation 0.043 index 147
residue id #1/A:149 conservation 0.043 index 148
residue id #1/A:150 conservation 0.609 index 149
residue id #1/A:151 conservation 0.217 index 150
residue id #1/A:152 conservation 1.0 index 151
residue id #1/A:153 conservation 0.478 index 152
residue id #1/A:154 conservation 0.435 index 153
residue id #1/A:155 conservation 0.913 index 154
residue id #1/A:156 conservation 0.957 index 155
residue id #1/A:157 conservation 0.261 index 156
residue id #1/A:158 conservation 0.174 index 157
residue id #1/A:159 conservation 0.826 index 158
residue id #1/A:160 conservation 0.783 index 159
residue id #1/A:161 conservation 0.87 index 160
residue id #1/A:162 conservation 0.261 index 161
residue id #1/A:163 conservation 0.783 index 162
residue id #1/A:164 conservation 1.0 index 163
residue id #1/A:165 conservation 1.0 index 164
residue id #1/A:166 conservation 0.304 index 165
residue id #1/A:167 conservation 0.348 index 166
residue id #1/A:168 conservation 0.261 index 167
residue id #1/A:169 conservation 0.043 index 168
residue id #1/A:170 conservation 0.217 index 169
residue id #1/A:171 conservation 0.043 index 170
residue id #1/A:172 conservation 0.13 index 171
residue id #1/A:173 conservation 0.043 index 172
residue id #1/A:174 conservation 0.174 index 173
residue id #1/A:175 conservation 0.087 index 174
residue id #1/A:176 conservation 0.087 index 175
residue id #1/A:177 conservation 0.174 index 176
residue id #1/A:178 conservation 0.261 index 177
residue id #1/A:179 conservation 0.087 index 178
residue id #1/A:180 conservation 0.043 index 179
residue id #1/A:181 conservation 0.087 index 180
residue id #1/A:182 conservation 0.652 index 181
residue id #1/A:183 conservation 0.043 index 182
residue id #1/A:184 conservation 0.217 index 183
residue id #1/A:185 conservation 0.13 index 184
residue id #1/A:186 conservation 0.087 index 185
residue id #1/A:187 conservation 0.043 index 186
residue id #1/A:188 conservation 0.739 index 187
residue id #1/A:189 conservation 0.13 index 188
residue id #1/A:190 conservation 0.087 index 189
residue id #1/A:191 conservation 0.87 index 190
residue id #1/A:192 conservation 0.522 index 191
residue id #1/A:193 conservation 0.261 index 192
residue id #1/A:194 conservation 0.087 index 193
residue id #1/A:195 conservation 0.348 index 194
residue id #1/A:196 conservation 0.304 index 195
residue id #1/A:197 conservation 0.739 index 196
residue id #1/A:198 conservation 0.696 index 197
residue id #1/A:199 conservation 0.565 index 198
residue id #1/A:200 conservation 0.435 index 199
residue id #1/A:201 conservation 0.13 index 200
residue id #1/A:202 conservation 0.304 index 201
residue id #1/A:203 conservation 0.348 index 202
residue id #1/A:204 conservation 0.739 index 203
residue id #1/A:205 conservation 0.609 index 204
residue id #1/A:206 conservation 0.652 index 205
residue id #1/A:207 conservation 0.043 index 206
residue id #1/A:208 conservation 0.174 index 207
residue id #1/A:209 conservation 0.435 index 208
residue id #1/A:210 conservation 0.87 index 209
residue id #1/A:211 conservation 0.87 index 210
residue id #1/A:212 conservation 0.522 index 211
residue id #1/A:213 conservation 0.522 index 212
residue id #1/A:214 conservation 0.174 index 213
residue id #1/A:215 conservation 0.565 index 214
residue id #1/A:216 conservation 0.826 index 215
residue id #1/A:217 conservation 0.696 index 216
residue id #1/A:218 conservation 0.13 index 217
residue id #1/A:219 conservation 0.217 index 218
residue id #1/A:220 conservation 0.087 index 219
residue id #1/A:221 conservation 0.043 index 220
residue id #1/A:222 conservation 0.087 index 221
residue id #1/A:223 conservation 0.13 index 222
residue id #1/A:224 conservation 0.174 index 223
residue id #1/A:225 conservation 0.13 index 224
residue id #1/A:226 conservation 0.304 index 225
residue id #1/A:227 conservation 0.087 index 226
residue id #1/A:228 conservation 0.087 index 227
residue id #1/A:229 conservation 0.348 index 228
