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Opened 5 months ago
Closed 5 months ago
#18191 closed defect (duplicate)
Crash saving atomic state
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sessions | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-5.14.0-162.6.1.el9_1.0.1.x86_64-x86_64-with-glibc2.34
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x0000146d773c4740 (most recent call first):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 2027 in save_state
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 219 in take_snapshot
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 1424 in take_snapshot
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/session.py", line 322 in process
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/session.py", line 297 in discovery
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/session.py", line 741 in save
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/session.py", line 1051 in save
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core_formats/__init__.py", line 95 in save
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/save_command/cmd.py", line 101 in provider_save
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3213 in run
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/save_command/cmd.py", line 86 in cmd_save
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3213 in run
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 319 in execute
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 146 in keyPressEvent
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 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.surface._surface, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, openmm._openmm, openmm.app.internal.compiled, lxml._elementpath, lxml.etree, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler (total: 58)
===== Log before crash start =====
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /yonath_group/andre/em_data/schultz_comparison/newest_overlap_ribosome_exitTunnel_take2.cxs
Log from Tue May 13 16:59:40 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open newest_overlap_ribosome_exitTunnel.cxs
Log from Tue May 13 16:17:56 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open new_overlap_ribosome_exitTunnel.cxs
Log from Wed Feb 9 12:18:56 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /Users/dede/schultz_comparison/new_overlap_ribosome_exitTunnel.cxs
Log from Mon Feb 7 17:21:35 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /Users/dede/schultz_comparison/new_overlap_bonds_waters_2.cxs
Log from Sun Feb 6 15:44:02 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /Users/dede/schultz_comparison/new_overlap_antibiotic_Anat.cxs
Log from Thu Feb 3 12:47:20 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /Users/dede/schultz_comparison/new_overlap_antibiotic_Anat.cxs
Log from Thu Feb 3 12:09:13 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /Users/dede/schultz_comparison/new_overlap_antibiotics_newcolors.cxs
Log from Tue Feb 1 18:36:14 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /Users/dede/schultz_comparison/new_overlap_antibiotics.cxs
Log from Tue Feb 1 16:51:39 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /Users/dede/schultz_comparison/overlap_antibiotics.cxs
Log from Sun Jan 30 17:00:34 2022UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
> open /yonath_group/andre/em_data/schultz_comparison/overlap_antibiotics.cxs
QXcbConnection: XCB error: 3 (BadWindow), sequence: 64517, resource id:
32032708, major code: 40 (TranslateCoords), minor code: 0
Log from Sun Jan 23 12:12:56 2022UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /yonath_group/andre/em_data/schultz_comparison/x10324.pdb
Chain information for x10324.pdb #1
---
Chain | Description
2 | No description available
3 | No description available
4 | No description available
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Z | No description available
QXcbConnection: XCB error: 3 (BadWindow), sequence: 24348, resource id:
32519754, major code: 40 (TranslateCoords), minor code: 0
> open /yonath_group/andre/em_data/schultz_comparison/x11066.pdb
Chain information for x11066.pdb #2
---
Chain | Description
1 | No description available
2 | No description available
3 | No description available
4 | No description available
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Z | No description available
> open /yonath_group/andre/em_data/schultz_comparison/X10305.pdb
Chain information for X10305.pdb #3
---
Chain | Description
1 | No description available
2 | No description available
3 | No description available
4 | No description available
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Z | No description available
> open /yonath_group/andre/em_data/schultz_comparison/X10350.pdb
Chain information for X10350.pdb #4
---
Chain | Description
0 | No description available
1 | No description available
2 | No description available
4 | No description available
6 | No description available
7 | No description available
9 | No description available
A | No description available
B | No description available
D | No description available
E | No description available
F | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
Z | No description available
QXcbConnection: XCB error: 3 (BadWindow), sequence: 29636, resource id:
32527352, major code: 40 (TranslateCoords), minor code: 0
> hide atoms
> show cartoons
> set bgColor white
> ui tool show "Color Actions"
> color dark cyan
> select #1
69569 atoms, 74328 bonds, 130 pseudobonds, 6160 residues, 2 models selected
> color sel dark cyan
> select #2
76873 atoms, 81429 bonds, 74 pseudobonds, 7395 residues, 2 models selected
> select #1
69569 atoms, 74328 bonds, 130 pseudobonds, 6160 residues, 2 models selected
> select #2
76873 atoms, 81429 bonds, 74 pseudobonds, 7395 residues, 2 models selected
> select #1
69569 atoms, 74328 bonds, 130 pseudobonds, 6160 residues, 2 models selected
> select #2
76873 atoms, 81429 bonds, 74 pseudobonds, 7395 residues, 2 models selected
> color sel magenta
> select #3
76870 atoms, 81415 bonds, 74 pseudobonds, 7403 residues, 2 models selected
> color sel lime
> select #4
78369 atoms, 85486 bonds, 22 pseudobonds, 5368 residues, 2 models selected
> color sel light salmon
> color sel deep sky blue
> color sel light salmon
> select #1
69569 atoms, 74328 bonds, 130 pseudobonds, 6160 residues, 2 models selected
> color sel deep sky blue
> cartoon style width 1 thickness 0.3
> view :XXX
> select :XXX
126 atoms, 133 bonds, 2 residues, 2 models selected
> show sel atoms
> select :LIG
130 atoms, 138 bonds, 2 residues, 2 models selected
> show sel atoms
> lighting soft
> show #1/A:2530, 2086, 2085, 2638, 797, 2636, 2089, 793, 2636, 2638
> select #1/A:2530, 2086, 2085, 2638, 797, 2636, 2089, 793, 2636, 2638
174 atoms, 189 bonds, 8 residues, 1 model selected
> style sel stick
Changed 174 atom styles
> select :XXX
126 atoms, 133 bonds, 2 residues, 2 models selected
> select add :LIG
256 atoms, 271 bonds, 4 residues, 4 models selected
> select ~ sel
301425 atoms, 322387 bonds, 300 pseudobonds, 26322 residues, 8 models selected
> hide sel
> hide sel cartoons
> graphics silhouettes true
> save /yonath_group/andre/em_data/schultz_comparison/overlap_antibiotics.cxs
> ui tool show "Color Actions"
> select #1
69569 atoms, 74328 bonds, 130 pseudobonds, 6160 residues, 2 models selected
> select #2
76873 atoms, 81429 bonds, 74 pseudobonds, 7395 residues, 2 models selected
> select #4
78369 atoms, 85486 bonds, 22 pseudobonds, 5368 residues, 2 models selected
> color sel light salmon
> select clear
> save /yonath_group/andre/em_data/schultz_comparison/overlap_antibiotics.png
> supersample 3
> save
> /yonath_group/andre/em_data/schultz_comparison/overlap_antibiotics_2.png
> supersample 3
> open
> /yonath_group/andre/em_data/schultz_66/comp-x11066_alternate_orientation.pdb
> ui tool show "Color Actions"
> color dark violet
> undo
> select #5
72 atoms, 77 bonds, 1 residue, 1 model selected
> color sel hot pink
> ui tool show Matchmaker
> matchmaker #5 to #2
Reference and/or match model contains no nucleic or amino acid chains.
Use the command-line 'align' command to superimpose small molecules/ligands.
> align #5 toAtoms #2
Unequal number of atoms to pair, 72 and 76873
> align #5 toAtoms #2:XXX
RMSD between 72 atom pairs is 2.923 angstroms
> select clear
> hide #5 models
> save /yonath_group/andre/em_data/schultz_comparison/overlap_antibiotics.cxs
opened ChimeraX session
> open
> /yonath_group/andre/em_data/schultz_comparison/FR_50S_SC_X10350_real_space_refined-
> coot-corrected.pdb
Chain information for FR_50S_SC_X10350_real_space_refined-coot-corrected.pdb
#6
---
Chain | Description
0 | No description available
1 | No description available
2 | No description available
4 | No description available
6 | No description available
7 | No description available
9 | No description available
A | No description available
B | No description available
D | No description available
E | No description available
F | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
Z | No description available
> select #6
78369 atoms, 85486 bonds, 22 pseudobonds, 5368 residues, 2 models selected
> select subtract #6/A:XXX
78296 atoms, 85408 bonds, 22 pseudobonds, 5367 residues, 2 models selected
> delete sel
> select #6
73 atoms, 78 bonds, 1 residue, 1 model selected
> color sel light salmon
> align #6 toAtoms #4
Unequal number of atoms to pair, 73 and 78369
> mmaker #6 to #4
Reference and/or match model contains no nucleic or amino acid chains.
Use the command-line 'align' command to superimpose small molecules/ligands.
