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Opened 5 years ago
Last modified 5 years ago
#3099 reopened enhancement
auto-wipe some commands?
| Reported by: | Tristan Croll | Owned by: | pett |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Command Line | Version: | |
| Keywords: | Cc: | Elaine Meng | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-3.10.0-1062.9.1.el7.x86_64-x86_64-with-centos-7.7.1908-Core
ChimeraX Version: 0.93 (2020-04-03)
Description
Just a thought: certain commands (in particular, "del selAtoms") can be really dangerous if accidentally repeated (by hitting return with them still in the command bar). Might be a good idea if those wipe themselves from the command history so they have to be explicitly typed every time?
Log:
Startup Messages
---
warning | 'clip' is a prefix of an existing command 'clipper'
UCSF ChimeraX version: 0.93 (2020-04-03)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 6jyt_refine_3.pdb
Summary of feedback from opening 6jyt_refine_3.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK Date 2020-04-21 Time 18:02:55 BST +0100 (1587488575.81 s)
Ignored bad PDB record found on line 2
REMARK PHENIX refinement
Ignored bad PDB record found on line 4
REMARK ****************** INPUT FILES AND LABELS
******************************
Ignored bad PDB record found on line 5
REMARK Reflections:
Ignored bad PDB record found on line 6
REMARK file name :
/run/media/tic20/storage/structure_dump/covid-19/sars/6jyt/6jyt.mtz
56 messages similar to the above omitted
Chain information for 6jyt_refine_3.pdb #1
---
Chain | Description
A | No description available
B | No description available
> isolde start
> set selectionWidth 4
Chain information for 6jyt_refine_3.pdb
---
Chain | Description
1.2/A | No description available
1.2/B | No description available
Done loading forcefield
WARNING: found multiple possible R-free arrays:
(dataset) R-free-flags,
(dataset) R-free-flags-1
Automatically choosing "(dataset) R-free-flags". If this is incorrect, please
either provide a file with a single flag array, or load the file again using
the free_flag_label argument.
> set bgColor white
> addh
Summary of feedback from adding hydrogens to 6jyt_refine_3.pdb #1.2
---
warnings | Not adding hydrogens to /B THR 188 CB because it is missing heavy-
atom bond partners
Unknown hybridization for atom (SE) of residue type MSE; not adding hydrogens
to it
notes | No usable SEQRES records for 6jyt_refine_3.pdb (#1.2) chain A;
guessing termini instead
No usable SEQRES records for 6jyt_refine_3.pdb (#1.2) chain B; guessing
termini instead
Chain-initial residues that are actual N termini: /A ASN -1, /B ASN -1
Chain-initial residues that are not actual N termini: /A THR 351, /B SER 350
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini: /A ASN 596, /A PRO 335, /B
ASN 596, /B VAL 340
1082 hydrogen bonds
Adding 'H' to /A THR 351
Adding 'H' to /B SER 350
/A ASN 596 is not terminus, removing H atom from 'C'
/A PRO 335 is not terminus, removing H atom from 'C'
/B ASN 596 is not terminus, removing H atom from 'C'
/B VAL 340 is not terminus, removing H atom from 'C'
9162 hydrogens added
> hide HC
> select :ZN
6 atoms, 1 model selected
> delete sel
> delete sel
> delete sel
> select #1
18354 atoms, 18516 bonds, 4 pseudobonds, 25 models selected
> select clear
> open2
> /run/media/tic20/storage/structure_dump/covid-19/mers/5wwp/Refine_2/5wwp_refine_2.pdb
Summary of feedback from opening <_io.textiowrapper
name="/run/media/tic20/storage/structure_dump/covid-19/mers/5wwp/Refine_2/5wwp_refine_2.pdb"
mode="rt" encoding="utf-8">
---
warnings | Ignored bad PDB record found on line 1
REMARK Date 2020-04-22 Time 19:00:08 BST +0100 (1587578408.41 s)
Ignored bad PDB record found on line 2
REMARK PHENIX refinement
Ignored bad PDB record found on line 4
REMARK ****************** INPUT FILES AND LABELS
******************************
Ignored bad PDB record found on line 5
REMARK Reflections:
Ignored bad PDB record found on line 6
REMARK file name :
/run/media/tic20/storage/structure_dump/covid-19/mers/5wwp/5wwp.mtz
72 messages similar to the above omitted
Chain information for 5wwp_refine_2.pdb #2
---
Chain | Description
A | No description available
B | No description available