residue id #1/A:230 conservation 0.565 index 229
residue id #1/A:231 conservation 0.304 index 230
residue id #1/A:232 conservation 0.087 index 231
residue id #1/A:233 conservation 0.565 index 232
residue id #1/A:234 conservation 0.826 index 233
residue id #1/A:235 conservation 0.478 index 234
residue id #1/A:236 conservation 0.217 index 235
residue id #1/A:237 conservation 0.826 index 236
residue id #1/A:238 conservation 0.826 index 237
residue id #1/A:239 conservation 0.217 index 238
residue id #1/A:240 conservation 0.043 index 239
residue id #1/A:241 conservation 0.261 index 240
residue id #1/A:242 conservation 0.522 index 241
residue id #1/A:243 conservation 0.739 index 242
residue id #1/A:244 conservation 0.652 index 243
residue id #1/A:245 conservation 0.652 index 244
residue id #1/A:246 conservation 0.696 index 245
residue id #1/A:247 conservation 0.13 index 246
residue id #1/A:248 conservation 0.043 index 247
residue id #1/A:249 conservation 0.174 index 248
residue id #1/A:250 conservation 0.304 index 249
residue id #1/A:251 conservation 0.304 index 250
residue id #1/A:252 conservation 0.13 index 251
residue id #1/A:253 conservation 0.174 index 252
residue id #1/A:254 conservation 0.261 index 253
residue id #1/A:255 conservation 0.13 index 254
residue id #1/A:256 conservation 0.87 index 255
residue id #1/A:257 conservation 0.609 index 256
residue id #1/A:258 conservation 0.783 index 257
residue id #1/A:259 conservation 0.304 index 258
residue id #1/A:260 conservation 0.087 index 259
residue id #1/A:261 conservation 0.217 index 260
residue id #1/A:262 conservation 0.87 index 261
residue id #1/A:263 conservation 0.217 index 262
residue id #1/A:264 conservation 0.174 index 263
residue id #1/A:265 conservation 0.261 index 264
residue id #1/A:266 conservation 0.435 index 265
residue id #1/A:267 conservation 0.13 index 266
residue id #1/A:268 conservation 0.087 index 267
residue id #1/A:269 conservation 0.304 index 268
residue id #1/A:270 conservation 0.087 index 269
residue id #1/A:271 conservation 0.087 index 270
residue id #1/A:272 conservation 0.696 index 271
residue id #1/A:273 conservation 0.609 index 272
residue id #1/A:274 conservation 0.826 index 273
residue id #1/A:275 conservation 0.261 index 274
residue id #1/A:276 conservation 0.087 index 275
residue id #1/A:277 conservation 0.435 index 276
residue id #1/A:278 conservation 0.174 index 277
residue id #1/A:279 conservation 0.174 index 278
residue id #1/A:280 conservation 0.478 index 279
residue id #1/A:281 conservation 0.783 index 280
residue id #1/A:282 conservation 0.348 index 281
residue id #1/A:283 conservation 0.565 index 282
residue id #1/A:284 conservation 0.217 index 283
residue id #1/A:285 conservation 0.13 index 284
residue id #1/A:286 conservation 0.043 index 285
residue id #1/A:287 conservation 0.13 index 286
residue id #1/A:288 conservation 0.261 index 287
residue id #1/A:289 conservation 0.565 index 288
residue id #1/A:290 conservation 0.739 index 289
residue id #1/A:291 conservation 0.652 index 290
residue id #1/A:292 conservation 0.826 index 291
residue id #1/A:293 conservation 0.261 index 292
residue id #1/A:294 conservation 0.261 index 293
residue id #1/A:295 conservation 0.174 index 294
residue id #1/A:296 conservation 0.13 index 295
residue id #1/A:297 conservation 0.174 index 296
residue id #1/A:298 conservation 0.13 index 297
residue id #1/A:299 conservation 0.13 index 298
residue id #1/A:300 conservation 0.652 index 299
residue id #1/A:301 conservation 0.652 index 300
residue id #1/A:302 conservation 0.609 index 301
residue id #1/A:303 conservation 0.609 index 302
residue id #1/A:304 conservation 0.826 index 303
residue id #1/A:305 conservation 0.087 index 304
residue id #1/A:306 conservation 0.087 index 305
residue id #1/A:307 conservation 0.304 index 306
residue id #1/A:308 conservation 0.217 index 307
residue id #1/A:309 conservation 0.609 index 308
residue id #1/A:310 conservation 0.696 index 309
residue id #1/A:311 conservation 0.739 index 310
