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Opened 14 months ago
Closed 14 months ago
#16029 closed defect (can't reproduce)
Crash while deleting atoms
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-3.10.0-1062.el7.x86_64-x86_64-with-glibc2.17
ChimeraX Version: 1.4.dev202205060510 (2022-05-06 05:10:33 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x00002ba2c6210700 (most recent call first):
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/multiprocessing/pool.py", line 576 in _handle_results
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/threading.py", line 910 in run
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00002ba2c600f700 (most recent call first):
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/multiprocessing/pool.py", line 528 in _handle_tasks
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/threading.py", line 910 in run
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00002ba2c5e0e700 (most recent call first):
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/selectors.py", line 416 in select
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/multiprocessing/connection.py", line 936 in wait
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/multiprocessing/pool.py", line 499 in _wait_for_updates
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/multiprocessing/pool.py", line 519 in _handle_workers
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/threading.py", line 910 in run
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00002ba2c5c0d700 (most recent call first):
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/threading.py", line 910 in run
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00002ba2c5a0c700 (most recent call first):
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/threading.py", line 910 in run
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00002ba2c580b700 (most recent call first):
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/threading.py", line 910 in run
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00002ba2c560a700 (most recent call first):
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/threading.py", line 910 in run
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00002ba2c5409700 (most recent call first):
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/threading.py", line 910 in run
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00002ba2c5208700 (most recent call first):
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/threading.py", line 910 in run
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00002ba2c5007700 (most recent call first):
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/threading.py", line 910 in run
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00002ba2c4e06700 (most recent call first):
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/threading.py", line 910 in run
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00002ba2c4c05700 (most recent call first):
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/threading.py", line 910 in run
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00002ba2c4a04700 (most recent call first):
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/threading.py", line 910 in run
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00002ba2c4803700 (most recent call first):
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/threading.py", line 910 in run
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00002ba2c4602700 (most recent call first):
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/threading.py", line 910 in run
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00002ba2c4401700 (most recent call first):
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/threading.py", line 910 in run
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00002ba2c4200700 (most recent call first):
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/threading.py", line 910 in run
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00002ba2b3e8f700 (most recent call first):
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/threading.py", line 910 in run
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00002ba2b3c8e700 (most recent call first):
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/threading.py", line 910 in run
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00002ba2b1781700 (most recent call first):
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/threading.py", line 910 in run
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00002ba2274e7700 (most recent call first):
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/threading.py", line 910 in run
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00002ba27ba14700 (most recent call first):
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/threading.py", line 910 in run
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00002ba213f38700 (most recent call first):
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/threading.py", line 910 in run
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/threading.py", line 930 in _bootstrap
Current thread 0x00002ba1d111a080 (most recent call first):
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-packages/chimerax/atomic/molarray.py", line 787 in delete
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-packages/chimerax/std_commands/delete.py", line 39 in delete_atoms
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-packages/chimerax/std_commands/delete.py", line 22 in delete
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2897 in run
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-packages/chimerax/cmd_line/tool.py", line 319 in execute
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-packages/chimerax/cmd_line/tool.py", line 146 in keyPressEvent
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-packages/chimerax/ui/gui.py", line 318 in event_loop
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-packages/ChimeraX_main.py", line 867 in init
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-packages/ChimeraX_main.py", line 1018 in
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/runpy.py", line 87 in _run_code
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/runpy.py", line 197 in _run_module_as_main
===== Log before crash start =====
UCSF ChimeraX version: 1.4.dev202205060510 (2022-05-06)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /home/songyanx/work/OME/ONIOM/r_2c19/extend/118_react_S/doublet/RC/RC.pdb
> format pdb
RC.pdb title:
Required [more info...]
Chain information for RC.pdb #1
---
Chain | Description
? | No description available
Non-standard residues in RC.pdb #1
---
CYP — (CYP)
HEM — (HEM)
OME — (OME)
> hide atoms
> show surfaces
> coulombic :1-462
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue CYP (net charge -1) with am1-bcc method
Running ANTECHAMBER command: /usr/libexec/UCSF-ChimeraX-
daily/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
/tmp/tmp4g8m3xtw/ante.in.mol2 -fi mol2 -o /tmp/tmp4g8m3xtw/ante.out.mol2 -fo
mol2 -c bcc -nc -1 -j 5 -s 2 -dr n
(CYP) ``
(CYP) `Welcome to antechamber 20.0: molecular input file processor.`
(CYP) ``
(CYP) `Info: Finished reading file (/tmp/tmp4g8m3xtw/ante.in.mol2); atoms read
(22), bonds read (21).`
(CYP) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(CYP) `Running: /usr/libexec/UCSF-ChimeraX-daily/bin/amber20/bin/bondtype -j
part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(CYP) ``
(CYP) ``
(CYP) `Running: /usr/libexec/UCSF-ChimeraX-daily/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(CYP) `Info: Total number of electrons: 94; net charge: -1`
(CYP) ``
(CYP) `Running: /usr/libexec/UCSF-ChimeraX-daily/bin/amber20/bin/sqm -O -i
sqm.in -o sqm.out`
(CYP) ``
(CYP) `Running: /usr/libexec/UCSF-ChimeraX-daily/bin/amber20/bin/am1bcc -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /usr/libexec/UCSF-
ChimeraX-daily/bin/amber20/dat/antechamber/BCCPARM.DAT -s 2 -j 1`
(CYP) ``
(CYP) `Running: /usr/libexec/UCSF-ChimeraX-daily/bin/amber20/bin/atomtype -f
ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`
(CYP) ``
Charges for residue CYP determined
Coulombic values for RC.pdb_ SES surface #1.2: minimum, -15.86, mean 0.22,
maximum 23.33
> select :OME,HEM
117 atoms, 121 bonds, 5 pseudobonds, 2 residues, 2 models selected
> show sel atoms
> ui tool show "Side View"
> lighting flat
> lighting simple
> lighting soft
> lighting full
> lighting flat
> graphics silhouettes false
> lighting shadows true intensity 0.5
> lighting flat
> lighting simple
> surface cap false
> select up
9095 atoms, 8681 bonds, 5 pseudobonds, 967 residues, 2 models selected
> select up
9095 atoms, 8681 bonds, 5 pseudobonds, 967 residues, 3 models selected
> select down
5 pseudobonds, 2 models selected
> select down
117 atoms, 121 bonds, 5 pseudobonds, 2 residues, 2 models selected
> coulombic :1-462 palette red-white-blue range -5,5
Coulombic values for RC.pdb_ SES surface #1.2: minimum, -15.86, mean 0.22,
maximum 23.33
> hide sel cartoons
> hide cartoons
> select :OME,HEM & @h
Nothing selected
> hide sel atoms
> hide sel
> select :OME,HEM & @H
Nothing selected
> hide sel
> select :OME,HEM & H
49 atoms, 2 residues, 1 model selected
> hide sel atoms
> select up
117 atoms, 121 bonds, 2 residues, 1 model selected
> select up
9095 atoms, 8681 bonds, 967 residues, 1 model selected
> select up
9095 atoms, 8681 bonds, 5 pseudobonds, 967 residues, 3 models selected
> select up
9095 atoms, 8681 bonds, 5 pseudobonds, 967 residues, 3 models selected
> select up
9095 atoms, 8681 bonds, 5 pseudobonds, 967 residues, 3 models selected
> select down
5 pseudobonds, 2 models selected
> select down
Nothing selected
> select down
117 atoms, 121 bonds, 2 residues, 1 model selected
> select down
49 atoms, 2 residues, 1 model selected
> select down
49 atoms, 2 residues, 1 model selected
> select down
49 atoms, 2 residues, 1 model selected
> select down
49 atoms, 2 residues, 1 model selected
> select down
49 atoms, 2 residues, 1 model selected
> select down
49 atoms, 2 residues, 1 model selected
> coulombic :1-462 palette red-white-blue range -3,3
Coulombic values for RC.pdb_ SES surface #1.2: minimum, -15.86, mean 0.22,
maximum 23.33
> rename RC RS
Missing or invalid "models" argument: invalid models specifier
> rename #RC RS
Missing or invalid "models" argument: invalid models specifier
> rename #RC.pdb RS
Missing or invalid "models" argument: invalid models specifier
> rename #1 RS
> open
> /home/songyanx/work/OME/ONIOM/s_2c19/extend/70_reactive_S/doublet/RC/RC.pdb
RC.pdb title:
Required [more info...]
