The following bug report has been submitted:
Platform: Linux-6.1.0-25-amd64-x86_64-with-glibc2.36
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Aborted
Thread 0x00007fdd83fff6c0 (most recent call first):
File "/usr/local/CAME/share/packages/chimerax/chimerax-1.8/lib/python3.11/threading.py", line 324 in wait
File "/usr/local/CAME/share/packages/chimerax/chimerax-1.8/lib/python3.11/threading.py", line 622 in wait
File "/usr/local/CAME/share/packages/chimerax/chimerax-1.8/lib/python3.11/threading.py", line 1392 in run
File "/usr/local/CAME/share/packages/chimerax/chimerax-1.8/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/local/CAME/share/packages/chimerax/chimerax-1.8/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007fde9aa98b80 (most recent call first):
File "/usr/local/CAME/share/packages/chimerax/chimerax-1.8/lib/python3.11/site-packages/chimerax/geometry/matrix.py", line 444 in normalize_vector
File "/usr/local/CAME/share/packages/chimerax/chimerax-1.8/lib/python3.11/site-packages/chimerax/geometry/matrix.py", line 301 in orthonormal_frame
File "/usr/local/CAME/share/packages/chimerax/chimerax-1.8/lib/python3.11/site-packages/chimerax/geometry/place.py", line 496 in orthonormal_frame
File "/usr/local/CAME/share/packages/chimerax/chimerax-1.8/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 1527 in _shadow_transforms
File "/usr/local/CAME/share/packages/chimerax/chimerax-1.8/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 1644 in use_multishadow_map
File "/usr/local/CAME/share/packages/chimerax/chimerax-1.8/lib/python3.11/site-packages/chimerax/graphics/view.py", line 633 in _compute_shadowmaps
File "/usr/local/CAME/share/packages/chimerax/chimerax-1.8/lib/python3.11/site-packages/chimerax/graphics/view.py", line 227 in _draw_scene
File "/usr/local/CAME/share/packages/chimerax/chimerax-1.8/lib/python3.11/site-packages/chimerax/graphics/view.py", line 188 in draw
File "/usr/local/CAME/share/packages/chimerax/chimerax-1.8/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 84 in draw_new_frame
File "/usr/local/CAME/share/packages/chimerax/chimerax-1.8/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 150 in _redraw_timer_callback
File "/usr/local/CAME/share/packages/chimerax/chimerax-1.8/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
File "/usr/local/CAME/share/packages/chimerax/chimerax-1.8/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
File "/usr/local/CAME/share/packages/chimerax/chimerax-1.8/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 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.pdb_lib._load_libs, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, lxml._elementpath, lxml.etree, chimerax.surface._surface, 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, lxml.builder, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.mlp._mlp, chimerax.coulombic._esp, psutil._psutil_linux, psutil._psutil_posix (total: 61)
===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> help help:quickstart
> open 2bbv
2bbv title:
The refined three-dimensional structure of an insect virus At 2.8 angstroms
resolution [more info...]
Chain information for 2bbv #1
---
Chain | Description | UniProt
A B C | PROTEIN (BLACK BEETLE VIRUS CAPSID PROTEIN) | COAT_BBV 1-363
D E F | PROTEIN (BLACK BEETLE VIRUS CAPSID PROTEIN) | COAT_BBV 364-407
N | RNA (5'-R(*UP*CP*UP*UP*AP*UP*AP*UP*CP*U)-3') |
Non-standard residues in 2bbv #1
---
CA — calcium ion
2bbv mmCIF Assemblies
---
1| complete icosahedral assembly
2| icosahedral asymmetric unit
3| icosahedral pentamer
4| icosahedral 23 hexamer
5| icosahedral asymmetric unit, std point frame
6| crystal asymmetric unit, crystal frame
> color bychain
> view
> measure buriedarea /a withAtoms2 /b
Buried area between /a and /b = 1900.4
area /a = 15385, area /b = 14989, area both = 26573
> measure sasa #1 & ~solvent
Solvent accessible area for #1 & ~solvent (7609 atoms) = 34093
> interfaces #1 & protein
6 buried areas: C A 1675, C B 1671, A B 1663, C F 739, A D 714, B E 699
> open 1080 fromDatabase emdb
Fetching url
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-1080/map/emd_1080.map.gz
failed:
> volume #1 level 0.9
No volumes specified
> open https://www.rbvi.ucsf.edu/chimerax/tutorials.html
Opened https://www.rbvi.ucsf.edu/chimerax/tutorials.html
> open 2LIS
Summary of feedback from opening 2LIS fetched from pdb
---
note | Fetching compressed mmCIF 2lis from http://files.rcsb.org/download/2lis.cif
2lis title:
High resolution structure of the red abalone lysin monomer [more info...]