residue id #1/A:312 conservation 0.348 index 311
residue id #1/A:313 conservation 0.565 index 312
residue id #1/A:314 conservation 0.565 index 313
residue id #1/A:315 conservation 0.087 index 314
residue id #1/A:316 conservation 0.043 index 315
residue id #1/A:317 conservation 0.261 index 316
residue id #1/A:318 conservation 0.13 index 317
residue id #1/A:319 conservation 0.478 index 318
residue id #1/A:320 conservation 0.217 index 319
residue id #1/A:321 conservation 0.043 index 320
residue id #1/A:322 conservation 0.522 index 321
residue id #1/A:323 conservation 0.174 index 322
residue id #1/A:324 conservation 0.826 index 323
residue id #1/A:325 conservation 0.217 index 324
residue id #1/A:326 conservation 0.174 index 325
residue id #1/A:327 conservation 0.565 index 326
residue id #1/A:328 conservation 0.174 index 327
residue id #1/A:329 conservation 0.087 index 328
residue id #1/A:330 conservation 0.261 index 329
residue id #1/A:331 conservation 0.478 index 330
residue id #1/A:332 conservation 0.348 index 331
residue id #1/A:333 conservation 0.783 index 332
residue id #1/A:334 conservation 0.304 index 333
residue id #1/A:335 conservation 0.087 index 334
residue id #1/A:336 conservation 0.174 index 335
residue id #1/A:337 conservation 0.261 index 336
residue id #1/A:338 conservation 0.261 index 337
residue id #1/A:339 conservation 0.522 index 338
residue id #1/A:340 conservation 0.478 index 339
residue id #1/A:341 conservation 0.391 index 340
residue id #1/A:342 conservation 0.087 index 341
residue id #1/A:343 conservation 0.217 index 342
residue id #1/A:344 conservation 0.043 index 343
residue id #1/A:345 conservation 0.087 index 344
residue id #1/A:346 conservation 0.522 index 345
residue id #1/A:347 conservation 0.304 index 346
residue id #1/A:348 conservation 0.217 index 347
residue id #1/A:349 conservation 0.696 index 348
residue id #1/A:350 conservation 0.826 index 349
residue id #1/A:351 conservation 0.565 index 350
residue id #1/A:352 conservation 0.13 index 351
residue id #1/A:353 conservation 0.783 index 352
residue id #1/A:354 conservation 0.174 index 353
residue id #1/A:355 conservation 0.087 index 354
residue id #1/A:356 conservation 0.261 index 355
residue id #1/A:357 conservation 0.174 index 356
residue id #1/A:358 conservation 0.217 index 357
residue id #1/A:359 conservation 0.435 index 358
residue id #1/A:360 conservation 0.478 index 359
residue id #1/A:361 conservation 0.174 index 360
residue id #1/A:362 conservation 0.13 index 361
residue id #1/A:363 conservation 0.13 index 362
residue id #1/A:364 conservation 0.087 index 363
residue id #1/A:365 conservation 0.043 index 364
residue id #1/A:366 conservation 0.217 index 365
residue id #1/A:367 conservation 0.217 index 366
residue id #1/A:368 conservation 0.087 index 367
residue id #1/A:369 conservation 0.087 index 368
residue id #1/A:370 conservation 0.174 index 369
residue id #1/A:371 conservation 0.217 index 370
residue id #1/A:372 conservation 0.261 index 371
residue id #1/A:373 conservation 0.304 index 372
residue id #1/A:374 conservation 0.261 index 373
residue id #1/A:375 conservation 0.652 index 374
residue id #1/A:376 conservation 0.348 index 375
residue id #1/A:377 conservation 0.087 index 376
residue id #1/A:378 conservation 0.826 index 377
> ui tool show "Render/Select by Attribute"
> color byattribute r:conservation #1 target cabs palette
> 0.0455251,red:0.524025,white:1,blue
3054 atoms, 378 residues, atom conservation range 0.043 to 1
> ui tool show "Scale Bar"
> scalebar
> scalebar off
> ui tool show "Render/Select by Attribute"
> key accent-3 :0.04 :0.52 :1.00 showTool true
> ui mousemode right "color key"
> color byattribute r:conservation #1 target cabs palette
> 0.043,#7fc97f:0.5215,#beaed4:1,#fdc086
3054 atoms, 378 residues, atom conservation range 0.043 to 1
> select subtract #1
Nothing selected
> save "/Users/paulminges/Library/CloudStorage/OneDrive-
> Personal/Documents/ResearchStuff/AG-Eder/2. Research/5. Endometriosis/1.