Chain information for RC.pdb #2
---
Chain | Description
? | No description available
Non-standard residues in RC.pdb #2
---
CYP — (CYP)
HEM — (HEM)
OME — (OME)
> hide #!2 models
> rename #2 SS
> open
> /home/songyanx/work/OME/ONIOM/s_2c19/extend/83_most_stable_R/doublet/RC/RC.pdb
RC.pdb title:
Required [more info...]
Chain information for RC.pdb #3
---
Chain | Description
? | No description available
Non-standard residues in RC.pdb #3
---
CYP — (CYP)
HEM — (HEM)
OME — (OME)
> hide #!3 models
> rename #3 SR
> open
> /home/songyanx/work/OME/ONIOM/r_2c19/extend/166_react_R/doublet/RC/RC.pdb
RC.pdb title:
Required [more info...]
Chain information for RC.pdb #4
---
Chain | Description
? | No description available
Non-standard residues in RC.pdb #4
---
CYP — (CYP)
HEM — (HEM)
OME — (OME)
> hide #!4 models
> rename #4 RR
> lighting simple
> lighting soft
> lighting flat
> graphics silhouettes false
> lighting shadows true intensity 0.5
> lighting simple
> lighting full
> lighting soft
> lighting simple
> lighting shadows true
> lighting shadows false
> lighting simple
> lighting shadows true
> lighting shadows false
> lighting flat
> lighting simple
> lighting soft
> lighting simple
> align #2 & :1-462 &! H toatoms #1 & :1-462 &! H
Expected a keyword
> align #2 & :1-462 ~H toatoms #1 & :1-462 ~H
Expected a keyword
> align #2 & :1-462 & ~H toAtoms #1 & :1-462 & ~H
Unequal number of atoms to pair, 3734 and 3732
> align #2 & :1-462 toAtoms #1 & :1-462
Unequal number of atoms to pair, 7523 and 7517
> align #2 & :1-462 & ~:WAT toAtoms #1 & :1-462 & ~:WAT
RMSD between 7469 atom pairs is 28.475 angstroms
> align #3 & :1-462 & ~:WAT toAtoms #1 & :1-462 & ~:WAT
RMSD between 7469 atom pairs is 28.183 angstroms
> align #4 & :1-462 & ~:WAT toAtoms #1 & :1-462 & ~:WAT
RMSD between 7469 atom pairs is 29.204 angstroms
> select FE
Expected an objects specifier or a keyword
> select @FE
4 atoms, 4 residues, 4 models selected
> bond #1 @FE,O1
Created 1 bond
> select :OME,HEM
468 atoms, 485 bonds, 20 pseudobonds, 8 residues, 8 models selected
> style sel & #!1 ball
Changed 117 atom styles
> ~bond #1 @FE,O1
> style sel & #!1 stick
Changed 117 atom styles
> select @FE
4 atoms, 4 residues, 4 models selected
> style sel & #!1 ball
Changed 1 atom style
> style sel & #!1 sphere
Changed 1 atom style
> lighting flat
> lighting depthCue false
> lignt ambientintensity 0.5
Unknown command: lignt ambientintensity 0.5
> lignt ambientIntensity 0.5
Unknown command: lignt ambientIntensity 0.5
> lignting ambientIntensity 0.5
Unknown command: lignting ambientIntensity 0.5
> lighting ambientIntensity 0.5
> lighting ambientIntensity 1
> lighting ambientIntensity 1.5
> lighting Intensity 1.5
Expected one of 'default', 'flat', 'full', 'gentle', 'simple', or 'soft' or a
keyword
> lighting Intensity 1.0
Expected one of 'default', 'flat', 'full', 'gentle', 'simple', or 'soft' or a
keyword
> lighting intensity 1.0
> lighting intensity 0.5
> lighting intensity 0.2
> lighting intensity 0.1
> lighting intensity 0.05
> lighting simple
> lighting intensity 0.1
> lighting intensity 0.5
> lighting intensity 1.5
> lighting intensity 1
> lighting ambientIntensity 1
> lighting ambientIntensity 0/3
Invalid "ambientIntensity" argument: Expected a number
> lighting ambientIntensity 0.3
> lighting shadows false
> lighting shadows true
> lighting shadows false
> material dull
> save /home/songyanx/Desktop/image1.png supersample 3
> set bgColor white
> set bgColor #ffffff00
> set bgColor black
> set bgColor transparent
> ui tool show Registration
Thank you for registering your copy of ChimeraX. By providing the information
requested you will be helping us document the impact this software is having
in the scientific community. The information you supplied will only be used
for reporting summary usage statistics; no individual data will be released.