Chain information for 2lis #2
---
Chain | Description | UniProt
A | SPERM LYSIN | ELYS_HALRU 1-136
10 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> close 2bbv
Expected a models specifier or a keyword
> help help:user
> close session
> open 2LIS format mmcif fromDatabase pdb
2lis title:
High resolution structure of the red abalone lysin monomer [more info...]
Chain information for 2lis #1
---
Chain | Description | UniProt
A | SPERM LYSIN | ELYS_HALRU 1-136
10 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> addcharge
> addh /A
Summary of feedback from adding hydrogens to 2lis #1
---
notes | Termini for 2lis (#1) chain A determined from SEQRES records
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini: /A HIS 4
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini: /A MET 134
832 hydrogen bonds
Adding 'H' to /A HIS 4
/A MET 134 is not terminus, removing H atom from 'C'
1700 hydrogens added
Using Amber 20 recommended default charges and atom types for standard
residues
> Dock Prep
Unknown command: Dock Prep
> dockprep
Starting dock prep
Deleting solvent
Deleting non-metal-complex ions
Deleting non-current alt locs
Summary of feedback from adding hydrogens to 2lis #1
---
notes | Termini for 2lis (#1) chain A determined from SEQRES records
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini: /A HIS 4
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini: /A MET 134
127 hydrogen bonds
/A MET 134 is not terminus, removing H atom from 'C'
0 hydrogens added
Using Amber 20 recommended default charges and atom types for standard
residues
Dock prep finished
> addcharge
Using Amber 20 recommended default charges and atom types for standard
residues
> volume style surface
No volumes specified
> volume style surface
No volumes specified
> volume style mesh
No volumes specified
> select /A:63
10 atoms, 9 bonds, 1 residue, 1 model selected
> select up
562 atoms, 570 bonds, 31 residues, 1 model selected
> select up
2236 atoms, 2266 bonds, 131 residues, 1 model selected
> volume style surface
No volumes specified
> volume style surface
No volumes specified
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> nucleotides sel fill
> style nucleic & sel stick
Changed 0 atom styles
> nucleotides sel tube/slab shape box
> open 1a0m
Summary of feedback from opening 1a0m fetched from pdb
---
note | Fetching compressed mmCIF 1a0m from http://files.rcsb.org/download/1a0m.cif
1a0m title:
1.1 angstrom crystal structure of A-conotoxin [TYR15]-epi [more info...]
Chain information for 1a0m #2
---
Chain | Description | UniProt
A B | ALPHA-CONOTOXIN [TYR15]-EPI | CXA1_CONEP 1-16
Non-standard residues in 1a0m #2
---
NH2 — amino group
8 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> hide ribbons
> show atoms
> volume #1 level 1.0 style
Missing "style" keyword's argument
> volume #1 level 1.0
No volumes specified
> volume #1 level
Missing "level" keyword's argument
> volume #1
No volumes specified
> mesh
Unknown command: mesh
> volume #1 level 1.0 style mesh
No volumes specified
> style mesh
Expected a keyword
> mlp sel
Map values for surface "2lis_A SES surface": minimum -24.11, mean -1.695,
maximum 25.63
To also show corresponding color key, enter the above mlp command and add key
true
> coulombic sel
Coulombic values for 2lis_A SES surface #1.1: minimum, -8.91, mean 4.34,
maximum 15.34
To also show corresponding color key, enter the above coulombic command and
add key true
> volume style surface
No volumes specified
> volume style mesh
No volumes specified
> volume style mesh
No volumes specified
> style sel sphere
Changed 2236 atom styles
> coulombic sel
Coulombic values for 2lis_A SES surface #1.1: minimum, -8.91, mean 4.34,
maximum 15.34
To also show corresponding color key, enter the above coulombic command and
add key true
> color bfactor sel