> mmaker #6 toAtoms #4
> matchmaker #6 toAtoms #4
Expected a keyword
> mmaker sel toAtoms #4
> matchmaker sel toAtoms #4
Expected a keyword
> align #6 toAtoms #4
Unequal number of atoms to pair, 73 and 78369
> align #6 toAtoms #4
Unequal number of atoms to pair, 73 and 78369
> open
> /yonath_group/andre/em_data/schultz_comparison/FR_50S_SC_X10350_real_space_refined-
> coot-corrected_Hydrogens.pdb
Chain information for FR_50S_SC_X10350_real_space_refined-coot-
corrected_Hydrogens.pdb #7
---
Chain | Description
0 | No description available
1 | No description available
2 | No description available
4 | No description available
6 | No description available
7 | No description available
9 | No description available
A | No description available
B | No description available
D | No description available
E | No description available
F | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
Z | No description available
> close #6
> close #7
> open
> /yonath_group/andre/em_data/schultz_comparison/FR_50S_SC_X10350_real_space_refined-
> coot-corrected_Hydrogens.pdb
Chain information for FR_50S_SC_X10350_real_space_refined-coot-
corrected_Hydrogens.pdb #6
---
Chain | Description
0 | No description available
1 | No description available
2 | No description available
4 | No description available
6 | No description available
7 | No description available
9 | No description available
A | No description available
B | No description available
D | No description available
E | No description available
F | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
Z | No description available
> select #6
78369 atoms, 85486 bonds, 22 pseudobonds, 5368 residues, 2 models selected
> select subtract #6/A:XXX
78296 atoms, 85408 bonds, 22 pseudobonds, 5367 residues, 2 models selected
> delete sel
> align #6 toAtoms #4
Unequal number of atoms to pair, 73 and 78369
> ui mousemode right "translate selected models"
> select #6
73 atoms, 78 bonds, 1 residue, 1 model selected
> ui mousemode right select
> align #6/A:XXX toAtoms #4/A:XXX
Unequal number of atoms to pair, 73 and 0
> align #6/A:XXX toAtoms #4/A:LIG
RMSD between 73 atom pairs is 3.681 angstroms
> show #5 models
> hide #5 models
> color #6 light salmon
> hide #!4 models
> save /yonath_group/andre/em_data/schultz_comparison/overlap_antibiotics.cxs
——— End of log from Sun Jan 30 17:00:34 2022 ———
opened ChimeraX session
> clear
Unknown command: clear
> select clear
> color #1 royal blue
> save /Users/dede/schultz_comparison/new_overlap_antibiotics.cxs
——— End of log from Tue Feb 1 16:51:39 2022 ———
opened ChimeraX session
> color #1 cyan
> color #1 #66ccee
> color #1 #33bbee
> color #2 #ee3377
> color #3 #009988
> color #1 #66ccee
> color #12#ee6677
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword
> color #2 #ee6677
> color #3 #228833
> color #3 #ccbb44
> color #3 #228833
> color #4 #228833
> color #6 #228833
> color #6 #ee6677
> color #2 #aa3377
> save /Users/dede/schultz_comparison/new_overlap_antibiotics_newcolors.cxs
——— End of log from Tue Feb 1 18:36:14 2022 ———
opened ChimeraX session
> color #6 orange
> color #6 mandarin
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword
> color #6 dark orange
> color byhetero
> hide #!2 models
> hide #!3 models
> hide #!6 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!6 models
> ui tool show "Color Actions"
> color #6 dark orange
> select #6
73 atoms, 78 bonds, 1 residue, 1 model selected
> select clear
> color #6 orange
> color byhetero
> show #!3 models
> hide #!6 models
> show #!6 models
> ui tool show "Color Actions"
> color #3 olive drab
> color #3 lawn green
> color #3 medium spring green
> color #3 lime
> color #3 gray
> color #3 dark olive green
> color #3 olive
> color #3 tan
> color #3 yellow green
> color byhetero
> color #3 dark khaki
> show #!2 models
> show #!1 models
> hide #!1 models
> hide #!2 models
> hide #!3 models
> show #!1 models
> color #1 pale turquoise
> color #1 sky blue
> show #!2 models
> color #2 tomato
> color #2 byhetero
> color #2 light coral
> color #2 byhetero
> show #!3 models
> hide #!3 models
> color #2 light coral
> color #1 sky blue
> color #6 orange
> ui tool show "Color Actions"
> color #2 tomato
> color #2 crimson
> select #2
76873 atoms, 81429 bonds, 74 pseudobonds, 7395 residues, 2 models selected
> color #2 #d33794 transparency 0
> color #2 #d33c81 transparency 0
> color #2 #d372a4 transparency 0
> show #!3 models
> select #3
76870 atoms, 81415 bonds, 74 pseudobonds, 7403 residues, 2 models selected
> color #3 #98c885 transparency 0
> select clear
> size stickRadius 0.15
Changed 322813 bond radii
> ui tool show "Side View"
> save /Users/dede/schultz_comparison/new_overlap_antibiotic_Anat.cxs
——— End of log from Thu Feb 3 12:09:13 2022 ———
opened ChimeraX session
> color #3 #8db27d
> save /Users/dede/schultz_comparison/new_overlap_antibiotic_Anat.cxs
——— End of log from Thu Feb 3 12:47:20 2022 ———
opened ChimeraX session
> select :XXX
271 atoms, 288 bonds, 4 residues, 4 models selected
> ui tool show H-Bonds
> hbonds sel interModel false reveal true log true
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: x10324.pdb #1/J PRO 93 N
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 x10324.pdb
2 x11066.pdb
5 comp-x11066_alternate_orientation.pdb
6 FR_50S_SC_X10350_real_space_refined-coot-corrected_Hydrogens.pdb
5 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
x10324.pdb #1/A C 2638 N4 x10324.pdb #1/A XXX 3230 O6 no hydrogen 3.307 N/A
x10324.pdb #1/A XXX 3230 O12 x10324.pdb #1/A A 2085 N1 no hydrogen 2.927 N/A
x11066.pdb #2/A XXX 3230 N5 x11066.pdb #2/Y HOH 1623 O no hydrogen 2.962 N/A
x11066.pdb #2/A XXX 3230 O12 x11066.pdb #2/A A 2085 N1 no hydrogen 3.006 N/A
FR_50S_SC_X10350_real_space_refined-coot-corrected_Hydrogens.pdb #6/A XXX 3060 O12 FR_50S_SC_X10350_real_space_refined-coot-corrected_Hydrogens.pdb #6/A XXX 3060 O7 no hydrogen 3.469 N/A
5 hydrogen bonds found
> select
301826 atoms, 322813 bonds, 305 pseudobonds, 26328 residues, 13 models
selected
> select subtract :XXX
301555 atoms, 322525 bonds, 304 pseudobonds, 26324 residues, 10 models
selected
> select subtract HOH
Expected an objects specifier or a keyword
> select subtract :HOH
296326 atoms, 322525 bonds, 304 pseudobonds, 21095 residues, 10 models
selected
> select style sticks
Expected an objects specifier or a keyword
> select style stick
Expected an objects specifier or a keyword
> style sel stick
Changed 296326 atom styles
> open /Users/dede/schultz_comparison/full_pdbs/X10305_new.pdb
Chain information for X10305_new.pdb #7
---
Chain | Description
1 | No description available
2 | No description available
3 | No description available
4 | No description available
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Z | No description available
> mmaker #7 to #1 matrix Nucleic
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
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 x10324.pdb, chain A (#1) with X10305_new.pdb, chain A (#7),
sequence alignment score = 8545.8
RMSD between 2231 pruned atom pairs is 0.497 angstroms; (across all 2267
pairs: 2.491)
> select clear
> hide #7
> show :XXX
> hide #3
> color #7 #8db27d
> select :XXX
328 atoms, 348 bonds, 1 pseudobond, 5 residues, 6 models selected
> hbonds sel interModel false reveal true log true
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: x10324.pdb #1/J PRO 93 N
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 x10324.pdb
2 x11066.pdb
5 comp-x11066_alternate_orientation.pdb
6 FR_50S_SC_X10350_real_space_refined-coot-corrected_Hydrogens.pdb
7 X10305_new.pdb
9 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
x10324.pdb #1/A C 2638 N4 x10324.pdb #1/A XXX 3230 O6 no hydrogen 3.307 N/A
x10324.pdb #1/A XXX 3230 O12 x10324.pdb #1/A A 2085 N1 no hydrogen 2.927 N/A
x11066.pdb #2/A XXX 3230 N5 x11066.pdb #2/Y HOH 1623 O no hydrogen 2.962 N/A
x11066.pdb #2/A XXX 3230 O12 x11066.pdb #2/A A 2085 N1 no hydrogen 3.006 N/A
FR_50S_SC_X10350_real_space_refined-coot-corrected_Hydrogens.pdb #6/A XXX 3060 O12 FR_50S_SC_X10350_real_space_refined-coot-corrected_Hydrogens.pdb #6/A XXX 3060 O7 no hydrogen 3.469 N/A
X10305_new.pdb #7/A XXX 3230 N2 X10305_new.pdb #7/Y HOH 1623 O no hydrogen 3.197 N/A
X10305_new.pdb #7/A XXX 3230 O12 X10305_new.pdb #7/A A 2085 N1 no hydrogen 3.110 N/A
X10305_new.pdb #7/Y HOH 1623 O X10305_new.pdb #7/A XXX 3230 O6 no hydrogen 2.290 N/A
X10305_new.pdb #7/Y HOH 1623 O X10305_new.pdb #7/A XXX 3230 O7 no hydrogen 2.851 N/A
9 hydrogen bonds found
> hide
> show #6
> close
> open /Users/dede/schultz_comparison/full_pdbs/X10324_new.pdb
Chain information for X10324_new.pdb #1
---
Chain | Description
2 | No description available
3 | No description available
4 | No description available
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Z | No description available
> open /Users/dede/schultz_comparison/full_pdbs/X11066_new.pdb
Chain information for X11066_new.pdb #2
---
Chain | Description
1 | No description available
2 | No description available
3 | No description available
4 | No description available
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Z | No description available
> open /Users/dede/schultz_comparison/full_pdbs/X10305_new.pdb
Chain information for X10305_new.pdb #3
---
Chain | Description
1 | No description available
2 | No description available
3 | No description available
4 | No description available
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Z | No description available
> open /Users/dede/schultz_comparison/full_pdbs/X10350_new_waters.pdb
No such file/path:
/Users/dede/schultz_comparison/full_pdbs/X10350_new_waters.pdb
> open /Users/dede/schultz_comparison/full_pdbs/X10350_new_water.pdb
No such file/path:
/Users/dede/schultz_comparison/full_pdbs/X10350_new_water.pdb
> open /Users/dede/schultz_comparison/full_pdbs/X10350_new-waters.pdb
Chain information for X10350_new-waters.pdb #4
---
Chain | Description
0 | No description available
1 | No description available
2 | No description available
4 | No description available
6 | No description available
7 | No description available
9 | No description available
A | No description available
B | No description available
D | No description available
E | No description available
F | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
Z | No description available
> open /Users/dede/schultz_comparison/full_pdbs/X11066_alternate.pdb
> style stick
Changed 306430 atom styles
> mmaker #2,3,4 to #1 matrix Nucleic
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
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 X10324_new.pdb, chain A (#1) with X11066_new.pdb, chain A (#2),
sequence alignment score = 8558.4
RMSD between 2231 pruned atom pairs is 0.499 angstroms; (across all 2267
pairs: 2.492)
Matchmaker X10324_new.pdb, chain A (#1) with X10305_new.pdb, chain A (#3),
sequence alignment score = 8558.4
RMSD between 2231 pruned atom pairs is 0.498 angstroms; (across all 2267
pairs: 2.491)
Matchmaker X10324_new.pdb, chain A (#1) with X10350_new-waters.pdb, chain A
(#4), sequence alignment score = 8447.3
RMSD between 2070 pruned atom pairs is 1.119 angstroms; (across all 2267
pairs: 2.894)
> mmaker #5 to #1 matrix Nucleic
Reference and/or match model contains no nucleic or amino acid chains.