> lighting ambientIntensity 1
> lighting ambientIntensity 0.5
> lighting ambientIntensity 0.4
> save test format png transparentBackground true
> save /home/songyanx/Desktop/test.png format png supersample 9
> transparentBackground true
> windowsize
window size 1979 1108
> save /home/songyanx/Desktop/test.png format png pixelSize 600 supersample 9
> transparentBackground true
> save /home/songyanx/Desktop/test.png format png pixelSize 0.5 supersample 9
> transparentBackground true
> save /home/songyanx/Desktop/test.png format png pixelSize 0.1 supersample 9
> transparentBackground true
> save /home/songyanx/Desktop/test.png format png pixelSize 0.0016 supersample
> 9 transparentBackground true
> save /home/songyanx/Desktop/test.png format png pixelSize 0.01 supersample 9
> transparentBackground true
> ~select
Nothing selected
> save /home/songyanx/Desktop/test.png format png pixelSize 0.01
> transparentBackground true
> surface #1 & :1-462 & ~:WAT
> surface #1 & :1-462 & ~:WAT probeRadius 2
> surface #1 & :1-462 & ~:WAT probeRadius 1.8
> surface #1 & :1-462 & ~:WAT probeRadius 1.6
> surface #1 & :1-462 & ~:WAT probeRadius 1.7
> surface #1 & :1-462 & ~:WAT probeRadius 1.8
> coulombic #1 & :1-462 & ~:WAT range -3,3
Coulombic values for RC.pdb_ SES surface #1.2: minimum, -12.86, mean 0.24,
maximum 12.41
> save /home/songyanx/work/OME/ONIOM/compare_2c19.cxs
FYI: command is replacing existing command: "build join peptide"
FYI: command is replacing existing command: "build modify"
FYI: command is replacing existing command: "build start"
FYI: command is replacing existing command: "bond"
FYI: command is replacing existing command: "~bond"
FYI: command is replacing existing command: "bond length"
> save
> /home/songyanx/work/OME/ONIOM/r_2c19/extend/118_react_S/doublet/RC/eps_1.png
> format png pixelSize 0.01 transparentBackground true
> hide surfaces
> select #1 & :HEM
74 atoms, 76 bonds, 5 pseudobonds, 1 residue, 2 models selected
> hide sel
> save
> /home/songyanx/work/OME/ONIOM/r_2c19/extend/118_react_S/doublet/RC/eps_2.png
> format png pixelSize 0.01 transparentBackground true
> show surfaces
> lighting ambientIntensity 0.4
> lighting ambientIntensity 0.3
> lighting ambientIntensity 0.2
> lighting ambientIntensity 0.1
> lighting ambientIntensity 0.2
> select #1 & :HEM
74 atoms, 76 bonds, 5 pseudobonds, 1 residue, 2 models selected
> select #1 & :HEM & ~H
44 atoms, 46 bonds, 5 pseudobonds, 1 residue, 2 models selected
> show sel
> ~select
Nothing selected
> save
> /home/songyanx/work/OME/ONIOM/r_2c19/extend/118_react_S/doublet/RC/eps_1.png
> format png pixelSize 0.01 transparentBackground true
> hide surfaces
> hide #1 & :HE hide #1 & :HEM
> save
> /home/songyanx/work/OME/ONIOM/r_2c19/extend/118_react_S/doublet/RC/eps_2.png
> format png pixelSize 0.01 transparentBackground true
> show surfaces
> lighting flat
> show #1 & :HEM & ~H
> save
> /home/songyanx/work/OME/ONIOM/r_2c19/extend/118_react_S/doublet/RC/eps_1.png
> format png pixelSize 0.01 transparentBackground true
> hide surfaces
> hide #1 & :HEM
> save
> /home/songyanx/work/OME/ONIOM/r_2c19/extend/118_react_S/doublet/RC/eps_2.png
> format png pixelSize 0.01 transparentBackground true
> lighting simple
> show surfaces
> lighting ambientIntensity 0.1
> lighting ambientIntensity 0.2
> show #1 & :HEM & ~h
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show #1 & :HEM & ~H
> save
> /home/songyanx/work/OME/ONIOM/r_2c19/extend/118_react_S/doublet/RC/eps_1.png
> format png pixelSize 0.01 transparentBackground true
> lighting ambientIntensity 1.45
> lighting intensity 0
> lighting intensity 1
> lighting intensity 0.1
> lighting intensity 0.2
> lighting intensity 0.3
> lighting intensity 0.4
> lighting intensity 0.5
> lighting ambientIntensity 0.5
> lighting ambientIntensity 1
> lighting ambientIntensity 0.2
> lighting ambientIntensity 0.5
> lighting intensity 0.7
> lighting intensity 0.6
> lighting ambientIntensity 0.7
> lighting ambientIntensity 0.4
> save
> /home/songyanx/work/OME/ONIOM/r_2c19/extend/118_react_S/doublet/RC/eps_1.png
> format png pixelSize 0.01 transparentBackground true
> hide surfaces
> lighting intensity 1
> lighting ambientIntensity 1
> lighting ambientIntensity 0.1
> lighting ambientIntensity 0.5
> lighting ambientIntensity 0.4
> lighting ambientIntensity 0.3
> save
> /home/songyanx/work/OME/ONIOM/r_2c19/extend/118_react_S/doublet/RC/eps_2.png
> format png pixelSize 0.01 transparentBackground true
> show surfaces
> save /home/songyanx/work/OME/ONIOM/compare_2c19.cxs
> mlp
/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/numpy/core/_methods.py:179: RuntimeWarning: overflow encountered in
reduce
ret = umr_sum(arr, axis, dtype, out, keepdims, where=where)
Map values for surface "RR_ SES surface": minimum -30.16, mean inf, maximum
1.005e+36
Map values for surface "RC.pdb_ SES surface": minimum -24.88, mean inf,
maximum 1.006e+36
Map values for surface "SR_ SES surface": minimum -28.73, mean inf, maximum
9.583e+35
Map values for surface "SS_ SES surface": minimum -26.85, mean inf, maximum
9.402e+35
> coulombic #1 & :1-462 & ~:WAT range -3,3
Coulombic values for RC.pdb_ SES surface #1.2: minimum, -12.86, mean 0.24,
maximum 12.41
> hide #!1 models
> show #!2 models
> show #!1 models
> align #2 & :1-462 & ~:WAT & ~H toAtoms #1 & :1-462 & ~:WAT & ~H
RMSD between 3716 atom pairs is 28.383 angstroms
> align #2 & :1-462 & ~:WAT & ~H toAtoms #1
Unequal number of atoms to pair, 3716 and 9095
> align #2 & :HEM & ~H toAtoms #1 & :HEM & ~H
RMSD between 44 atom pairs is 0.329 angstroms
> hide #!1 models
> show #!1 models
> hide #!1 models
> align #3 & :1-462 & ~:WAT & ~H toAtoms #1
Unequal number of atoms to pair, 3716 and 9095
> align #3 & :HEM & ~H toAtoms #1 & :HEM & ~H
RMSD between 44 atom pairs is 0.381 angstroms
> align #4 & :HEM & ~H toAtoms #1 & :HEM & ~H
RMSD between 44 atom pairs is 0.390 angstroms
> save /home/songyanx/work/OME/ONIOM/compare_2c19.cxs
> hide cartoons
> hide atoms
> show #2 & :OME,HEM & ~H
> surface #2 & :1-462 & ~:WAT probeRadius 1.8
> surface #2 & :1-462 & ~:WAT probeRadius 1.7
> surface #2 & :1-462 & ~:WAT probeRadius 1.8
> coulombic #2 & :1-462 & ~:WAT range -3,3
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue CYP (net charge -1) with am1-bcc method
Running ANTECHAMBER command: /usr/libexec/UCSF-ChimeraX-
daily/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
/tmp/tmpu3mgzshr/ante.in.mol2 -fi mol2 -o /tmp/tmpu3mgzshr/ante.out.mol2 -fo
mol2 -c bcc -nc -1 -j 5 -s 2 -dr n
(CYP) ``
(CYP) `Welcome to antechamber 20.0: molecular input file processor.`
(CYP) ``
(CYP) `Info: Finished reading file (/tmp/tmpu3mgzshr/ante.in.mol2); atoms read
(22), bonds read (21).`
(CYP) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(CYP) `Running: /usr/libexec/UCSF-ChimeraX-daily/bin/amber20/bin/bondtype -j
part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(CYP) ``
(CYP) ``