2236 atoms, 131 residues, 1 surfaces, atom bfactor range 2.18 to 93.9
> color bfactor sel
2236 atoms, 131 residues, 1 surfaces, atom bfactor range 2.18 to 93.9
> mlp sel
Map values for surface "2lis_A SES surface": minimum -24.11, mean -1.695,
maximum 25.63
To also show corresponding color key, enter the above mlp command and add key
true
> hide sel surfaces
> show sel surfaces
> hide sel surfaces
> hide sel cartoons
> hide sel atoms
> show sel atoms
> style sel sphere
Changed 2236 atom styles
> style sel stick
Changed 2236 atom styles
> style sel ball
Changed 2236 atom styles
> color bfactor sel
2236 atoms, 131 residues, 1 surfaces, atom bfactor range 2.18 to 93.9
> coulombic sel
Coulombic values for 2lis_A SES surface #1.1: minimum, -8.91, mean 4.34,
maximum 15.34
To also show corresponding color key, enter the above coulombic command and
add key true
> coulombic sel
Coulombic values for 2lis_A SES surface #1.1: minimum, -8.91, mean 4.34,
maximum 15.34
To also show corresponding color key, enter the above coulombic command and
add key true
> close coulombic
Expected a models specifier or a keyword
> hbonds sel reveal true
127 hydrogen bonds found
> color bfactor sel
2236 atoms, 131 residues, 1 surfaces, atom bfactor range 2.18 to 93.9
> hide sel surfaces
> hide sel cartoons
> color bfactor sel
2236 atoms, 131 residues, 1 surfaces, atom bfactor range 2.18 to 93.9
> hbonds sel reveal true
127 hydrogen bonds found
> ~hbonds
> hbonds sel reveal true
127 hydrogen bonds found
> hbonds sel reveal true
127 hydrogen bonds found
> rainbow sel
> show sel cartoons
> hide sel atoms
> select clear
> select #1/A:12
14 atoms, 13 bonds, 1 residue, 1 model selected
> select #1/A:11
19 atoms, 18 bonds, 1 residue, 1 model selected
> hbonds sel reveal true
0 hydrogen bonds found
> hbonds sel reveal true
0 hydrogen bonds found
> hbonds sel reveal true
0 hydrogen bonds found
> hbonds sel reveal true
0 hydrogen bonds found
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> select #1/A:61
17 atoms, 17 bonds, 1 residue, 1 model selected
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> interfaces #1 & protein
0 buried areas:
> close
> set bgColor black
> set silhouettes false
> open 1a0m format mmcif fromDatabase pdb
1a0m title:
1.1 angstrom crystal structure of A-conotoxin [TYR15]-epi [more info...]
Chain information for 1a0m #1
---
Chain | Description | UniProt
A B | ALPHA-CONOTOXIN [TYR15]-EPI | CXA1_CONEP 1-16
Non-standard residues in 1a0m #1
---
NH2 — amino group
8 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> close
> set bgColor black
> set silhouettes false
> open 2LIS format mmcif fromDatabase pdb
2lis title:
High resolution structure of the red abalone lysin monomer [more info...]
Chain information for 2lis #1
---
Chain | Description | UniProt
A | SPERM LYSIN | ELYS_HALRU 1-136
10 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> close
> set bgColor black
> set silhouettes false
> open 1080 fromDatabase emdb
Summary of feedback from opening 1080 fetched from emdb
---
warning | Could not read metadata for EMDB 1080: Fetching url ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-1080/header/emd-1080.xml failed:
note | Fetching compressed map 1080 from ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-1080/map/emd_1080.map.gz
Opened emdb 1080 as #1, grid size 100,100,100, pixel 2.7, shown at level 1.68,
step 1, values float32
> lighting full
> volume #1 level 0.9
> mousemode rightMode "contour level"
> volume #1 level 0.622
Drag select of 1 emdb 1080
> volume #1 encloseVolume 1e6 step 1 color tan
> set bgColor gray
> set bgColor #80808000
> set silhouettes true
> open 1grl
Summary of feedback from opening 1grl fetched from pdb
---
note | Fetching compressed mmCIF 1grl from http://files.rcsb.org/download/1grl.cif
1grl title:
The crystal structure of the bacterial chaperonin groel At 2.8 angstroms [more
info...]