> Target Development/Structure_Analysis/MMP-10.cxs"
> select add #2
11423 atoms, 3163 bonds, 405 residues, 31 models selected
> ui tool show "Render/Select by Attribute"
> ui tool show "Color Key"
> ui mousemode right "color key"
> ui tool show "Color Key"
> ui mousemode right "color key"
> ui tool show "Color Key"
> ui mousemode right "color key"
> select subtract #2
27 models selected
> select add #2
11423 atoms, 3163 bonds, 405 residues, 31 models selected
> ui tool show "Color Key"
> ui mousemode right "color key"
> key accent-3 :0.04 :0.52 :1.00
> key pos 0.69000,0.08000
> key pos 0.68000,0.08000
> key pos 0.67000,0.08000
> key pos 0.66000,0.08000
> key pos 0.65000,0.08000
> key pos 0.64000,0.08000
> key pos 0.63000,0.08000
> key pos 0.62000,0.08000
> key pos 0.61000,0.08000
> key pos 0.60000,0.08000
> key pos 0.59000,0.08000
> key pos 0.58000,0.08000
> key pos 0.57000,0.08000
> key pos 0.56000,0.08000
> key pos 0.55000,0.08000
> key pos 0.54000,0.08000
> key pos 0.53000,0.08000
> key pos 0.52000,0.08000
> key pos 0.51000,0.08000
> key pos 0.50000,0.08000
> key pos 0.49000,0.08000
> key pos 0.48000,0.08000
> key pos 0.47000,0.08000
> key pos 0.46000,0.08000
> key pos 0.45000,0.08000
> key pos 0.44000,0.08000
> key pos 0.43000,0.08000
> key pos 0.42000,0.08000
> key pos 0.41000,0.08000
> key pos 0.40000,0.08000
> key pos 0.39000,0.08000
> key pos 0.38000,0.08000
> key pos 0.37000,0.08000
> key pos 0.36000,0.08000
> key pos 0.35000,0.08000
> key pos 0.34000,0.08000
> key pos 0.33000,0.08000
> key pos 0.32000,0.08000
> key pos 0.31000,0.08000
> key pos 0.30000,0.08000
> key pos 0.29000,0.08000
> key pos 0.28000,0.08000
> key pos 0.28000,0.07000
> key pos 0.28000,0.06000
> key pos 0.28000,0.05000
> key pos 0.28000,0.04000
> key pos 0.28000,0.05000
> key pos 0.28000,0.06000
> key pos 0.28000,0.07000
> key pos 0.28000,0.08000
> key pos 0.28000,0.09000
> key pos 0.28000,0.10000
> key pos 0.28000,0.09000
> select subtract #2
27 models selected
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.11.1 (2026-01-23)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M4
OpenGL vendor: Apple
Python: 3.11.9
Locale: en_US.UTF-8
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: Mac16,13
Model Number: MC6L4D/A
Chip: Apple M4
Total Number of Cores: 10 (4 performance and 6 efficiency)
Memory: 24 GB
System Firmware Version: 13822.61.10
OS Loader Version: 13822.61.10
Software:
System Software Overview:
System Version: macOS 26.2 (25C56)
Kernel Version: Darwin 25.2.0
Time since boot: 11 days, 17 hours, 40 minutes
Graphics/Displays:
Apple M4:
Chipset Model: Apple M4
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 4
Displays:
N27p:
Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus)
UI Looks like: 2560 x 1440 @ 60.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Automatically Adjust Brightness: No
Color LCD:
Display Type: Built-in Liquid Retina Display
Resolution: 2880 x 1864 Retina
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
aiohappyeyeballs: 2.6.1
aiohttp: 3.13.1
aiosignal: 1.4.0
alabaster: 1.0.0
annotated-types: 0.7.0
anyio: 4.12.1
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.1
attrs: 25.4.0
babel: 2.17.0
beautifulsoup4: 4.13.5
blockdiag: 3.0.0
blosc2: 3.12.2
build: 1.3.0
certifi: 2025.7.14
cftime: 1.6.5
charset-normalizer: 3.4.4
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.2.8
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.1.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Animations: 1.0
ChimeraX-Aniso: 1.3.2
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.61.4
ChimeraX-AtomicLibrary: 14.2.1
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.1
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.6.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3.0
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.11.1
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5.3
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.4