(CYP) `Running: /usr/libexec/UCSF-ChimeraX-daily/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(CYP) `Info: Total number of electrons: 94; net charge: -1`
(CYP) ``
(CYP) `Running: /usr/libexec/UCSF-ChimeraX-daily/bin/amber20/bin/sqm -O -i
sqm.in -o sqm.out`
(CYP) ``
(CYP) `Running: /usr/libexec/UCSF-ChimeraX-daily/bin/amber20/bin/am1bcc -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /usr/libexec/UCSF-
ChimeraX-daily/bin/amber20/dat/antechamber/BCCPARM.DAT -s 2 -j 1`
(CYP) ``
(CYP) `Running: /usr/libexec/UCSF-ChimeraX-daily/bin/amber20/bin/atomtype -f
ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`
(CYP) ``
Charges for residue CYP determined
Coulombic values for SS_ SES surface #2.2: minimum, -10.89, mean 0.23, maximum
12.05
> select :OME,HEM
468 atoms, 484 bonds, 20 pseudobonds, 8 residues, 8 models selected
> color #2 tan transparency 0
> color #2 skyblue transparency 0
> color #2 tan transparency 0
> color (#!2 & sel) byelement
> ui tool show "Color Actions"
> color sel byelement
> color sel tan target a
> color sel byelement
> color sel tan target a
> color (#!2 & sel) byelement
> color sel & C tan
> ~select
Nothing selected
> coulombic #2 & :1-462 & ~:WAT range -3,3
Coulombic values for SS_ SES surface #2.2: minimum, -10.89, mean 0.23, maximum
12.05
> lighting ambientIntensity 0.4
> lighting intensity 0.6
> save
> /home/songyanx/work/OME/ONIOM/s_2c19/extend/70_reactive_S/doublet/RC/eps_1.png
> format png pixelSize 0.01 transparentBackground true
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> hide surfaces
> lighting intensity 1
> lighting ambientIntensity 0.3
> save
> /home/songyanx/work/OME/ONIOM/s_2c19/extend/70_reactive_S/doublet/RC/eps_2.png
> format png pixelSize 0.01 transparentBackground true
> show surfaces
> lighting ambientIntensity 0.4
> lighting intensity 0.6
> save
> /home/songyanx/work/OME/ONIOM/s_2c19/extend/70_reactive_S/doublet/RC/eps_1.png
> format png pixelSize 0.01 transparentBackground true
> color bond purple
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword
> show #!1 models
> hide #!1 models
> select pseudobonds
Expected an objects specifier or a keyword
> select pseudobond
Expected an objects specifier or a keyword
> select halfbonds
Expected an objects specifier or a keyword
> select halfbond
Expected an objects specifier or a keyword
> select pbonds
20 pseudobonds, 4 models selected
> color sel megenta
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword
> color pbonds megenta
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword
> color pbonds purple
> color pbonds blue violet
> color pbonds medium purple
> ~select
Nothing selected
> color pbonds medium slate blue
> color pbonds medium purple
> hide surfaces
> lighting intensity 1
> lighting ambientIntensity 0.3
> save
> /home/songyanx/work/OME/ONIOM/s_2c19/extend/70_reactive_S/doublet/RC/eps_2.png
> format png pixelSize 0.01 transparentBackground true
> show #!1 models
> show #1 & :OME,HEM & ~H
> select #1,2 & :334,463,464 & ~:WAT & ~H
152 atoms, 158 bonds, 10 pseudobonds, 6 residues, 4 models selected
> show sel
> color sel byelement
> select #1,2
18154 atoms, 17338 bonds, 10 pseudobonds, 1922 residues, 4 models selected
> show #1,2 cartoons
> color #1 sky blue
> color #2 tomato
> hide atoms
> cartoon style (#!1-2 & sel) xsection oval modeHelix default
> cartoon style (#!1-2 & sel) xsection rectangle modeHelix default
> cartoon style (#!1-2 & sel & coil) xsection oval
> cartoon style (#!1-2 & sel) xsection barbell modeHelix default
> cartoon style (#!1-2 & sel) modeHelix tube sides 20
> cartoon style (#!1-2 & sel) xsection oval modeHelix default
> select #1,2 & :299,463,464 & ~:WAT & ~H & ~CA,C,O,N
Expected a keyword
> select #1,2 & :299,463,464 & ~:WAT & ~H & ~@CA,C,O,N
144 atoms, 266 bonds, 10 pseudobonds, 6 residues, 4 models selected
> show sel atoms
> hide atoms
> select #1,2 & :334,463,464 & ~:WAT & ~H & ~@CA,C,O,N
144 atoms, 266 bonds, 10 pseudobonds, 6 residues, 4 models selected
> show sel atoms
> color pbonds medium purple
> color sel byelement
> color #1 & :334,463,464 & ~:WAT & ~H & ~@CA,C,O,N & C sky blue
> color #2 & :334,463,464 & ~:WAT & ~H & ~@CA,C,O,N & C salmon
> color #2 & :334,463,464 & ~:WAT & ~H & ~@CA,C,O,N & C tomato
> transparency cartoon 80
Missing or invalid "percent" argument: Expected a number
> transparency 80 target c
> material dull
> ~select
Nothing selected
> camera ortho
> hide #1,2 :336-338
> ~#1,2 :336-338
Unknown command: ~#1,2 :336-338
> hide #1,2 :336-338
> hide #1,2 :336-338 cartoons
> transparency 90 target c
> ui mousemode right select
> select #1/?:463@CMA
1 atom, 1 residue, 1 model selected
> distance #1 & :334 & @CG2 sel symbol false
Expected a keyword
> distance #1 & :334 & @CG2 #1 & :HEM & @CMA symbol false
Expected exactly two atoms and/or measurable objects (e.g. axes, planes), got
0
> select #1/?:334@CG2
1 atom, 1 residue, 1 model selected
> select #1/?:463@CMA
1 atom, 1 residue, 1 model selected
> select add #1/?:334@CG2
2 atoms, 2 residues, 1 model selected
> distance sel
Distance between RS #1/? HEM 463 CMA and ILE 334 CG2: 3.541Å
> distance sel symbol false
Distance already exists; modify distance properties with 'distance style'
> distance style symbol false
> distance sel
Distance already exists; modify distance properties with 'distance style'
> distance delete sel
> distance sel
Distance between RS #1/? HEM 463 CMA and ILE 334 CG2: 3.541
> distance delete sel
> hbonds sel
0 hydrogen bonds found
> pbonds sel
Unknown command: pbonds sel
> distance sel monitor false
Expected a keyword
> distance sel
Distance between RS #1/? HEM 463 CMA and ILE 334 CG2: 3.541
> ~distance
> ui mousemode right "tape measure"
> marker segment #6 position 47.3,37.47,48.52 toPosition 43.86,36.66,48.36
> color yellow radius 0.1 label 3.541 labelHeight 0.3541 labelColor yellow
> undo
> ui mousemode right "map eraser"
> ui mousemode right "pick blobs"
> ui mousemode right "tape measure"
> marker delete #6
> ui mousemode right select
> select add #1/?:334@CG2
2 atoms, 2 residues, 1 model selected
> pbond sel
Unknown command: pbond sel
> pbond
Unknown command: pbond
> pbonds
Unknown command: pbonds
> select pbonds
20 pseudobonds, 4 models selected
> pbond
Unknown command: pbond
> pbonds
Unknown command: pbonds
> pseudobonds
Unknown command: pseudobonds
> pseudo bonds
Unknown command: pseudo bonds
> ui mousemode right distance
> ui mousemode right label
> ui mousemode right "move label"
> ui mousemode right "color key"
> ui mousemode right "move label"
> ui mousemode right distance
> ui mousemode right "clip rotate"
> ui mousemode right clip
> ui mousemode right label
> ui mousemode right "color key"
> ui mousemode right label
> select subtract #5
20 pseudobonds, 4 models selected
> hide #5 models
> hide #6 models
> ui tool show "Selection Inspector"
> ui mousemode right select
> select #1/?:334@CG2
1 atom, 1 residue, 1 model selected