Chain information for 1grl #2
---
Chain | Description | UniProt
A B C D E F G | GROEL (HSP60 CLASS) | CH60_ECOLI 2-548
1grl mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| software_defined_assembly
> lighting default
> open /tmp/ChimeraX-DpiaUZ/move_h2o.png
Image mode RGBA is not supported (L, P, I;16, I;16B, I;16L, I;16S, F, F;32BF,
I, RGB)
> fitmap #2 inMap #1
Fit molecule 1grl (#2) to map emdb 1080 (#1) using 29274 atoms
average map value = 1.33, steps = 160
shifted from previous position = 43.6
rotated from previous position = 25.7 degrees
atoms outside contour = 3704, contour level = 0.82501
Position of 1grl (#2) relative to emdb 1080 (#1) coordinates:
Matrix rotation and translation
0.90168160 -0.43226797 -0.01070926 39.38378225
0.43239643 0.90128739 0.02672781 18.93321539
-0.00190145 -0.02873062 0.99958538 -0.07505929
Axis -0.06400385 -0.01016498 0.99789788
Axis point -21.87971538 95.67332351 0.00000000
Rotation angle (degrees) 25.67354134
Shift along axis -2.78807077
> volume #1 transparency 0.5
> molmap #2 10
Opened 1grl map 10 as #3, grid size 63,63,41, pixel 3.33, shown at level
0.0611, step 1, values float32
> volume #3 style mesh
> volume sel style mesh
> volume sel style surface
> volume sel hide
> volume sel show
> close
> set bgColor black
> set bgColor transparent
> set silhouettes false
> open 1a0m fromDatabase eds
Summary of feedback from opening 1a0m fetched from eds
---
note | Fetching map 1a0m from http://www.ebi.ac.uk/pdbe/coordinates/files/1a0m.ccp4
Opened eds 1a0m as #1, grid size 120,120,64, pixel 0.37,0.37,0.367, shown at
level 2.4, step 1, values float32
> open 1a0m
1a0m title:
1.1 angstrom crystal structure of A-conotoxin [TYR15]-epi [more info...]
Chain information for 1a0m #2
---
Chain | Description | UniProt
A B | ALPHA-CONOTOXIN [TYR15]-EPI | CXA1_CONEP 1-16
Non-standard residues in 1a0m #2
---
NH2 — amino group
8 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> hide ribbons
> show
> volume #1 level 1.0 style mesh
> close
> open 2LIS format mmcif fromDatabase pdb
2lis title:
High resolution structure of the red abalone lysin monomer [more info...]
Chain information for 2lis #1
---
Chain | Description | UniProt
A | SPERM LYSIN | ELYS_HALRU 1-136
10 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> addh
Summary of feedback from adding hydrogens to 2lis #1
---
notes | Termini for 2lis (#1) chain A determined from SEQRES records
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini: /A HIS 4
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini: /A MET 134
832 hydrogen bonds
Adding 'H' to /A HIS 4
/A MET 134 is not terminus, removing H atom from 'C'
1700 hydrogens added
> ui tool show "Color Zone"
> ui tool show "Fit in Map"
> ui tool show AlphaFold
> ui tool show "Surface Color"
No surface chosen for coloring
> select /A:23
19 atoms, 18 bonds, 1 residue, 1 model selected
No surface chosen for coloring
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 1 atomic models, 0 maps.
Color zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic
models, 0 maps.