Use the command-line 'align' command to superimpose small molecules/ligands.
> mmaker #5 to #1
Reference and/or match model contains no nucleic or amino acid chains.
Use the command-line 'align' command to superimpose small molecules/ligands.
> align #5 toAtoms #1
Unequal number of atoms to pair, 72 and 69535
> align #5/A:XXX toAtoms #1/A:XXX
Unequal number of atoms to pair, 72 and 54
> align #5/A:XXX toAtoms #2/A:XXX
RMSD between 72 atom pairs is 2.923 angstroms
> hide
> show :XXXX
> show :XXX
> view :XXX
> size :XXX stickRadius 0.15
Changed 348 bond radii
> color #1/A:XXX sky blue
> color #2/A:XXX #d372a4
> color #5/A:XXX #d372a4
> color #3/A:XXX #8db27d
> color #4/A:XXX orange
> close #5
> open /Users/dede/schultz_comparison/full_pdbs/X11066_alternate_new.pdb
Chain information for X11066_alternate_new.pdb #5
---
Chain | Description
1 | No description available
2 | No description available
3 | No description available
4 | No description available
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Z | No description available
> style #5 stick
Changed 76873 atom styles
> mmaker #5 to #2 matrix Nucleic
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
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 X11066_new.pdb, chain A (#2) with X11066_alternate_new.pdb, chain A
(#5), sequence alignment score = 9892
RMSD between 2473 pruned atom pairs is 0.000 angstroms; (across all 2473
pairs: 0.000)
> color #5 dark grey
> color #5/A:XXX #d372a4
> hide#5
Unknown command: hide#5
> hide #5
> show #5/A:XXX
> hide #5
> show #5/A:XXX@n,C8,c9,c10,c11,n1,c12,c13,c19,n3,c14,c18,c17,c16,n2,c15
> size stickRadius #5 0.15
Invalid "stickRadius" argument: Expected a number
> size #0.15 stickRadius 0.15
Changed 0 bond radii
> size #5 stickRadius 0.15
Changed 81429 bond radii
> color :XXX byhetero
> undo
> select :XXX
328 atoms, 348 bonds, 5 residues, 5 models selected
> ui tool show H-Bonds
> hbonds sel interModel false reveal true log true
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: X10324_new.pdb #1/J PRO 93 N
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 X10324_new.pdb
2 X11066_new.pdb
3 X10305_new.pdb
4 X10350_new-waters.pdb
5 X11066_alternate_new.pdb
27 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
X10324_new.pdb #1/A C 2638 N4 X10324_new.pdb #1/A XXX 3230 O6 no hydrogen 3.307 N/A
X10324_new.pdb #1/A XXX 3230 N1 X10324_new.pdb #1/G HOH 1205 O no hydrogen 2.930 N/A
X10324_new.pdb #1/A XXX 3230 O12 X10324_new.pdb #1/A A 2085 N1 no hydrogen 2.927 N/A
X10324_new.pdb #1/A XXX 3230 O12 X10324_new.pdb #1/G HOH 1205 O no hydrogen 3.412 N/A
X10324_new.pdb #1/G HOH 1205 O X10324_new.pdb #1/A XXX 3230 O12 no hydrogen 3.412 N/A
X10324_new.pdb #1/G HOH 1205 O X10324_new.pdb #1/A XXX 3230 O6 no hydrogen 3.580 N/A
X10324_new.pdb #1/G HOH 1205 O X10324_new.pdb #1/A XXX 3230 O7 no hydrogen 2.693 N/A
X11066_new.pdb #2/A XXX 3230 N5 X11066_new.pdb #2/Y HOH 1623 O no hydrogen 2.966 N/A
X11066_new.pdb #2/A XXX 3230 O12 X11066_new.pdb #2/A A 2085 N1 no hydrogen 3.000 N/A
X10305_new.pdb #3/A XXX 3230 N2 X10305_new.pdb #3/Y HOH 1623 O no hydrogen 3.197 N/A
X10305_new.pdb #3/A XXX 3230 O12 X10305_new.pdb #3/A A 2085 N1 no hydrogen 3.110 N/A
X10305_new.pdb #3/Y HOH 1623 O X10305_new.pdb #3/A XXX 3230 O6 no hydrogen 2.290 N/A
X10305_new.pdb #3/Y HOH 1623 O X10305_new.pdb #3/A XXX 3230 O7 no hydrogen 2.851 N/A
X10350_new-waters.pdb #4/A C 2638 N4 X10350_new-waters.pdb #4/A XXX 3060 O6 no hydrogen 2.951 N/A
X10350_new-waters.pdb #4/A XXX 3060 N2 X10350_new-waters.pdb #4/G HOH 4057 O no hydrogen 2.557 N/A
X10350_new-waters.pdb #4/A XXX 3060 O12 X10350_new-waters.pdb #4/A A 2085 N1 no hydrogen 3.002 N/A
X10350_new-waters.pdb #4/A XXX 3060 O12 X10350_new-waters.pdb #4/A XXX 3060 O7 no hydrogen 3.469 N/A
X10350_new-waters.pdb #4/A XXX 3060 O12 X10350_new-waters.pdb #4/G HOH 1081 O no hydrogen 3.351 N/A
X10350_new-waters.pdb #4/G HOH 319 O X10350_new-waters.pdb #4/A XXX 3060 O6 no hydrogen 2.434 N/A
X10350_new-waters.pdb #4/G HOH 1081 O X10350_new-waters.pdb #4/A XXX 3060 O12 no hydrogen 3.351 N/A
X10350_new-waters.pdb #4/G HOH 1081 O X10350_new-waters.pdb #4/A XXX 3060 O7 no hydrogen 2.904 N/A
X10350_new-waters.pdb #4/G HOH 2244 O X10350_new-waters.pdb #4/A XXX 3060 O4 no hydrogen 3.179 N/A
X10350_new-waters.pdb #4/G HOH 3098 O X10350_new-waters.pdb #4/A XXX 3060 N3 no hydrogen 2.414 N/A
X10350_new-waters.pdb #4/G HOH 4057 O X10350_new-waters.pdb #4/A XXX 3060 N2 no hydrogen 2.557 N/A
X10350_new-waters.pdb #4/G HOH 4516 O X10350_new-waters.pdb #4/A XXX 3060 O1 no hydrogen 3.182 N/A
X11066_alternate_new.pdb #5/A XXX 3230 N5 X11066_alternate_new.pdb #5/Y HOH 1623 O no hydrogen 2.966 N/A
X11066_alternate_new.pdb #5/A XXX 3230 O12 X11066_alternate_new.pdb #5/A A 2085 N1 no hydrogen 2.913 N/A
27 hydrogen bonds found
> select :XXX
328 atoms, 348 bonds, 1 pseudobond, 5 residues, 6 models selected
> select
383231 atoms, 404088 bonds, 220 pseudobonds, 38397 residues, 15 models
selected
> select subtract :XXX
382903 atoms, 403740 bonds, 219 pseudobonds, 38392 residues, 15 models
selected
> size sel stickRadius 0.1
Changed 403740 bond radii
> size sel stickRadius 0.08
Changed 403740 bond radii
> select :HOH
11920 atoms, 11920 residues, 5 models selected
> style sel ball
Changed 11920 atom styles
> select clear
> lighting simple
> color #1 sky blue
> color #2,5 #d372a4
> color #3 #8db27d
> color #4 orange
> hide #5
> show #5/A:XXX@n,C8,c9,c10,c11,n1,c12,c13,c19,n3,c14,c18,c17,c16,n2,c15
> ui tool show H-Bonds
> color #1.2 deepskyblue models transparency 0
> color #2.2,3.2,4.2 deepskyblue models transparency 0
> color #2.2 deepskyblue models transparency 0
> color #3.2 deepskyblue models transparency 0
> color #4.2 deepskyblue models transparency 0
> save /Users/dede/schultz_comparison/new_overlap_bonds_waters.cxs
> nucleotides fill
> select
383231 atoms, 404088 bonds, 220 pseudobonds, 38397 residues, 15 models
selected
> select subtract :XXX
382903 atoms, 403740 bonds, 219 pseudobonds, 38392 residues, 15 models
selected
> select subtract :HOH
370983 atoms, 403740 bonds, 219 pseudobonds, 26472 residues, 15 models
selected
> color sel dark grey
> undo
> color sel dark grey
> color #2.2 deepskyblue models transparency 0
> color #1.2 deepskyblue models transparency 0
> color #3.2 deepskyblue models transparency 0
> color #4.2 deepskyblue models transparency 0
> select clear
> save /Users/dede/schultz_comparison/new_overlap_bonds_waters.cxs
> save /Users/dede/schultz_comparison/new_overlap_bonds_waters_2.cxs
——— End of log from Sun Feb 6 15:44:02 2022 ———
opened ChimeraX session
> hide #!5 models
> hide :HOH
> hide hbonds
> hide
> show :XXX
> lighting soft
> lighting simple
[Repeated 1 time(s)]
> lighting soft
[Repeated 1 time(s)]