> select add #1/?:463@CMA
2 atoms, 2 residues, 2 models selected
> distance sel
Distance between RS #1/? ILE 334 CG2 and HEM 463 CMA: 3.541
> hide label
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide labels
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> ~label
> hide #2 & :74-75 cartoons
> select clear
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> save
> /home/songyanx/work/OME/ONIOM/s_2c19/extend/70_reactive_S/doublet/RC/compare.png
> format png pixelSize 0.01 transparentBackground true
> color cartoon white
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword
> ui tool show "Color Actions"
> color white target c
> save
> /home/songyanx/work/OME/ONIOM/s_2c19/extend/70_reactive_S/doublet/RC/compare.png
> format png pixelSize 0.01 transparentBackground true
> show label
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> label
> ui mousemode right select
> select #1/?:334@CG2
1 atom, 1 residue, 1 model selected
> select add #1/?:463@CMA
2 atoms, 2 residues, 2 models selected
> distance sel
Distance already exists; modify distance properties with 'distance style'
> ui mousemode right distance
> distance #1/?:334@CG2 #1/?:463@CMA
Distance already exists; modify distance properties with 'distance style'
> ui mousemode right "tape measure"
> marker segment #8 position 47.3,37.47,48.52 toPosition 46.94,35.41,49.96
> color yellow radius 0.1 label 2.532 labelHeight 0.2532 labelColor yellow
> undo
> hide #!8 models
> ~label
> ui tool show "Color Actions"
> color white target c
> hide #7 models
> select #1,2 & :334
38 atoms, 36 bonds, 2 residues, 2 models selected
> hide sel atoms
> show #!3 models
> show #!4 models
> show #1,2,3,4 cartoons
> select #3,4 & :OME,HEM & ~H
136 atoms, 144 bonds, 10 pseudobonds, 4 residues, 4 models selected
> show sel atoms
> color sel byelement
> ui tool show "Color Actions"
> select #1,2,3,4 & :463,464,448 & ~H & ~@CA,C,O,N
300 atoms, 540 bonds, 20 pseudobonds, 12 residues, 8 models selected
> show sel atoms
> color sel byelement
> color #1 & :334,463,464 & ~:WAT & ~H & ~@CA,C,O,N & C sky blue
> color #1 & :448,463,464 & ~:WAT & ~H & ~@CA,C,O,N & C sky blue
> color #2 & :448,463,464 & ~:WAT & ~H & ~@CA,C,O,N & C tomato
> color #3 & :448,463,464 & ~:WAT & ~H & ~@CA,C,O,N & C lawn green
> color #3 & :448,463,464 & ~:WAT & ~H & ~@CA,C,O,N & C pale green
> ui tool show "Side View"
> hide #!1 models
> hide #!4 models
> marker delete #8
> ui mousemode right rotate
> hide #!3 models
> show #!3 models
> hide #!2 models
> show #!4 models
> ~select
Nothing selected
> camera pers
Expected one of '360', '360sbs', '360tb', 'dome', 'mono', 'ortho', 'sbs',
'stereo', or 'tb' or a keyword
> camera mono
> color #4 & :448,463,464 & ~:WAT & ~H & ~@CA,C,O,N & C gray
> color #4 & :448,463,464 & ~:WAT & ~H & ~@CA,C,O,N & C dark gray
> color #4 & :448,463,464 & ~:WAT & ~H & ~@CA,C,O,N & C dim gray
> ui mousemode right select
> select #3/?:448@CD1
1 atom, 1 residue, 1 model selected
> select add #3/?:448@CE1
2 atoms, 1 residue, 2 models selected
> select add #3/?:448@CZ
3 atoms, 1 residue, 2 models selected
> select add #3/?:448@CE2
4 atoms, 1 residue, 2 models selected
> select add #3/?:448@CD2
5 atoms, 1 residue, 2 models selected
> select add #3/?:448@CG
6 atoms, 1 residue, 2 models selected
> define centroid sel
Centroid 'centroid' placed at [37.88133333 41.955 46.24466667]
> select #3.3/centroid:1@centroid
1 atom, 1 residue, 1 model selected
> show sel atoms
> hide sel sphere
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> ~select
Nothing selected
> select #3.3/centroid:1@centroid
1 atom, 1 residue, 1 model selected
> hide sle
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide sel
> show sel atoms
> hide sel
> marker #3 position 37.8813,41.955,46.2446 color lawn green radius 1
Cannot create a marker set #3 with same model id as another model
> marker #8 position 37.8813,41.955,46.2446 color lawn green radius 1
> marker #8 position 37.8813,41.955,46.2446 color lawn green radius 0.2
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> select up
1 atom, 1 residue, 1 model selected
> select up
1 atom, 1 residue, 1 model selected
> select up
1 atom, 1 residue, 1 model selected
> select up
1 atom, 1 residue, 1 model selected
> select #!3/?:448@CD1
1 atom, 1 residue, 1 model selected
> select add #!3/?:448@CE1
2 atoms, 1 residue, 2 models selected
> select add #!3/?:448@CZ
3 atoms, 1 residue, 2 models selected
> select add #!3/?:448@CE2
4 atoms, 1 residue, 2 models selected
> select add #!3/?:448@CD2
5 atoms, 1 residue, 2 models selected
> select add #!3/?:448@CG
6 atoms, 1 residue, 2 models selected
> define centroid sel
Centroid 'centroid' placed at [37.88133333 41.955 46.24466667]
> select #3.4/centroid:1@centroid
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> size sel atomRadius 1
Changed 1 atom radii
> size sel atomRadius 0.5
Changed 1 atom radii
> size sel atomRadius 0.2
Changed 1 atom radii
> color sel yellow
> size sel atomRadius 0.1
Changed 1 atom radii
> size sel atomRadius 0.2
Changed 1 atom radii
> select #!3/?:464@C2
1 atom, 1 residue, 1 model selected
> select add #!3/?:464@N3
2 atoms, 1 residue, 1 model selected
> select add #!3/?:464@C11
3 atoms, 1 residue, 1 model selected
> select add #!3/?:464@C8
4 atoms, 1 residue, 1 model selected
> select add #!3/?:464@C6
5 atoms, 1 residue, 1 model selected
> select add #!3/?:464@C3
6 atoms, 1 residue, 1 model selected
> define centroid sel
Centroid 'centroid' placed at [39.11283333 40.17533333 40.75666667]
> select #3.5/centroid:1@centroid
1 atom, 1 residue, 1 model selected
> size sel atomRadius 0.2
Changed 1 atom radii
> color sel yellow
> select add #3.4/centroid:1@centroid
2 atoms, 2 residues, 2 models selected
> marker link sel
marker link: Cannot link markers from different models (#3.5:1, #3.4:1)
> distance #3.5:1 #3.4:1
Distance between centroid #3.5/centroid centroid 1 centroid and centroid
#3.4/centroid centroid 1 centroid: 5.899
> select #1,2,3,4 & :OME & H & ~CH
Expected a keyword
> select #1,2,3,4 & :OME & H & ~HC
4 atoms, 4 residues, 4 models selected
> show sel atoms
> color sel white
> ui mousemode right distance
> distance #1/?:334@CG2 #3.5/centroid:1@centroid
Distance between RS #1/? ILE 334 CG2 and centroid #3.5/centroid centroid 1
centroid: 8.874
> distance #3.4/centroid:1@centroid #3.5/centroid:1@centroid
Distance already exists; modify distance properties with 'distance style'
> distance #3.5/centroid:1@centroid #3.4/centroid:1@centroid
Distance already exists; modify distance properties with 'distance style'
> show #!7 models
> hide #7.1 models
> show #7.1 models
> hide #7.1 models
> show #7.1 models
> hide #7.1 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> delete #3
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.4.dev202205060510 (2022-05-06)
© 2016-2022 Regents of the University of California. All rights reserved.