> matchmaker #2/A to #1/A
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6jyt_refine_3.pdb, chain A (#1.2) with 5wwp_refine_2.pdb, chain A
(#2), sequence alignment score = 1865.5
RMSD between 375 pruned atom pairs is 0.913 angstroms; (across all 498 pairs:
1.884)
> isolde restrain torsions #1/A:439-600 templateResidues #2/A angleRange 120
> isolde restrain torsions #1/B:439-600 templateResidues #2/A angleRange 120
> isolde restrain distances #1/B:439-600 templateAtoms #2/A
RMSD between 156 pruned atom pairs is 1.638 angstroms; (across all 158 pairs:
1.750)
> isolde restrain distances #1/A:439-600 templateAtoms #2/A
RMSD between 156 pruned atom pairs is 1.541 angstroms; (across all 158 pairs:
1.787)
> hide #1.2.6 models
> hide #1.2.5 models
> hide #!2 models
> close #1.2.5-6
> movie record
> show #!2 models
> isolde restrain distances #1/A:439-600 templateAtoms #2/A
RMSD between 156 pruned atom pairs is 1.541 angstroms; (across all 158 pairs:
1.787)
> isolde restrain distances #1/B:439-600 templateAtoms #2/A
RMSD between 156 pruned atom pairs is 1.638 angstroms; (across all 158 pairs:
1.750)
> isolde restrain torsions #1/A:439-600 templateResidues #2/A angleRange 120
> isolde restrain torsions #1/B:439-600 templateResidues #2/A angleRange 120
> select #1/A,B:439-600
5012 atoms, 5058 bonds, 1 model selected
> isolde adjust distances #1 displayThreshold 0.5
Loading residue template for SO4 from internal database
> select clear
> select clear
> isolde release distances #1/A
> isolde restrain distances #1/A:439-600 templateAtoms #2/A
RMSD between 156 pruned atom pairs is 0.544 angstroms; (across all 158 pairs:
1.192)
> isolde adjust distances #1 displayThreshold 0.5
Updating bulk solvent parameters...
> select clear
> movie stop
> movie reset
> close #1.2.5-6
> hide #!2 models
> movie record
> hide ~@CA
> show #!2 models
> show #1&~HC
> isolde restrain distances #1/A:439-600 templateAtoms #2/A kappa 50
RMSD between 156 pruned atom pairs is 1.541 angstroms; (across all 158 pairs:
1.787)
> isolde restrain distances #1/B:439-600 templateAtoms #2/A kappa 50
RMSD between 156 pruned atom pairs is 1.638 angstroms; (across all 158 pairs:
1.750)
> isolde restrain torsions #1/A:439-600 templateResidues #2/A angleRange 120
> isolde restrain torsions #1/B:439-600 templateResidues #2/A angleRange 120
> hide ~@CA
> hide #!2 models
> select #1:439-600
5012 atoms, 5058 bonds, 1 model selected
> select clear
> show #1&~HC
> isolde adjust distances #1 displayThreshold 0.5
> show #!2 models
> movie stop
> movie encode restrain_to_5wwp.mp4
Movie saved to restrain_to_5wwp.mp4
> select up
24 atoms, 23 bonds, 1 model selected
> select up
210 atoms, 211 bonds, 1 model selected
> isolde release torsions sel
> isolde release distances sel
Updating bulk solvent parameters...
> select clear
> show #1&~HC
Updating bulk solvent parameters...
> delete sel
> select #1/B:436-600
2562 atoms, 2586 bonds, 1 model selected
> hide #!2 models
> select clear
> isolde release distances sel
> isolde release torsions sel
> isolde release distances #1/B
> isolde restrain distances #1/B:439-600 templateAtoms #2/A kappa 50
RMSD between 151 pruned atom pairs is 1.175 angstroms; (across all 156 pairs:
1.588)
RMSD between 5 pruned atom pairs is 3.095 angstroms; (across all 5 pairs:
3.095)
> isolde adjust distances #1 displayThreshold 0.5
> isolde release distances sel
> isolde release torsions sel
> isolde release distances sel
> isolde release torsions sel
> select clear
> isolde release distances #1/B
> isolde restrain distances #1/B:439-600 templateAtoms #2/A
RMSD between 150 pruned atom pairs is 0.242 angstroms; (across all 156 pairs:
1.270)
RMSD between 6 pruned atom pairs is 3.234 angstroms; (across all 6 pairs:
3.234)
> isolde adjust distances #1 displayThreshold 0.5
> select up
20 atoms, 20 bonds, 1 model selected
> isolde release distances sel
> isolde release distances #1/B
> isolde restrain distances #1/B:439-600 templateAtoms #2/A
RMSD between 150 pruned atom pairs is 0.618 angstroms; (across all 156 pairs:
1.394)
RMSD between 6 pruned atom pairs is 3.204 angstroms; (across all 6 pairs:
3.204)
> isolde release distances sel
> isolde release distances #1/B
Updating bulk solvent parameters...