> lighting full
> lighting soft
> show ribbons
> view
> hide #!1 models
> hide #!2 models
> hide #!3 models
> show #!3 models
> hide #!4 models
> hide #!3 models
> show #!4 models
> show #!3 models
> show #!2 models
> show #!1 models
> select
383231 atoms, 404088 bonds, 220 pseudobonds, 38397 residues, 15 models
selected
> select subtract :XXX
382903 atoms, 403740 bonds, 219 pseudobonds, 38392 residues, 15 models
selected
> select subtract #4
299896 atoms, 318331 bonds, 191 pseudobonds, 28315 residues, 12 models
selected
> hide sel ribbons
> lighting simple
> save /Users/dede/schultz_comparison/new_overlap_ribosome_exitTunnel.cxs
——— End of log from Mon Feb 7 17:21:35 2022 ———
opened ChimeraX session
> select
383231 atoms, 404088 bonds, 220 pseudobonds, 38397 residues, 15 models
selected
> select subtract :XXX
382903 atoms, 403740 bonds, 219 pseudobonds, 38392 residues, 15 models
selected
> color sel lightblue gret
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color sel light grey
> select clear
> select :XXX
328 atoms, 348 bonds, 1 pseudobond, 5 residues, 6 models selected
> style sel & #!1-4 sphere
Changed 256 atom styles
> select clear
> save /Users/dede/schultz_comparison/new_overlap_ribosome_exitTunnel.cxs
——— End of log from Wed Feb 9 12:18:56 2022 ———
opened ChimeraX session
> select :XXX
328 atoms, 348 bonds, 1 pseudobond, 5 residues, 6 models selected
> select ~ sel
382903 atoms, 403740 bonds, 193 pseudobonds, 38392 residues, 10 models
selected
> color cartoon darkgrey transparency 50
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color sel transparency 50
> transparency sel 50 target c
> transparency sel 65 target c
> select clear
> select :XXX
328 atoms, 348 bonds, 1 pseudobond, 5 residues, 6 models selected
> select ~ sel
382903 atoms, 403740 bonds, 193 pseudobonds, 38392 residues, 10 models
selected
> transparency sel 75 target c
> transparency sel 85 target c
> select clear
> save newest_overlap_ribosome_exitTunnel.cxs
——— End of log from Tue May 13 16:17:56 2025 ———
opened ChimeraX session
> save newest_overlap_ribosome_exitTunnel.cxs
> save newest_overlap_ribosome_exitTunnel.png supersample 3
> graphics silhouettes false
> select :XXX
328 atoms, 348 bonds, 1 pseudobond, 5 residues, 6 models selected
> select ~ sel
382903 atoms, 403740 bonds, 193 pseudobonds, 38392 residues, 10 models
selected
> transparency sel 65 target c
> select clear
> select :XXX
328 atoms, 348 bonds, 1 pseudobond, 5 residues, 6 models selected
> select ~ sel
382903 atoms, 403740 bonds, 193 pseudobonds, 38392 residues, 10 models
selected
> transparency sel 55 target c
> select clear
> select :XXX
328 atoms, 348 bonds, 1 pseudobond, 5 residues, 6 models selected
> select ~ sel
382903 atoms, 403740 bonds, 193 pseudobonds, 38392 residues, 10 models
selected
> transparency sel 40 target c
> select clear
> lighting soft
> lighting full
> lighting simple
> lighting soft
> select :XXX
328 atoms, 348 bonds, 1 pseudobond, 5 residues, 6 models selected
> select ~ sel
382903 atoms, 403740 bonds, 193 pseudobonds, 38392 residues, 10 models
selected
> transparency sel 10 target c
> select clear
> select :XXX
328 atoms, 348 bonds, 1 pseudobond, 5 residues, 6 models selected
> select ~ sel
382903 atoms, 403740 bonds, 193 pseudobonds, 38392 residues, 10 models
selected
> color sel grey
> select clear
> select :XXX
328 atoms, 348 bonds, 1 pseudobond, 5 residues, 6 models selected
> select ~ sel
382903 atoms, 403740 bonds, 193 pseudobonds, 38392 residues, 10 models
selected
> nucleotides sel & #!1-4 stubs
> nucleotides sel & #!1-4 tube/slab shape ellipsoid
> nucleotides sel & #!1-4 tube/slab shape box
> nucleotides sel & #!1-4 fill
> style nucleic & sel & #!1-4 stick
Changed 217244 atom styles
> preset "molecular surfaces" "ghostly white"
Using preset: Molecular Surfaces / Ghostly White
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color white targ s trans 80
> set bgColor white
> set bgColor black
> select clear
> set bgColor white
> select :XXX
328 atoms, 348 bonds, 1 pseudobond, 5 residues, 6 models selected
> select ~ sel
382903 atoms, 403740 bonds, 193 pseudobonds, 38392 residues, 10 models
selected
> color sel dark grey
> transparency sel 60 target s
> select clear
> transparency sel 75 target s
> select clear
> select :XXX
328 atoms, 348 bonds, 1 pseudobond, 5 residues, 6 models selected
> select ~ sel
382903 atoms, 403740 bonds, 193 pseudobonds, 38392 residues, 10 models
selected
> transparency sel 75 target s
> select clear
> select :XXX
328 atoms, 348 bonds, 1 pseudobond, 5 residues, 6 models selected
> select ~ sel
382903 atoms, 403740 bonds, 193 pseudobonds, 38392 residues, 10 models
selected
> show sel & #!1-4 cartoons
> close #5
> select clear
> save newest_overlap_ribosome_exitTunnel_take2.cxs
> save newest_overlap_ribosome_exitTunnel_take2.png supersample 3
[Repeated 1 time(s)]
> save newest_overlap_ribosome_exitTunnel_take2.cxs
> select :XXX
256 atoms, 271 bonds, 1 pseudobond, 4 residues, 5 models selected
> select ~ sel
306102 atoms, 322388 bonds, 156 pseudobonds, 30998 residues, 8 models selected
> transparency sel 85 target s
> select clear
> save newest_overlap_ribosome_exitTunnel_take2.png supersample 3
> save newest_overlap_ribosome_exitTunnel_take2.cxs
——— End of log from Tue May 13 16:59:40 2025 ———
opened ChimeraX session
> select :XXX
256 atoms, 271 bonds, 1 pseudobond, 4 residues, 5 models selected
> select ~ sel
306102 atoms, 322388 bonds, 156 pseudobonds, 30998 residues, 8 models selected
> select subtract #4
223095 atoms, 236979 bonds, 139 pseudobonds, 20921 residues, 112 models
selected
> delete sel
> save /yonath_group/andre/figure_for_yeda_50S_only.cxs
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /yonath_group/andre/em_data/schultz_comparison/newest_overlap_ribosome_exitTunnel_take2.cxs
Log from Tue May 13 16:59:40 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open newest_overlap_ribosome_exitTunnel.cxs
Log from Tue May 13 16:17:56 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open new_overlap_ribosome_exitTunnel.cxs
Log from Wed Feb 9 12:18:56 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /Users/dede/schultz_comparison/new_overlap_ribosome_exitTunnel.cxs
Log from Mon Feb 7 17:21:35 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /Users/dede/schultz_comparison/new_overlap_bonds_waters_2.cxs
Log from Sun Feb 6 15:44:02 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /Users/dede/schultz_comparison/new_overlap_antibiotic_Anat.cxs
Log from Thu Feb 3 12:47:20 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /Users/dede/schultz_comparison/new_overlap_antibiotic_Anat.cxs