> surface cap false
Log from Thu Sep 26 16:57:38 2024UCSF ChimeraX version: 1.4.dev202205060510
(2022-05-06)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /home/songyanx/work/OME/ONIOM/r_2c19/extend/118_react_S/doublet/RC/RC.pdb
> format pdb
RC.pdb title:
Required [more info...]
Chain information for RC.pdb #1
---
Chain | Description
? | No description available
Non-standard residues in RC.pdb #1
---
CYP — (CYP)
HEM — (HEM)
OME — (OME)
> hide atoms
> show surfaces
> coulombic :1-462
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue CYP (net charge -1) with am1-bcc method
Running ANTECHAMBER command: /usr/libexec/UCSF-ChimeraX-
daily/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
/tmp/tmp4g8m3xtw/ante.in.mol2 -fi mol2 -o /tmp/tmp4g8m3xtw/ante.out.mol2 -fo
mol2 -c bcc -nc -1 -j 5 -s 2 -dr n
(CYP) ``
(CYP) `Welcome to antechamber 20.0: molecular input file processor.`
(CYP) ``
(CYP) `Info: Finished reading file (/tmp/tmp4g8m3xtw/ante.in.mol2); atoms read
(22), bonds read (21).`
(CYP) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(CYP) `Running: /usr/libexec/UCSF-ChimeraX-daily/bin/amber20/bin/bondtype -j
part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(CYP) ``
(CYP) ``
(CYP) `Running: /usr/libexec/UCSF-ChimeraX-daily/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(CYP) `Info: Total number of electrons: 94; net charge: -1`
(CYP) ``
(CYP) `Running: /usr/libexec/UCSF-ChimeraX-daily/bin/amber20/bin/sqm -O -i
sqm.in -o sqm.out`
(CYP) ``
(CYP) `Running: /usr/libexec/UCSF-ChimeraX-daily/bin/amber20/bin/am1bcc -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /usr/libexec/UCSF-
ChimeraX-daily/bin/amber20/dat/antechamber/BCCPARM.DAT -s 2 -j 1`
(CYP) ``
(CYP) `Running: /usr/libexec/UCSF-ChimeraX-daily/bin/amber20/bin/atomtype -f
ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`
(CYP) ``
Charges for residue CYP determined
Coulombic values for RC.pdb_ SES surface #1.2: minimum, -15.86, mean 0.22,
maximum 23.33
> select :OME,HEM
117 atoms, 121 bonds, 5 pseudobonds, 2 residues, 2 models selected
> show sel atoms
> ui tool show "Side View"
> lighting flat
> lighting simple
> lighting soft
> lighting full
> lighting flat
> graphics silhouettes false
> lighting shadows true intensity 0.5
> lighting flat
> lighting simple
> surface cap false
[Repeated 1 time(s)]
> select up
9095 atoms, 8681 bonds, 5 pseudobonds, 967 residues, 2 models selected
> select up
9095 atoms, 8681 bonds, 5 pseudobonds, 967 residues, 3 models selected
> select down
5 pseudobonds, 2 models selected
> select down
117 atoms, 121 bonds, 5 pseudobonds, 2 residues, 2 models selected
> coulombic :1-462 palette red-white-blue range -5,5
Coulombic values for RC.pdb_ SES surface #1.2: minimum, -15.86, mean 0.22,
maximum 23.33
> hide sel cartoons
> hide cartoons
> select :OME,HEM & @h
Nothing selected
> hide sel atoms
> hide sel
> select :OME,HEM & @H
Nothing selected
> hide sel
> select :OME,HEM & H
49 atoms, 2 residues, 1 model selected
> hide sel atoms
> select up
117 atoms, 121 bonds, 2 residues, 1 model selected
> select up
9095 atoms, 8681 bonds, 967 residues, 1 model selected
> select up
9095 atoms, 8681 bonds, 5 pseudobonds, 967 residues, 3 models selected
> select up
9095 atoms, 8681 bonds, 5 pseudobonds, 967 residues, 3 models selected
> select up
9095 atoms, 8681 bonds, 5 pseudobonds, 967 residues, 3 models selected
> select down
5 pseudobonds, 2 models selected
> select down
Nothing selected
> select down
117 atoms, 121 bonds, 2 residues, 1 model selected
> select down
49 atoms, 2 residues, 1 model selected
> select down
49 atoms, 2 residues, 1 model selected
> select down
49 atoms, 2 residues, 1 model selected
> select down
49 atoms, 2 residues, 1 model selected
> select down
49 atoms, 2 residues, 1 model selected
> select down
49 atoms, 2 residues, 1 model selected
> coulombic :1-462 palette red-white-blue range -3,3
Coulombic values for RC.pdb_ SES surface #1.2: minimum, -15.86, mean 0.22,
maximum 23.33
> rename RC RS
Missing or invalid "models" argument: invalid models specifier
> rename #RC RS
Missing or invalid "models" argument: invalid models specifier
> rename #RC.pdb RS
Missing or invalid "models" argument: invalid models specifier
> rename #1 RS
> open
> /home/songyanx/work/OME/ONIOM/s_2c19/extend/70_reactive_S/doublet/RC/RC.pdb
RC.pdb title:
Required [more info...]
Chain information for RC.pdb #2
---
Chain | Description
? | No description available
Non-standard residues in RC.pdb #2
---
CYP — (CYP)
HEM — (HEM)
OME — (OME)
> hide #!2 models
> rename #2 SS
> open
> /home/songyanx/work/OME/ONIOM/s_2c19/extend/83_most_stable_R/doublet/RC/RC.pdb
RC.pdb title:
Required [more info...]
Chain information for RC.pdb #3
---
Chain | Description
? | No description available
Non-standard residues in RC.pdb #3
---
CYP — (CYP)
HEM — (HEM)
OME — (OME)
> hide #!3 models
> rename #3 SR
> open
> /home/songyanx/work/OME/ONIOM/r_2c19/extend/166_react_R/doublet/RC/RC.pdb
RC.pdb title:
Required [more info...]