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.7.3
ChimeraX-Label: 1.2
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.2
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MCPServer: 0.1.0
ChimeraX-MDcrds: 2.17.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.3.2
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.22
ChimeraX-ModelPanel: 1.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0.1
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.15.2
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.12
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.5
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.4
ChimeraX-ProfileGrids: 1.4.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.5
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.3
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.2
ChimeraX-Scenes: 0.3.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.10
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.3
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
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: 2.5.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.49.1
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.5.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.5
ChimeraX-Zone: 1.0.1
click: 8.3.1
colorama: 0.4.6
comm: 0.2.3
contourpy: 1.3.3
coverage: 7.13.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.1.4
debugpy: 1.8.19
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.1
filelock: 3.19.1
fonttools: 4.61.1
frozenlist: 1.8.0
funcparserlib: 2.0.0a0
glfw: 2.10.0
grako: 3.16.5
h11: 0.16.0
h5py: 3.15.1
html2text: 2025.4.15
httpcore: 1.0.9
httpx: 0.28.1
httpx-sse: 0.4.3
idna: 3.11
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.3.0
ipykernel: 6.30.1
ipython: 9.5.0
ipython_pygments_lexers: 1.1.1
ipywidgets: 8.1.8
jedi: 0.19.2
Jinja2: 3.1.6
jsonschema: 4.26.0
jsonschema-specifications: 2025.9.1
jupyter_client: 8.6.3
jupyter_core: 5.9.1
jupyterlab_widgets: 3.0.16
kiwisolver: 1.4.9
line_profiler: 5.0.0
lxml: 6.0.2
lz4: 4.3.2
Markdown: 3.8.2
MarkupSafe: 3.0.3
matplotlib: 3.10.7
matplotlib-inline: 0.2.1
mcp: 1.18.0
msgpack: 1.1.1
multidict: 6.7.0
narwhals: 2.16.0
ndindex: 1.10.1
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.14.1
numpy: 2.4.2
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 25.0
ParmEd: 4.2.2
parso: 0.8.5
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 11.3.0
pip: 25.2
pkginfo: 1.12.1.2
platformdirs: 4.5.1
plotly: 6.5.2
pluggy: 1.6.0
prompt_toolkit: 3.0.52
propcache: 0.4.1
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pybind11: 3.0.1
pycollada: 0.8
pydantic: 2.12.5
pydantic-settings: 2.12.0
pydantic_core: 2.41.5
pydicom: 2.4.4
Pygments: 2.18.0
pyKVFinder: 0.9.0
pynmrstar: 3.3.6
pynrrd: 1.0.0
PyOpenGL: 3.1.10
PyOpenGL-accelerate: 3.1.10
pyopenxr: 1.1.4501
pyparsing: 3.3.2
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.9.1
PyQt6-Qt6: 6.9.2
PyQt6-WebEngine-commercial: 6.9.0
PyQt6-WebEngine-Qt6: 6.9.2
PyQt6_sip: 13.10.2
pytest: 9.0.2
pytest-cov: 7.0.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.2.1
python-multipart: 0.0.21
pyzmq: 27.1.0
qtconsole: 5.7.0
QtPy: 2.4.3
qtshim: 1.2
RandomWords: 0.4.0
referencing: 0.37.0
requests: 2.32.5
roman-numerals: 4.1.0
roman-numerals-py: 4.1.0
rpds-py: 0.30.0
scipy: 1.14.0
setuptools: 80.9.0
sfftk-rw: 0.8.1
six: 1.17.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.8.3
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.2.0
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
sse-starlette: 3.2.0
stack-data: 0.6.3
starlette: 0.52.1
superqt: 0.7.6
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.5
tomlkit: 0.14.0
tornado: 6.5.4
traitlets: 5.14.3
typing-inspection: 0.4.2
typing_extensions: 4.15.0
urllib3: 2.6.3
uvicorn: 0.40.0
wcwidth: 0.3.2
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.15
yarl: 1.22.0
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