Log from Thu Feb 3 12:09:13 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /Users/dede/schultz_comparison/new_overlap_antibiotics_newcolors.cxs
Log from Tue Feb 1 18:36:14 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /Users/dede/schultz_comparison/new_overlap_antibiotics.cxs
Log from Tue Feb 1 16:51:39 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /Users/dede/schultz_comparison/overlap_antibiotics.cxs
Log from Sun Jan 30 17:00:34 2022UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
> open /yonath_group/andre/em_data/schultz_comparison/overlap_antibiotics.cxs
QXcbConnection: XCB error: 3 (BadWindow), sequence: 64517, resource id:
32032708, major code: 40 (TranslateCoords), minor code: 0
Log from Sun Jan 23 12:12:56 2022UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /yonath_group/andre/em_data/schultz_comparison/x10324.pdb
Chain information for x10324.pdb #1
---
Chain | Description
2 | No description available
3 | No description available
4 | No description available
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Z | No description available
QXcbConnection: XCB error: 3 (BadWindow), sequence: 24348, resource id:
32519754, major code: 40 (TranslateCoords), minor code: 0
> open /yonath_group/andre/em_data/schultz_comparison/x11066.pdb
Chain information for x11066.pdb #2
---
Chain | Description
1 | No description available
2 | No description available
3 | No description available
4 | No description available
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Z | No description available
> open /yonath_group/andre/em_data/schultz_comparison/X10305.pdb
Chain information for X10305.pdb #3
---
Chain | Description
1 | No description available
2 | No description available
3 | No description available
4 | No description available
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Z | No description available
> open /yonath_group/andre/em_data/schultz_comparison/X10350.pdb
Chain information for X10350.pdb #4
---
Chain | Description
0 | No description available
1 | No description available
2 | No description available
4 | No description available
6 | No description available
7 | No description available
9 | No description available
A | No description available
B | No description available
D | No description available
E | No description available
F | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
Z | No description available
QXcbConnection: XCB error: 3 (BadWindow), sequence: 29636, resource id:
32527352, major code: 40 (TranslateCoords), minor code: 0
> hide atoms
> show cartoons
> set bgColor white
> ui tool show "Color Actions"
> color dark cyan
> select #1
69569 atoms, 74328 bonds, 130 pseudobonds, 6160 residues, 2 models selected
> color sel dark cyan
> select #2
76873 atoms, 81429 bonds, 74 pseudobonds, 7395 residues, 2 models selected
> select #1
69569 atoms, 74328 bonds, 130 pseudobonds, 6160 residues, 2 models selected
> select #2
76873 atoms, 81429 bonds, 74 pseudobonds, 7395 residues, 2 models selected
> select #1
69569 atoms, 74328 bonds, 130 pseudobonds, 6160 residues, 2 models selected
> select #2
76873 atoms, 81429 bonds, 74 pseudobonds, 7395 residues, 2 models selected
> color sel magenta
> select #3
76870 atoms, 81415 bonds, 74 pseudobonds, 7403 residues, 2 models selected
> color sel lime
> select #4
78369 atoms, 85486 bonds, 22 pseudobonds, 5368 residues, 2 models selected
> color sel light salmon
> color sel deep sky blue
> color sel light salmon
> select #1
69569 atoms, 74328 bonds, 130 pseudobonds, 6160 residues, 2 models selected
> color sel deep sky blue
> cartoon style width 1 thickness 0.3
> view :XXX
> select :XXX
126 atoms, 133 bonds, 2 residues, 2 models selected
> show sel atoms
> select :LIG
130 atoms, 138 bonds, 2 residues, 2 models selected
> show sel atoms
> lighting soft
> show #1/A:2530, 2086, 2085, 2638, 797, 2636, 2089, 793, 2636, 2638
> select #1/A:2530, 2086, 2085, 2638, 797, 2636, 2089, 793, 2636, 2638
174 atoms, 189 bonds, 8 residues, 1 model selected
> style sel stick
Changed 174 atom styles
> select :XXX
126 atoms, 133 bonds, 2 residues, 2 models selected
> select add :LIG
256 atoms, 271 bonds, 4 residues, 4 models selected
> select ~ sel
301425 atoms, 322387 bonds, 300 pseudobonds, 26322 residues, 8 models selected
> hide sel
> hide sel cartoons
> graphics silhouettes true
> save /yonath_group/andre/em_data/schultz_comparison/overlap_antibiotics.cxs
> ui tool show "Color Actions"
> select #1
69569 atoms, 74328 bonds, 130 pseudobonds, 6160 residues, 2 models selected
> select #2
76873 atoms, 81429 bonds, 74 pseudobonds, 7395 residues, 2 models selected
> select #4
78369 atoms, 85486 bonds, 22 pseudobonds, 5368 residues, 2 models selected
> color sel light salmon
> select clear
> save /yonath_group/andre/em_data/schultz_comparison/overlap_antibiotics.png
> supersample 3
> save
> /yonath_group/andre/em_data/schultz_comparison/overlap_antibiotics_2.png
> supersample 3
> open
> /yonath_group/andre/em_data/schultz_66/comp-x11066_alternate_orientation.pdb
> ui tool show "Color Actions"
> color dark violet
> undo
> select #5
72 atoms, 77 bonds, 1 residue, 1 model selected
> color sel hot pink
> ui tool show Matchmaker
> matchmaker #5 to #2
Reference and/or match model contains no nucleic or amino acid chains.
Use the command-line 'align' command to superimpose small molecules/ligands.
> align #5 toAtoms #2
Unequal number of atoms to pair, 72 and 76873
> align #5 toAtoms #2:XXX
RMSD between 72 atom pairs is 2.923 angstroms
> select clear
> hide #5 models
> save /yonath_group/andre/em_data/schultz_comparison/overlap_antibiotics.cxs
opened ChimeraX session
> open
> /yonath_group/andre/em_data/schultz_comparison/FR_50S_SC_X10350_real_space_refined-
> coot-corrected.pdb
Chain information for FR_50S_SC_X10350_real_space_refined-coot-corrected.pdb
#6
---
Chain | Description
0 | No description available
1 | No description available
2 | No description available
4 | No description available
6 | No description available
7 | No description available
9 | No description available
A | No description available
B | No description available
D | No description available
E | No description available
F | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
Z | No description available
> select #6
78369 atoms, 85486 bonds, 22 pseudobonds, 5368 residues, 2 models selected
> select subtract #6/A:XXX
78296 atoms, 85408 bonds, 22 pseudobonds, 5367 residues, 2 models selected
> delete sel
> select #6
73 atoms, 78 bonds, 1 residue, 1 model selected
> color sel light salmon
> align #6 toAtoms #4
Unequal number of atoms to pair, 73 and 78369
> mmaker #6 to #4
Reference and/or match model contains no nucleic or amino acid chains.
Use the command-line 'align' command to superimpose small molecules/ligands.