Chain information for RC.pdb #4
---
Chain | Description
? | No description available
Non-standard residues in RC.pdb #4
---
CYP — (CYP)
HEM — (HEM)
OME — (OME)
> hide #!4 models
> rename #4 RR
> lighting simple
[Repeated 1 time(s)]
> lighting soft
> lighting flat
> graphics silhouettes false
> lighting shadows true intensity 0.5
> lighting simple
> lighting full
> lighting soft
> lighting simple
> lighting shadows true
> lighting shadows false
> lighting simple
[Repeated 2 time(s)]
> lighting shadows true
> lighting shadows false
> lighting flat
[Repeated 1 time(s)]
> lighting simple
> lighting soft
[Repeated 1 time(s)]
> lighting simple
> align #2 & :1-462 &! H toatoms #1 & :1-462 &! H
Expected a keyword
> align #2 & :1-462 ~H toatoms #1 & :1-462 ~H
Expected a keyword
> align #2 & :1-462 & ~H toAtoms #1 & :1-462 & ~H
Unequal number of atoms to pair, 3734 and 3732
> align #2 & :1-462 toAtoms #1 & :1-462
Unequal number of atoms to pair, 7523 and 7517
> align #2 & :1-462 & ~:WAT toAtoms #1 & :1-462 & ~:WAT
RMSD between 7469 atom pairs is 28.475 angstroms
> align #3 & :1-462 & ~:WAT toAtoms #1 & :1-462 & ~:WAT
RMSD between 7469 atom pairs is 28.183 angstroms
> align #4 & :1-462 & ~:WAT toAtoms #1 & :1-462 & ~:WAT
RMSD between 7469 atom pairs is 29.204 angstroms
> select FE
Expected an objects specifier or a keyword
> select @FE
4 atoms, 4 residues, 4 models selected
> bond #1 @FE,O1
Created 1 bond
> select :OME,HEM
468 atoms, 485 bonds, 20 pseudobonds, 8 residues, 8 models selected
> style sel & #!1 ball
Changed 117 atom styles
> ~bond #1 @FE,O1
> style sel & #!1 stick
Changed 117 atom styles
> select @FE
4 atoms, 4 residues, 4 models selected
> style sel & #!1 ball
Changed 1 atom style
> style sel & #!1 sphere
Changed 1 atom style
> lighting flat
> lighting depthCue false
> lignt ambientintensity 0.5
Unknown command: lignt ambientintensity 0.5
> lignt ambientIntensity 0.5
Unknown command: lignt ambientIntensity 0.5
> lignting ambientIntensity 0.5
Unknown command: lignting ambientIntensity 0.5
> lighting ambientIntensity 0.5
> lighting ambientIntensity 1
> lighting ambientIntensity 1.5
> lighting Intensity 1.5
Expected one of 'default', 'flat', 'full', 'gentle', 'simple', or 'soft' or a
keyword
> lighting Intensity 1.0
Expected one of 'default', 'flat', 'full', 'gentle', 'simple', or 'soft' or a
keyword
> lighting intensity 1.0
> lighting intensity 0.5
> lighting intensity 0.2
> lighting intensity 0.1
> lighting intensity 0.05
> lighting simple
> lighting intensity 0.1
> lighting intensity 0.5
> lighting intensity 1.5
> lighting intensity 1
> lighting ambientIntensity 1
> lighting ambientIntensity 0/3
Invalid "ambientIntensity" argument: Expected a number
> lighting ambientIntensity 0.3
> lighting shadows false
> lighting shadows true
> lighting shadows false
> material dull
> save /home/songyanx/Desktop/image1.png supersample 3
> set bgColor white
> set bgColor #ffffff00
> set bgColor black
> set bgColor transparent
> ui tool show Registration
Thank you for registering your copy of ChimeraX. By providing the information
requested you will be helping us document the impact this software is having
in the scientific community. The information you supplied will only be used
for reporting summary usage statistics; no individual data will be released.
> lighting ambientIntensity 1
> lighting ambientIntensity 0.5
> lighting ambientIntensity 0.4
> save test format png transparentBackground true
> save /home/songyanx/Desktop/test.png format png supersample 9
> transparentBackground true
> windowsize
window size 1979 1108
> save /home/songyanx/Desktop/test.png format png pixelSize 600 supersample 9
> transparentBackground true
> save /home/songyanx/Desktop/test.png format png pixelSize 0.5 supersample 9
> transparentBackground true
> save /home/songyanx/Desktop/test.png format png pixelSize 0.1 supersample 9
> transparentBackground true
> save /home/songyanx/Desktop/test.png format png pixelSize 0.0016 supersample
> 9 transparentBackground true
> save /home/songyanx/Desktop/test.png format png pixelSize 0.01 supersample 9
> transparentBackground true
> ~select
Nothing selected
> save /home/songyanx/Desktop/test.png format png pixelSize 0.01
> transparentBackground true
> surface #1 & :1-462 & ~:WAT
> surface #1 & :1-462 & ~:WAT probeRadius 2
> surface #1 & :1-462 & ~:WAT probeRadius 1.8
> surface #1 & :1-462 & ~:WAT probeRadius 1.6
> surface #1 & :1-462 & ~:WAT probeRadius 1.7
> surface #1 & :1-462 & ~:WAT probeRadius 1.8
> coulombic #1 & :1-462 & ~:WAT range -3,3
Coulombic values for RC.pdb_ SES surface #1.2: minimum, -12.86, mean 0.24,
maximum 12.41
> save /home/songyanx/work/OME/ONIOM/compare_2c19.cxs
FYI: command is replacing existing command: "build join peptide"
FYI: command is replacing existing command: "build modify"
FYI: command is replacing existing command: "build start"
FYI: command is replacing existing command: "bond"
FYI: command is replacing existing command: "~bond"
FYI: command is replacing existing command: "bond length"
> save
> /home/songyanx/work/OME/ONIOM/r_2c19/extend/118_react_S/doublet/RC/eps_1.png
> format png pixelSize 0.01 transparentBackground true
> hide surfaces
> select #1 & :HEM
74 atoms, 76 bonds, 5 pseudobonds, 1 residue, 2 models selected
> hide sel
> save
> /home/songyanx/work/OME/ONIOM/r_2c19/extend/118_react_S/doublet/RC/eps_2.png
> format png pixelSize 0.01 transparentBackground true
> show surfaces
> lighting ambientIntensity 0.4
> lighting ambientIntensity 0.3
> lighting ambientIntensity 0.2
> lighting ambientIntensity 0.1
> lighting ambientIntensity 0.2
> select #1 & :HEM
74 atoms, 76 bonds, 5 pseudobonds, 1 residue, 2 models selected
> select #1 & :HEM & ~H
44 atoms, 46 bonds, 5 pseudobonds, 1 residue, 2 models selected
> show sel
> ~select
Nothing selected
> save
> /home/songyanx/work/OME/ONIOM/r_2c19/extend/118_react_S/doublet/RC/eps_1.png
> format png pixelSize 0.01 transparentBackground true
> hide surfaces
> hide #1 & :HE<
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide #1 & :HEM
> save
> /home/songyanx/work/OME/ONIOM/r_2c19/extend/118_react_S/doublet/RC/eps_2.png
> format png pixelSize 0.01 transparentBackground true
> show surfaces
> lighting flat
> show #1 & :HEM & ~H
> save
> /home/songyanx/work/OME/ONIOM/r_2c19/extend/118_react_S/doublet/RC/eps_1.png
> format png pixelSize 0.01 transparentBackground true
> hide surfaces
> hide #1 & :HEM
> save
> /home/songyanx/work/OME/ONIOM/r_2c19/extend/118_react_S/doublet/RC/eps_2.png
> format png pixelSize 0.01 transparentBackground true
> lighting simple
> show surfaces
> lighting ambientIntensity 0.1
> lighting ambientIntensity 0.2
> show #1 & :HEM & ~h