> volume style surface
No volumes specified
> volume style mesh
No volumes specified
> color sel byhetero
> color sel bychain
> color sel bypolymer
> rainbow sel
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 2lis_A SES surface #1.1: minimum, -8.91, mean 4.34,
maximum 15.34
To also show corresponding color key, enter the above coulombic command and
add key true
> mlp sel
Map values for surface "2lis_A SES surface": minimum -24.11, mean -1.695,
maximum 25.63
To also show corresponding color key, enter the above mlp command and add key
true
> color bfactor sel
19 atoms, 1 residues, 1 surfaces, atom bfactor range 8.45 to 11.3
> color sel bynucleotide
> hide sel surfaces
> volume #1 style mesh level 0.8 color red level 1.2 color 0,50,80
No volumes specified
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> ui mousemode right distance
> ui mousemode right "translate selected atoms"
> select /A:4
17 atoms, 17 bonds, 1 residue, 1 model selected
> ui mousemode right distance
> ui mousemode right "translate selected models"
> ui mousemode right zoom
> ui mousemode right translate
> ui mousemode right select
> ui mousemode right "contour level"
> ui mousemode right windowing
> ui mousemode right tug
> ui mousemode right "mark center"
> ui mousemode right "link markers"
> ui mousemode right "move markers"
> ui mousemode right "resize markers"
> ui mousemode right "mark point"
> ui mousemode right "mark center"
> ui mousemode right "mark point"
> ui mousemode right "mark maximum"
> ui mousemode right "mark surface"
> style sel ball
Changed 17 atom styles
> hide sel cartoons
> style sel stick
Changed 17 atom styles
> style sel ball
Changed 17 atom styles
> select #1/A:25
10 atoms, 9 bonds, 1 residue, 1 model selected
> select up
488 atoms, 492 bonds, 29 residues, 2 models selected
> select up
2236 atoms, 2266 bonds, 131 residues, 2 models selected
> style sel ball
Changed 2236 atom styles
> hide sel cartoons
> style sel ball
Changed 2236 atom styles
> style sel stick
Changed 2236 atom styles
> style sel sphere
Changed 2236 atom styles
> show sel cartoons
> color bfactor sel
2236 atoms, 131 residues, 1 surfaces, atom bfactor range 2.18 to 93.9
> style sel sphere
Changed 2236 atom styles
> style sel ball
Changed 2236 atom styles
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> style sel stick
Changed 2236 atom styles
> rainbow sel
> style sel ball
Changed 2236 atom styles
> style sel sphere
Changed 2236 atom styles
> style sel stick
Changed 2236 atom styles
> show sel cartoons
> hide sel cartoons
> show sel cartoons
> show sel atoms
> hide sel atoms
> show sel atoms
> hide sel cartoons
> style sel ball
Changed 2236 atom styles
> style sel stick
Changed 2236 atom styles
> style sel ball
Changed 2236 atom styles
> color bfactor sel
2236 atoms, 131 residues, 1 surfaces, atom bfactor range 2.18 to 93.9
> ui mousemode right "mark surface"
> ui mousemode right "mark point"
> select down
488 atoms, 492 bonds, 29 residues, 2 models selected
> select down
10 atoms, 9 bonds, 1 residue, 2 models selected
> ui mousemode right "mark surface"
> marker #2 position 16.06,-9.172,116.5 color yellow radius 1
> marker change #2:3 position 2.021,-29.09,121 color blue radius 2
> ui mousemode right "resize markers"
> marker change #2:3 position 2.021,-29.09,121 color red radius 2
> marker change #2/A PRO 130 color red
Expected a keyword
> color red #2/A PRO 130
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> help help:quickstart
> close
> open 1273 fromDatabase emdb
Summary of feedback from opening 1273 fetched from emdb
---
notes | Fetching compressed map 1273 from ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-1273/map/emd_1273.map.gz
Fetching map header 1273 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-1273/header/emd-1273.xml
Opened emdb 1273 as #1, grid size 2048,2048,76, pixel 22.5, shown at step 1,
values int8
> close
> open 1273 fromDatabase emdb
Opened emdb 1273 as #1, grid size 2048,2048,76, pixel 22.5, shown at step 1,
values int8
> volume #1 region all showOutlineBox true
> close
> open 2LIS format mmcif fromDatabase pdb
2lis title:
High resolution structure of the red abalone lysin monomer [more info...]
Chain information for 2lis #1
---
Chain | Description | UniProt
A | SPERM LYSIN | ELYS_HALRU 1-136
10 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> style ball
Changed 1388 atom styles
> show cartoons
> show atoms
> hide cartoons
> hbonds reveal true
830 hydrogen bonds found
> coulombic
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 2lis_A SES surface #1.2: minimum, -8.90, mean 3.27,
maximum 13.89
To also show corresponding color key, enter the above coulombic command and
add key true
> interfaces ~solvent
0 buried areas:
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> lighting flat
> lighting shadows true intensity 0.5
> lighting full
> lighting soft
> lighting simple
> close
> open 2LIS format mmcif fromDatabase pdb
2lis title:
High resolution structure of the red abalone lysin monomer [more info...]