> mmaker #6 toAtoms #4
> matchmaker #6 toAtoms #4
Expected a keyword
> mmaker sel toAtoms #4
> matchmaker sel toAtoms #4
Expected a keyword
> align #6 toAtoms #4
Unequal number of atoms to pair, 73 and 78369
> align #6 toAtoms #4
Unequal number of atoms to pair, 73 and 78369
> open
> /yonath_group/andre/em_data/schultz_comparison/FR_50S_SC_X10350_real_space_refined-
> coot-corrected_Hydrogens.pdb
Chain information for FR_50S_SC_X10350_real_space_refined-coot-
corrected_Hydrogens.pdb #7
---
Chain | Description
0 | No description available
1 | No description available
2 | No description available
4 | No description available
6 | No description available
7 | No description available
9 | No description available
A | No description available
B | No description available
D | No description available
E | No description available
F | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
Z | No description available
> close #6
> close #7
> open
> /yonath_group/andre/em_data/schultz_comparison/FR_50S_SC_X10350_real_space_refined-
> coot-corrected_Hydrogens.pdb
Chain information for FR_50S_SC_X10350_real_space_refined-coot-
corrected_Hydrogens.pdb #6
---
Chain | Description
0 | No description available
1 | No description available
2 | No description available
4 | No description available
6 | No description available
7 | No description available
9 | No description available
A | No description available
B | No description available
D | No description available
E | No description available
F | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
Z | No description available
> select #6
78369 atoms, 85486 bonds, 22 pseudobonds, 5368 residues, 2 models selected
> select subtract #6/A:XXX
78296 atoms, 85408 bonds, 22 pseudobonds, 5367 residues, 2 models selected
> delete sel
> align #6 toAtoms #4
Unequal number of atoms to pair, 73 and 78369
> ui mousemode right "translate selected models"
> select #6
73 atoms, 78 bonds, 1 residue, 1 model selected
> ui mousemode right select
> align #6/A:XXX toAtoms #4/A:XXX
Unequal number of atoms to pair, 73 and 0
> align #6/A:XXX toAtoms #4/A:LIG
RMSD between 73 atom pairs is 3.681 angstroms
> show #5 models
> hide #5 models
> color #6 light salmon
> hide #!4 models
> save /yonath_group/andre/em_data/schultz_comparison/overlap_antibiotics.cxs
——— End of log from Sun Jan 30 17:00:34 2022 ———
opened ChimeraX session
> clear
Unknown command: clear
> select clear
> color #1 royal blue
> save /Users/dede/schultz_comparison/new_overlap_antibiotics.cxs
——— End of log from Tue Feb 1 16:51:39 2022 ———
opened ChimeraX session
> color #1 cyan
> color #1 #66ccee
> color #1 #33bbee
> color #2 #ee3377
> color #3 #009988
> color #1 #66ccee
> color #12#ee6677
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword
> color #2 #ee6677
> color #3 #228833
> color #3 #ccbb44
> color #3 #228833
> color #4 #228833
> color #6 #228833
> color #6 #ee6677
> color #2 #aa3377
> save /Users/dede/schultz_comparison/new_overlap_antibiotics_newcolors.cxs
——— End of log from Tue Feb 1 18:36:14 2022 ———
opened ChimeraX session
> color #6 orange
> color #6 mandarin
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword
> color #6 dark orange
> color byhetero
> hide #!2 models
> hide #!3 models
> hide #!6 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!6 models
> ui tool show "Color Actions"
> color #6 dark orange
> select #6
73 atoms, 78 bonds, 1 residue, 1 model selected
> select clear
> color #6 orange
> color byhetero
> show #!3 models
> hide #!6 models
> show #!6 models
> ui tool show "Color Actions"
> color #3 olive drab
> color #3 lawn green
> color #3 medium spring green
> color #3 lime
> color #3 gray
> color #3 dark olive green
> color #3 olive
> color #3 tan
> color #3 yellow green
> color byhetero
> color #3 dark khaki
> show #!2 models
> show #!1 models
> hide #!1 models
> hide #!2 models
> hide #!3 models
> show #!1 models
> color #1 pale turquoise
> color #1 sky blue
> show #!2 models
> color #2 tomato
> color #2 byhetero
> color #2 light coral
> color #2 byhetero
> show #!3 models
> hide #!3 models
> color #2 light coral
> color #1 sky blue
> color #6 orange
> ui tool show "Color Actions"
> color #2 tomato
> color #2 crimson
> select #2
76873 atoms, 81429 bonds, 74 pseudobonds, 7395 residues, 2 models selected
> color #2 #d33794 transparency 0
> color #2 #d33c81 transparency 0
> color #2 #d372a4 transparency 0
> show #!3 models
> select #3
76870 atoms, 81415 bonds, 74 pseudobonds, 7403 residues, 2 models selected
> color #3 #98c885 transparency 0
> select clear
> size stickRadius 0.15
Changed 322813 bond radii
> ui tool show "Side View"
> save /Users/dede/schultz_comparison/new_overlap_antibiotic_Anat.cxs
——— End of log from Thu Feb 3 12:09:13 2022 ———
opened ChimeraX session
> color #3 #8db27d
> save /Users/dede/schultz_comparison/new_overlap_antibiotic_Anat.cxs
——— End of log from Thu Feb 3 12:47:20 2022 ———
opened ChimeraX session
> select :XXX
271 atoms, 288 bonds, 4 residues, 4 models selected
> ui tool show H-Bonds
> hbonds sel interModel false reveal true log true
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: x10324.pdb #1/J PRO 93 N
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 x10324.pdb
2 x11066.pdb
5 comp-x11066_alternate_orientation.pdb
6 FR_50S_SC_X10350_real_space_refined-coot-corrected_Hydrogens.pdb
5 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
x10324.pdb #1/A C 2638 N4 x10324.pdb #1/A XXX 3230 O6 no hydrogen 3.307 N/A
x10324.pdb #1/A XXX 3230 O12 x10324.pdb #1/A A 2085 N1 no hydrogen 2.927 N/A
x11066.pdb #2/A XXX 3230 N5 x11066.pdb #2/Y HOH 1623 O no hydrogen 2.962 N/A
x11066.pdb #2/A XXX 3230 O12 x11066.pdb #2/A A 2085 N1 no hydrogen 3.006 N/A
FR_50S_SC_X10350_real_space_refined-coot-corrected_Hydrogens.pdb #6/A XXX 3060 O12 FR_50S_SC_X10350_real_space_refined-coot-corrected_Hydrogens.pdb #6/A XXX 3060 O7 no hydrogen 3.469 N/A
5 hydrogen bonds found
> select
301826 atoms, 322813 bonds, 305 pseudobonds, 26328 residues, 13 models
selected
> select subtract :XXX
301555 atoms, 322525 bonds, 304 pseudobonds, 26324 residues, 10 models
selected
> select subtract HOH
Expected an objects specifier or a keyword
> select subtract :HOH
296326 atoms, 322525 bonds, 304 pseudobonds, 21095 residues, 10 models
selected
> select style sticks
Expected an objects specifier or a keyword
> select style stick
Expected an objects specifier or a keyword
> style sel stick
Changed 296326 atom styles
> open /Users/dede/schultz_comparison/full_pdbs/X10305_new.pdb
Chain information for X10305_new.pdb #7
---
Chain | Description
1 | No description available
2 | No description available
3 | No description available
4 | No description available
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Z | No description available
> mmaker #7 to #1 matrix Nucleic
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
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 x10324.pdb, chain A (#1) with X10305_new.pdb, chain A (#7),
sequence alignment score = 8545.8
RMSD between 2231 pruned atom pairs is 0.497 angstroms; (across all 2267
pairs: 2.491)
> select clear
> hide #7
> show :XXX
> hide #3
> color #7 #8db27d
> select :XXX
328 atoms, 348 bonds, 1 pseudobond, 5 residues, 6 models selected
> hbonds sel interModel false reveal true log true
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: x10324.pdb #1/J PRO 93 N
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 x10324.pdb
2 x11066.pdb
5 comp-x11066_alternate_orientation.pdb
6 FR_50S_SC_X10350_real_space_refined-coot-corrected_Hydrogens.pdb
7 X10305_new.pdb
9 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
x10324.pdb #1/A C 2638 N4 x10324.pdb #1/A XXX 3230 O6 no hydrogen 3.307 N/A
x10324.pdb #1/A XXX 3230 O12 x10324.pdb #1/A A 2085 N1 no hydrogen 2.927 N/A
x11066.pdb #2/A XXX 3230 N5 x11066.pdb #2/Y HOH 1623 O no hydrogen 2.962 N/A
x11066.pdb #2/A XXX 3230 O12 x11066.pdb #2/A A 2085 N1 no hydrogen 3.006 N/A
FR_50S_SC_X10350_real_space_refined-coot-corrected_Hydrogens.pdb #6/A XXX 3060 O12 FR_50S_SC_X10350_real_space_refined-coot-corrected_Hydrogens.pdb #6/A XXX 3060 O7 no hydrogen 3.469 N/A
X10305_new.pdb #7/A XXX 3230 N2 X10305_new.pdb #7/Y HOH 1623 O no hydrogen 3.197 N/A
X10305_new.pdb #7/A XXX 3230 O12 X10305_new.pdb #7/A A 2085 N1 no hydrogen 3.110 N/A
X10305_new.pdb #7/Y HOH 1623 O X10305_new.pdb #7/A XXX 3230 O6 no hydrogen 2.290 N/A
X10305_new.pdb #7/Y HOH 1623 O X10305_new.pdb #7/A XXX 3230 O7 no hydrogen 2.851 N/A
9 hydrogen bonds found
> hide
> show #6
> close
> open /Users/dede/schultz_comparison/full_pdbs/X10324_new.pdb
Chain information for X10324_new.pdb #1
---
Chain | Description
2 | No description available
3 | No description available
4 | No description available
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Z | No description available
> open /Users/dede/schultz_comparison/full_pdbs/X11066_new.pdb
Chain information for X11066_new.pdb #2
---
Chain | Description
1 | No description available
2 | No description available
3 | No description available
4 | No description available
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Z | No description available
> open /Users/dede/schultz_comparison/full_pdbs/X10305_new.pdb
Chain information for X10305_new.pdb #3
---
Chain | Description
1 | No description available
2 | No description available
3 | No description available
4 | No description available
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Z | No description available
> open /Users/dede/schultz_comparison/full_pdbs/X10350_new_waters.pdb
No such file/path:
/Users/dede/schultz_comparison/full_pdbs/X10350_new_waters.pdb
> open /Users/dede/schultz_comparison/full_pdbs/X10350_new_water.pdb
No such file/path:
/Users/dede/schultz_comparison/full_pdbs/X10350_new_water.pdb
> open /Users/dede/schultz_comparison/full_pdbs/X10350_new-waters.pdb
Chain information for X10350_new-waters.pdb #4
---
Chain | Description
0 | No description available
1 | No description available
2 | No description available
4 | No description available
6 | No description available
7 | No description available
9 | No description available
A | No description available
B | No description available
D | No description available
E | No description available
F | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
Z | No description available
> open /Users/dede/schultz_comparison/full_pdbs/X11066_alternate.pdb
> style stick
Changed 306430 atom styles
> mmaker #2,3,4 to #1 matrix Nucleic
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
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 X10324_new.pdb, chain A (#1) with X11066_new.pdb, chain A (#2),
sequence alignment score = 8558.4
RMSD between 2231 pruned atom pairs is 0.499 angstroms; (across all 2267
pairs: 2.492)
Matchmaker X10324_new.pdb, chain A (#1) with X10305_new.pdb, chain A (#3),
sequence alignment score = 8558.4
RMSD between 2231 pruned atom pairs is 0.498 angstroms; (across all 2267
pairs: 2.491)
Matchmaker X10324_new.pdb, chain A (#1) with X10350_new-waters.pdb, chain A
(#4), sequence alignment score = 8447.3
RMSD between 2070 pruned atom pairs is 1.119 angstroms; (across all 2267
pairs: 2.894)
> mmaker #5 to #1 matrix Nucleic
Reference and/or match model contains no nucleic or amino acid chains.