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show #1 & :HEM & ~H
> save
> /home/songyanx/work/OME/ONIOM/r_2c19/extend/118_react_S/doublet/RC/eps_1.png
> format png pixelSize 0.01 transparentBackground true
> lighting ambientIntensity 1.45
> lighting intensity 0
> lighting intensity 1
> lighting intensity 0.1
> lighting intensity 0.2
> lighting intensity 0.3
> lighting intensity 0.4
> lighting intensity 0.5
> lighting ambientIntensity 0.5
> lighting ambientIntensity 1
> lighting ambientIntensity 0.2
> lighting ambientIntensity 0.5
> lighting intensity 0.7
> lighting intensity 0.6
> lighting ambientIntensity 0.7
> lighting ambientIntensity 0.4
> save
> /home/songyanx/work/OME/ONIOM/r_2c19/extend/118_react_S/doublet/RC/eps_1.png
> format png pixelSize 0.01 transparentBackground true
> hide surfaces
> lighting intensity 1
> lighting ambientIntensity 1
> lighting ambientIntensity 0.1
> lighting ambientIntensity 0.5
> lighting ambientIntensity 0.4
> lighting ambientIntensity 0.3
> save
> /home/songyanx/work/OME/ONIOM/r_2c19/extend/118_react_S/doublet/RC/eps_2.png
> format png pixelSize 0.01 transparentBackground true
> show surfaces
> save /home/songyanx/work/OME/ONIOM/compare_2c19.cxs
> mlp
/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/numpy/core/_methods.py:179: RuntimeWarning: overflow encountered in
reduce
ret = umr_sum(arr, axis, dtype, out, keepdims, where=where)
Map values for surface "RR_ SES surface": minimum -30.16, mean inf, maximum
1.005e+36
Map values for surface "RC.pdb_ SES surface": minimum -24.88, mean inf,
maximum 1.006e+36
Map values for surface "SR_ SES surface": minimum -28.73, mean inf, maximum
9.583e+35
Map values for surface "SS_ SES surface": minimum -26.85, mean inf, maximum
9.402e+35
> coulombic #1 & :1-462 & ~:WAT range -3,3
Coulombic values for RC.pdb_ SES surface #1.2: minimum, -12.86, mean 0.24,
maximum 12.41
> hide #!1 models
> show #!2 models
> show #!1 models
> align #2 & :1-462 & ~:WAT & ~H toAtoms #1 & :1-462 & ~:WAT & ~H
RMSD between 3716 atom pairs is 28.383 angstroms
> align #2 & :1-462 & ~:WAT & ~H toAtoms #1
Unequal number of atoms to pair, 3716 and 9095
> align #2 & :HEM & ~H toAtoms #1 & :HEM & ~H
RMSD between 44 atom pairs is 0.329 angstroms
> hide #!1 models
> show #!1 models
> hide #!1 models
> align #3 & :1-462 & ~:WAT & ~H toAtoms #1
Unequal number of atoms to pair, 3716 and 9095
> align #3 & :HEM & ~H toAtoms #1 & :HEM & ~H
RMSD between 44 atom pairs is 0.381 angstroms
> align #4 & :HEM & ~H toAtoms #1 & :HEM & ~H
RMSD between 44 atom pairs is 0.390 angstroms
> save /home/songyanx/work/OME/ONIOM/compare_2c19.cxs
——— End of log from Thu Sep 26 16:57:38 2024 ———
opened ChimeraX session
OpenGL version: 3.3.0 NVIDIA 510.60.02
OpenGL renderer: NVIDIA GeForce RTX 3070 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.9.11
Locale: en_US.UTF-8
Qt version: PyQt5 5.15.2, Qt 5.15.2
Qt runtime version: 5.15.2
Qt platform: xcb
XDG_SESSION_TYPE=x11
DESKTOP_SESSION=gnome-classic
XDG_SESSION_DESKTOP=gnome-classic
XDG_CURRENT_DESKTOP=GNOME-Classic:GNOME
DISPLAY=:0
Manufacturer: LENOVO
Model: 90S2002RCP
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
Virtual Machine: none
CPU: 20 12th Gen Intel(R) Core(TM) i7-12700KF
Cache Size: 25600 KB
Memory:
total used free shared buff/cache available
Mem: 31G 14G 10G 107M 6.1G 16G
Swap: 7.7G 343M 7.4G
Graphics:
01:00.0 VGA compatible controller [0300]: NVIDIA Corporation Device [10de:2482] (rev a1)
Subsystem: Lenovo Device [17aa:5050]
Kernel driver in use: nvidia
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.10.1
backcall: 0.2.0
blockdiag: 3.0.0
certifi: 2021.10.8
cftime: 1.6.0
charset-normalizer: 2.0.12
ChimeraX-AddCharge: 1.2.3
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.4.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.39.1
ChimeraX-AtomicLibrary: 7.0
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.1
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.7
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.1
ChimeraX-CommandLine: 1.2.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.4.dev202205060510
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.1.5
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.1.2
ChimeraX-Help: 1.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0
ChimeraX-Label: 1.1.1
ChimeraX-LinuxSupport: 1.0
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.6
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.7
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.5.5
ChimeraX-ModelPanel: 1.3.2
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.2
ChimeraX-OpenCommand: 1.9
ChimeraX-PDB: 2.6.6
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.6
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.8
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.0.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.1
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.18.2
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.26
debugpy: 1.6.0
decorator: 5.1.1
distro: 1.6.0
docutils: 0.17.1
entrypoints: 0.4
filelock: 3.4.2
fonttools: 4.33.3
funcparserlib: 1.0.0
grako: 3.16.5
h5py: 3.6.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.27
imagecodecs: 2021.11.20
imagesize: 1.3.0
ipykernel: 6.6.1
ipython: 7.31.1
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.0.3
jupyter-client: 7.1.0
jupyter-core: 4.10.0
kiwisolver: 1.4.2
line-profiler: 3.4.0
lxml: 4.7.1
lz4: 3.1.10
MarkupSafe: 2.1.1
matplotlib: 3.5.1
matplotlib-inline: 0.1.3
msgpack: 1.0.3
nest-asyncio: 1.5.5
netCDF4: 1.5.8
networkx: 2.6.3
numexpr: 2.8.1
numpy: 1.22.1
openvr: 1.16.802
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.0.1
pip: 21.3.1
pkginfo: 1.8.2
prompt-toolkit: 3.0.29
psutil: 5.9.0
ptyprocess: 0.7.0
pycollada: 0.7.2
pydicom: 2.2.2
Pygments: 2.11.2
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.8
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.2
pytz: 2022.1
pyzmq: 22.3.0
qtconsole: 5.3.0
QtPy: 2.1.0
RandomWords: 0.3.0
requests: 2.27.1
scipy: 1.7.3
setuptools: 59.8.0
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.3.2
sphinx-autodoc-typehints: 1.15.2
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
suds-community: 1.0.0
tables: 3.7.0
tifffile: 2021.11.2
tinyarray: 1.2.4
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.9
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.1
wheel-filename: 1.3.0
Change History (2)
comment:1 by , 14 months ago
| Component: | Unassigned → Core |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash while deleting atoms |
comment:2 by , 14 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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