> select #1
18292 atoms, 18454 bonds, 4 pseudobonds, 31 models selected
Map is too large for fast cubic interpolation on the GPU! Switching to slower,
more memory-efficient implementation.
> select clear
> select clear
> isolde release distances #1/A
> isolde restrain distances #1/A:439-600 templateAtoms #2/A
RMSD between 155 pruned atom pairs is 0.722 angstroms; (across all 155 pairs:
0.722)
> select clear
> isolde release distances #1/A
Updating bulk solvent parameters...
> save working.pdb #1
> view /B:188
> close #1
Deleting atomic symmetry model...
Deleting atomic symmetry model...
Chain information for 5wwp_refine_2.pdb
---
Chain | Description
1.2/A | No description available
1.2/B | No description available
Deleting (LIVE) mFo-DFc
Deleting (LIVE) MDFF potential
Deleting (LIVE) 2mFo-DFc
Deleting (LIVE) 2mFo-DFc_sharp_22
Deleting Crystallographic maps (6jyt.mtz)
> close #1
Deleting atomic symmetry model...
> open2
> /run/media/tic20/storage/structure_dump/covid-19/sars/6jyt/Refine_4/6jyt_refine_4.pdb
Summary of feedback from opening <_io.textiowrapper
name="/run/media/tic20/storage/structure_dump/covid-19/sars/6jyt/Refine_4/6jyt_refine_4.pdb"
mode="rt" encoding="utf-8">
---
warnings | Ignored bad PDB record found on line 1
REMARK Date 2020-04-23 Time 09:40:22 BST +0100 (1587631222.72 s)
Ignored bad PDB record found on line 2
REMARK PHENIX refinement
Ignored bad PDB record found on line 4
REMARK ****************** INPUT FILES AND LABELS
******************************
Ignored bad PDB record found on line 5
REMARK Reflections:
Ignored bad PDB record found on line 6
REMARK file name :
/run/media/tic20/storage/structure_dump/covid-19/sars/6jyt/6jyt.mtz
60 messages similar to the above omitted
Chain information for 6jyt_refine_4.pdb #1
---
Chain | Description
A | No description available
B | No description available
Chain information for 6jyt_refine_4.pdb
---
Chain | Description
1.2/A | No description available
1.2/B | No description available
> dssp
WARNING: found multiple possible R-free arrays:
(dataset) R-free-flags,
(dataset) R-free-flags-1
Automatically choosing "(dataset) R-free-flags". If this is incorrect, please
either provide a file with a single flag array, or load the file again using
the free_flag_label argument.
> open2
> /run/media/tic20/storage/structure_dump/covid-19/mers/5wwp/Refine_2/5wwp_refine_2.pdb
Summary of feedback from opening <_io.textiowrapper
name="/run/media/tic20/storage/structure_dump/covid-19/mers/5wwp/Refine_2/5wwp_refine_2.pdb"
mode="rt" encoding="utf-8">
---
warnings | Ignored bad PDB record found on line 1
REMARK Date 2020-04-22 Time 19:00:08 BST +0100 (1587578408.41 s)
Ignored bad PDB record found on line 2
REMARK PHENIX refinement
Ignored bad PDB record found on line 4
REMARK ****************** INPUT FILES AND LABELS
******************************
Ignored bad PDB record found on line 5
REMARK Reflections:
Ignored bad PDB record found on line 6
REMARK file name :
/run/media/tic20/storage/structure_dump/covid-19/mers/5wwp/5wwp.mtz
72 messages similar to the above omitted
Chain information for 5wwp_refine_2.pdb #2
---
Chain | Description
A | No description available
B | No description available
> select #1
18292 atoms, 18454 bonds, 4 pseudobonds, 25 models selected
> select clear
> isolde restrain torsions #1/A:439-600 templateResidues #2/A
> isolde restrain torsions #1/A:439-600 templateResidues #2/A angleRange 120
> isolde restrain torsions #1/B:439-600 templateResidues #2/A angleRange 120
> select #1
18292 atoms, 18454 bonds, 4 pseudobonds, 26 models selected
Map is too large for fast cubic interpolation on the GPU! Switching to slower,
more memory-efficient implementation.