Chain information for 2lis #1
---
Chain | Description | UniProt
A | SPERM LYSIN | ELYS_HALRU 1-136
10 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> show atoms
> hide cartoons
> hbonds reveal true
830 hydrogen bonds found
> coulombic
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 2lis_A SES surface #1.2: minimum, -8.90, mean 3.27,
maximum 13.89
To also show corresponding color key, enter the above coulombic command and
add key true
Alignment identifier is 1/A
> select clear
> select /A:13-41,44-74,82-95,98-107,116-123,126-128
806 atoms, 822 bonds, 95 pseudobonds, 95 residues, 2 models selected
> select clear
> select /A:13-41,44-74,82-95,98-107,116-123,126-128
806 atoms, 822 bonds, 95 pseudobonds, 95 residues, 2 models selected
> select clear
> select /A:13-41,44-74,82-95,98-107,116-123,126-128
806 atoms, 822 bonds, 95 pseudobonds, 95 residues, 2 models selected
> volume step 2
No volumes specified
Volume zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic
models, 0 maps.
> ui mousemode right rotate
> ui mousemode right translate
> ui mousemode right zoom
> ui mousemode right pivot
> ui mousemode right minimize
> ui mousemode right "next docked"
> ui mousemode right "play coordinates"
> ui mousemode right swapaa
> select /A
1388 atoms, 1134 bonds, 830 pseudobonds, 415 residues, 2 models selected
> select C
723 atoms, 590 bonds, 131 residues, 1 model selected
> select C1
Nothing selected
> hide surfaces
> select C3
431 atoms, 293 bonds, 131 residues, 1 model selected
> select backbone
524 atoms, 523 bonds, 89 pseudobonds, 131 residues, 2 models selected
> select clear
> hide #* target a
> show target ab
> color white
> color bfactor
1388 atoms, 415 residues, 1 surfaces, atom bfactor range 2.18 to 93.9
> rainbow
> surface style mesh
> transparency 40
> ui tool show "Selection Inspector"
> help help:user/tools/inspector.html
> label #1 text "/{0.chain_id} {0.name} {0.number}{0.insertion_code}"
> ~label #1 atoms
> ~label #1 residues
> view
> cofr frontCenter
> cartoon style modeHelix tube sides 20
> style sphere
Changed 1388 atom styles
> hide surfaces
> style sphere
Changed 1388 atom styles
> style stick
Changed 1388 atom styles
> style ball
Changed 1388 atom styles
> set bgColor white
> set bgColor #ffffff00
> set bgColor gray
> set bgColor #80808000
> lighting full
> view orient
> ui tool show "Side View"
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 3.3 (Core Profile) Mesa 22.3.6
OpenGL renderer: Mesa Intel(R) HD Graphics 2000 (SNB GT1)
OpenGL vendor: Intel
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: xcb
XDG_SESSION_TYPE=x11
DESKTOP_SESSION=xfce
XDG_SESSION_DESKTOP=xfce
XDG_CURRENT_DESKTOP=XFCE
DISPLAY=:0.0
Manufacturer:
Model:
OS: Debian GNU/Linux 12 bookworm
Architecture: 64bit ELF
Virtual Machine: none
CPU: 8 Intel(R) Core(TM) i7-2600 CPU @ 3.40GHz
Cache Size: 8192 KB
Memory:
total used free shared buff/cache available
Mem: 15Gi 3.0Gi 6.1Gi 695Mi 7.5Gi 12Gi
Swap: 8.0Gi 72Ki 8.0Gi
Graphics:
00:02.0 VGA compatible controller [0300]: Intel Corporation 2nd Generation Core Processor Family Integrated Graphics Controller [8086:0102] (rev 09)
DeviceName: Intel(R) HD Graphics Device
Subsystem: Intel Corporation 2nd Generation Core Processor Family Integrated Graphics Controller [8086:2008]
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2024.6.2
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-LinuxSupport: 1.0.1
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.5
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
distro: 1.9.0
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 24.1
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Need a reproducible test case. Tried everything from the last close command.