Use the command-line 'align' command to superimpose small molecules/ligands.
> mmaker #5 to #1
Reference and/or match model contains no nucleic or amino acid chains.
Use the command-line 'align' command to superimpose small molecules/ligands.
> align #5 toAtoms #1
Unequal number of atoms to pair, 72 and 69535
> align #5/A:XXX toAtoms #1/A:XXX
Unequal number of atoms to pair, 72 and 54
> align #5/A:XXX toAtoms #2/A:XXX
RMSD between 72 atom pairs is 2.923 angstroms
> hide
> show :XXXX
> show :XXX
> view :XXX
> size :XXX stickRadius 0.15
Changed 348 bond radii
> color #1/A:XXX sky blue
> color #2/A:XXX #d372a4
> color #5/A:XXX #d372a4
> color #3/A:XXX #8db27d
> color #4/A:XXX orange
> close #5
> open /Users/dede/schultz_comparison/full_pdbs/X11066_alternate_new.pdb
Chain information for X11066_alternate_new.pdb #5
---
Chain | Description
1 | No description available
2 | No description available
3 | No description available
4 | No description available
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Z | No description available
> style #5 stick
Changed 76873 atom styles
> mmaker #5 to #2 matrix Nucleic
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
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 X11066_new.pdb, chain A (#2) with X11066_alternate_new.pdb, chain A
(#5), sequence alignment score = 9892
RMSD between 2473 pruned atom pairs is 0.000 angstroms; (across all 2473
pairs: 0.000)
> color #5 dark grey
> color #5/A:XXX #d372a4
> hide#5
Unknown command: hide#5
> hide #5
> show #5/A:XXX
> hide #5
> show #5/A:XXX@n,C8,c9,c10,c11,n1,c12,c13,c19,n3,c14,c18,c17,c16,n2,c15
> size stickRadius #5 0.15
Invalid "stickRadius" argument: Expected a number
> size #0.15 stickRadius 0.15
Changed 0 bond radii
> size #5 stickRadius 0.15
Changed 81429 bond radii
> color :XXX byhetero
> undo
> select :XXX
328 atoms, 348 bonds, 5 residues, 5 models selected
> ui tool show H-Bonds
> hbonds sel interModel false reveal true log true
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: X10324_new.pdb #1/J PRO 93 N
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 X10324_new.pdb
2 X11066_new.pdb
3 X10305_new.pdb
4 X10350_new-waters.pdb
5 X11066_alternate_new.pdb
27 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
X10324_new.pdb #1/A C 2638 N4 X10324_new.pdb #1/A XXX 3230 O6 no hydrogen 3.307 N/A
X10324_new.pdb #1/A XXX 3230 N1 X10324_new.pdb #1/G HOH 1205 O no hydrogen 2.930 N/A
X10324_new.pdb #1/A XXX 3230 O12 X10324_new.pdb #1/A A 2085 N1 no hydrogen 2.927 N/A
X10324_new.pdb #1/A XXX 3230 O12 X10324_new.pdb #1/G HOH 1205 O no hydrogen 3.412 N/A
X10324_new.pdb #1/G HOH 1205 O X10324_new.pdb #1/A XXX 3230 O12 no hydrogen 3.412 N/A
X10324_new.pdb #1/G HOH 1205 O X10324_new.pdb #1/A XXX 3230 O6 no hydrogen 3.580 N/A
X10324_new.pdb #1/G HOH 1205 O X10324_new.pdb #1/A XXX 3230 O7 no hydrogen 2.693 N/A
X11066_new.pdb #2/A XXX 3230 N5 X11066_new.pdb #2/Y HOH 1623 O no hydrogen 2.966 N/A
X11066_new.pdb #2/A XXX 3230 O12 X11066_new.pdb #2/A A 2085 N1 no hydrogen 3.000 N/A
X10305_new.pdb #3/A XXX 3230 N2 X10305_new.pdb #3/Y HOH 1623 O no hydrogen 3.197 N/A
X10305_new.pdb #3/A XXX 3230 O12 X10305_new.pdb #3/A A 2085 N1 no hydrogen 3.110 N/A
X10305_new.pdb #3/Y HOH 1623 O X10305_new.pdb #3/A XXX 3230 O6 no hydrogen 2.290 N/A
X10305_new.pdb #3/Y HOH 1623 O X10305_new.pdb #3/A XXX 3230 O7 no hydrogen 2.851 N/A
X10350_new-waters.pdb #4/A C 2638 N4 X10350_new-waters.pdb #4/A XXX 3060 O6 no hydrogen 2.951 N/A
X10350_new-waters.pdb #4/A XXX 3060 N2 X10350_new-waters.pdb #4/G HOH 4057 O no hydrogen 2.557 N/A
X10350_new-waters.pdb #4/A XXX 3060 O12 X10350_new-waters.pdb #4/A A 2085 N1 no hydrogen 3.002 N/A
X10350_new-waters.pdb #4/A XXX 3060 O12 X10350_new-waters.pdb #4/A XXX 3060 O7 no hydrogen 3.469 N/A
X10350_new-waters.pdb #4/A XXX 3060 O12 X10350_new-waters.pdb #4/G HOH 1081 O no hydrogen 3.351 N/A
X10350_new-waters.pdb #4/G HOH 319 O X10350_new-waters.pdb #4/A XXX 3060 O6 no hydrogen 2.434 N/A
X10350_new-waters.pdb #4/G HOH 1081 O X10350_new-waters.pdb #4/A XXX 3060 O12 no hydrogen 3.351 N/A
X10350_new-waters.pdb #4/G HOH 1081 O X10350_new-waters.pdb #4/A XXX 3060 O7 no hydrogen 2.904 N/A
X10350_new-waters.pdb #4/G HOH 2244 O X10350_new-waters.pdb #4/A XXX 3060 O4 no hydrogen 3.179 N/A
X10350_new-waters.pdb #4/G HOH 3098 O X10350_new-waters.pdb #4/A XXX 3060 N3 no hydrogen 2.414 N/A
X10350_new-waters.pdb #4/G HOH 4057 O X10350_new-waters.pdb #4/A XXX 3060 N2 no hydrogen 2.557 N/A
X10350_new-waters.pdb #4/G HOH 4516 O X10350_new-waters.pdb #4/A XXX 3060 O1 no hydrogen 3.182 N/A
X11066_alternate_new.pdb #5/A XXX 3230 N5 X11066_alternate_new.pdb #5/Y HOH 1623 O no hydrogen 2.966 N/A
X11066_alternate_new.pdb #5/A XXX 3230 O12 X11066_alternate_new.pdb #5/A A 2085 N1 no hydrogen 2.913 N/A
27 hydrogen bonds found
> select :XXX
328 atoms, 348 bonds, 1 pseudobond, 5 residues, 6 models selected
> select
383231 atoms, 404088 bonds, 220 pseudobonds, 38397 residues, 15 models
selected
> select subtract :XXX
382903 atoms, 403740 bonds, 219 pseudobonds, 38392 residues, 15 models
selected
> size sel stickRadius 0.1
Changed 403740 bond radii
> size sel stickRadius 0.08
Changed 403740 bond radii
> select :HOH
11920 atoms, 11920 residues, 5 models selected
> style sel ball
Changed 11920 atom styles
> select clear
> lighting simple
> color #1 sky blue
> color #2,5 #d372a4
> color #3 #8db27d
> color #4 orange
> hide #5
> show #5/A:XXX@n,C8,c9,c10,c11,n1,c12,c13,c19,n3,c14,c18,c17,c16,n2,c15
> ui tool show H-Bonds
> color #1.2 deepskyblue models transparency 0
> color #2.2,3.2,4.2 deepskyblue models transparency 0
> color #2.2 deepskyblue models transparency 0
> color #3.2 deepskyblue models transparency 0
> color #4.2 deepskyblue models transparency 0
> save /Users/dede/schultz_comparison/new_overlap_bonds_waters.cxs
> nucleotides fill
> select
383231 atoms, 404088 bonds, 220 pseudobonds, 38397 residues, 15 models
selected
> select subtract :XXX
382903 atoms, 403740 bonds, 219 pseudobonds, 38392 residues, 15 models
selected
> select subtract :HOH
370983 atoms, 403740 bonds, 219 pseudobonds, 26472 residues, 15 models
selected
> color sel dark grey
> undo
> color sel dark grey
> color #2.2 deepskyblue models transparency 0
> color #1.2 deepskyblue models transparency 0
> color #3.2 deepskyblue models transparency 0
> color #4.2 deepskyblue models transparency 0
> select clear
> save /Users/dede/schultz_comparison/new_overlap_bonds_waters.cxs
> save /Users/dede/schultz_comparison/new_overlap_bonds_waters_2.cxs
——— End of log from Sun Feb 6 15:44:02 2022 ———
opened ChimeraX session
> hide #!5 models
> hide :HOH
> hide hbonds
> hide
> show :XXX
> lighting soft
> lighting simple
[Repeated 1 time(s)]
> lighting soft
[Repeated 1 time(s)]
> lighting full
> lighting soft
> show ribbons
> view
> hide #!1 models
> hide #!2 models
> hide #!3 models
> show #!3 models
> hide #!4 models
> hide #!3 models
> show #!4 models
> show #!3 models
> show #!2 models
> show #!1 models
> select
383231 atoms, 404088 bonds, 220 pseudobonds, 38397 residues, 15 models
selected
> select subtract :XXX
382903 atoms, 403740 bonds, 219 pseudobonds, 38392 residues, 15 models
selected
> select subtract #4
299896 atoms, 318331 bonds, 191 pseudobonds, 28315 residues, 12 models
selected
> hide sel ribbons
> lighting simple
> save /Users/dede/schultz_comparison/new_overlap_ribosome_exitTunnel.cxs
——— End of log from Mon Feb 7 17:21:35 2022 ———
opened ChimeraX session
> select
383231 atoms, 404088 bonds, 220 pseudobonds, 38397 residues, 15 models
selected
> select subtract :XXX
382903 atoms, 403740 bonds, 219 pseudobonds, 38392 residues, 15 models
selected
> color sel lightblue gret
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color sel light grey
> select clear
> select :XXX
328 atoms, 348 bonds, 1 pseudobond, 5 residues, 6 models selected
> style sel & #!1-4 sphere
Changed 256 atom styles
> select clear
> save /Users/dede/schultz_comparison/new_overlap_ribosome_exitTunnel.cxs
——— End of log from Wed Feb 9 12:18:56 2022 ———
opened ChimeraX session
> select :XXX
328 atoms, 348 bonds, 1 pseudobond, 5 residues, 6 models selected
> select ~ sel
382903 atoms, 403740 bonds, 193 pseudobonds, 38392 residues, 10 models
selected
> color cartoon darkgrey transparency 50
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color sel transparency 50
> transparency sel 50 target c
> transparency sel 65 target c
> select clear
> select :XXX
328 atoms, 348 bonds, 1 pseudobond, 5 residues, 6 models selected
> select ~ sel
382903 atoms, 403740 bonds, 193 pseudobonds, 38392 residues, 10 models
selected
> transparency sel 75 target c
> transparency sel 85 target c
> select clear
> save newest_overlap_ribosome_exitTunnel.cxs
——— End of log from Tue May 13 16:17:56 2025 ———
opened ChimeraX session
> save newest_overlap_ribosome_exitTunnel.cxs
> save newest_overlap_ribosome_exitTunnel.png supersample 3
> graphics silhouettes false
> select :XXX
328 atoms, 348 bonds, 1 pseudobond, 5 residues, 6 models selected
> select ~ sel
382903 atoms, 403740 bonds, 193 pseudobonds, 38392 residues, 10 models
selected
> transparency sel 65 target c
> select clear
> select :XXX
328 atoms, 348 bonds, 1 pseudobond, 5 residues, 6 models selected
> select ~ sel
382903 atoms, 403740 bonds, 193 pseudobonds, 38392 residues, 10 models
selected
> transparency sel 55 target c
> select clear
> select :XXX
328 atoms, 348 bonds, 1 pseudobond, 5 residues, 6 models selected
> select ~ sel
382903 atoms, 403740 bonds, 193 pseudobonds, 38392 residues, 10 models
selected
> transparency sel 40 target c
> select clear
> lighting soft
> lighting full
> lighting simple
> lighting soft
> select :XXX
328 atoms, 348 bonds, 1 pseudobond, 5 residues, 6 models selected
> select ~ sel
382903 atoms, 403740 bonds, 193 pseudobonds, 38392 residues, 10 models
selected
> transparency sel 10 target c
> select clear
> select :XXX
328 atoms, 348 bonds, 1 pseudobond, 5 residues, 6 models selected
> select ~ sel
382903 atoms, 403740 bonds, 193 pseudobonds, 38392 residues, 10 models
selected
> color sel grey
> select clear
> select :XXX
328 atoms, 348 bonds, 1 pseudobond, 5 residues, 6 models selected
> select ~ sel
382903 atoms, 403740 bonds, 193 pseudobonds, 38392 residues, 10 models
selected
> nucleotides sel & #!1-4 stubs
> nucleotides sel & #!1-4 tube/slab shape ellipsoid
> nucleotides sel & #!1-4 tube/slab shape box
> nucleotides sel & #!1-4 fill
> style nucleic & sel & #!1-4 stick
Changed 217244 atom styles
> preset "molecular surfaces" "ghostly white"
Using preset: Molecular Surfaces / Ghostly White
Changed 0 atom styles
Preset expands to these ChimeraX commands:
style (protein|nucleic|solvent) & @@draw_mode=0 stick
surface
color white targ s trans 80
> set bgColor white
> set bgColor black
> select clear
> set bgColor white
> select :XXX
328 atoms, 348 bonds, 1 pseudobond, 5 residues, 6 models selected
> select ~ sel
382903 atoms, 403740 bonds, 193 pseudobonds, 38392 residues, 10 models
selected
> color sel dark grey
> transparency sel 60 target s
> select clear
> transparency sel 75 target s
> select clear
> select :XXX
328 atoms, 348 bonds, 1 pseudobond, 5 residues, 6 models selected
> select ~ sel
382903 atoms, 403740 bonds, 193 pseudobonds, 38392 residues, 10 models
selected
> transparency sel 75 target s
> select clear
> select :XXX
328 atoms, 348 bonds, 1 pseudobond, 5 residues, 6 models selected
> select ~ sel
382903 atoms, 403740 bonds, 193 pseudobonds, 38392 residues, 10 models
selected
> show sel & #!1-4 cartoons
> close #5
> select clear
> save newest_overlap_ribosome_exitTunnel_take2.cxs
> save newest_overlap_ribosome_exitTunnel_take2.png supersample 3
[Repeated 1 time(s)]
> save newest_overlap_ribosome_exitTunnel_take2.cxs
> select :XXX
256 atoms, 271 bonds, 1 pseudobond, 4 residues, 5 models selected
> select ~ sel
306102 atoms, 322388 bonds, 156 pseudobonds, 30998 residues, 8 models selected
> transparency sel 85 target s
> select clear
> save newest_overlap_ribosome_exitTunnel_take2.png supersample 3
> save newest_overlap_ribosome_exitTunnel_take2.cxs
——— End of log from Tue May 13 16:59:40 2025 ———
opened ChimeraX session
OpenGL version: 3.3.0 NVIDIA 525.60.11
OpenGL renderer: Quadro RTX 4000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: xcb
XDG_SESSION_TYPE=x11
DESKTOP_SESSION=gnome
XDG_SESSION_DESKTOP=gnome
XDG_CURRENT_DESKTOP=GNOME
DISPLAY=:1
Manufacturer: System manufacturer
Model: System Product Name
OS: Rocky Linux 9.1
Architecture: 64bit ELF
Virtual Machine: none
CPU: 16 AMD Ryzen 7 3700X 8-Core Processor
Cache Size: 512 KB
Memory:
total used free shared buff/cache available
Mem: 62Gi 11Gi 38Gi 521Mi 13Gi 51Gi
Swap: 31Gi 0B 31Gi
Graphics:
07:00.0 VGA compatible controller [0300]: NVIDIA Corporation TU104GL [Quadro RTX 4000] [10de:1eb1] (rev a1)
Subsystem: NVIDIA Corporation Device [10de:12a0]
Kernel driver in use: nvidia
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
asttokens: 3.0.0
auditwheel: 6.1.0
autocommand: 2.2.2
babel: 2.16.0
backports.tarfile: 1.2.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2024.8.30
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-Clipper: 0.24.0
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: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
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: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ISOLDE: 1.9
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-LinuxSupport: 1.0.1
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
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: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
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-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: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
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: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-QScore: 1.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
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: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
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: 1.18.1
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
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: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
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: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
distro: 1.9.0
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
importlib_metadata: 8.0.0
importlib_resources: 6.4.0
inflect: 7.3.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jaraco.context: 5.3.0
jaraco.functools: 4.0.1
jaraco.text: 3.12.1
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
more-itertools: 10.3.0
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
openvr: 1.26.701
ordered-set: 4.1.0
packaging: 23.2
packaging: 24.1
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
platformdirs: 4.2.2
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
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
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4.2
traitlets: 5.14.3
typeguard: 4.3.0
typing_extensions: 4.12.2
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
zipp: 3.19.2
Change History (2)
comment:1 by , 5 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Sessions |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash saving atomic state |
comment:2 by , 5 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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