> select clear
> isolde restrain distances #1/B:439-600 templateAtoms #2/A
RMSD between 150 pruned atom pairs is 0.626 angstroms; (across all 156 pairs:
1.387)
RMSD between 5 pruned atom pairs is 2.303 angstroms; (across all 6 pairs:
3.516)
> isolde restrain distances #1/A:439-600 templateAtoms #2/A
RMSD between 155 pruned atom pairs is 0.801 angstroms; (across all 155 pairs:
0.801)
Updating bulk solvent parameters...
> sequence chain /A
Chains must have same sequence
> sequence chain #1/A
Alignment identifier is 1.2.A
> view sel
Updating bulk solvent parameters...
> isolde add water
> color sel bychain
> color sel byhetero
> isolde sim start sel
Updating bulk solvent parameters...
> toolshed show Shell
/opt/UCSF/ChimeraX/lib/python3.7/site-packages/IPython/core/history.py:226:
UserWarning: IPython History requires SQLite, your history will not be saved
warn("IPython History requires SQLite, your history will not be saved")
Updating bulk solvent parameters...
> isolde add water
> color sel bychain
> color sel byhetero
> isolde sim start sel
Updating bulk solvent parameters...
> isolde add water
> color sel bychain
> color sel byhetero
> isolde sim start sel
Updating bulk solvent parameters...
> isolde add ligand SO4
> color sel bychain
> color sel byhetero
Updating bulk solvent parameters...
> isolde add water
> color sel bychain
> color sel byhetero
> isolde sim start sel
Updating bulk solvent parameters...
> isolde add water
> color sel bychain
> color sel byhetero
> isolde sim start sel
Updating bulk solvent parameters...
> isolde add water
> color sel bychain
> color sel byhetero
> isolde sim start sel
Updating bulk solvent parameters...
> select clear
> isolde add water
> color sel bychain
> color sel byhetero
> isolde sim start sel
Updating bulk solvent parameters...
Updating bulk solvent parameters...
Updating bulk solvent parameters...
> isolde add water
> color sel bychain
> color sel byhetero
> isolde sim start sel
Updating bulk solvent parameters...
> select up
3 atoms, 2 bonds, 1 model selected
> delete sel
Updating bulk solvent parameters...
> isolde add water
> color sel bychain
> color sel byhetero
> isolde sim start sel
> select clear
Updating bulk solvent parameters...
> isolde add water
> color sel bychain
> color sel byhetero
> isolde sim start sel
Updating bulk solvent parameters...
> isolde add water
> color sel bychain
> color sel byhetero
> isolde sim start sel
Updating bulk solvent parameters...
> isolde add water
> color sel bychain
> color sel byhetero
> isolde sim start sel
Updating bulk solvent parameters...
> isolde add water
> color sel bychain
> color sel byhetero
> isolde sim start sel
Updating bulk solvent parameters...
> isolde add water
> color sel bychain
> color sel byhetero
> isolde sim start sel
Updating bulk solvent parameters...
> isolde add water
> color sel bychain
> color sel byhetero
> isolde sim start sel
Updating bulk solvent parameters...
> isolde add water
> color sel bychain
> color sel byhetero
> isolde sim start sel
Updating bulk solvent parameters...
> isolde add water
> color sel bychain
> color sel byhetero
> isolde sim start sel
Updating bulk solvent parameters...
> select up
3 atoms, 2 bonds, 1 model selected
> delete sel
Updating bulk solvent parameters...
> isolde add water
> color sel bychain
> color sel byhetero
> isolde sim start sel
Updating bulk solvent parameters...
Updating bulk solvent parameters...
> isolde add water
> color sel bychain
> color sel byhetero
> isolde sim start sel
Updating bulk solvent parameters...
> select up
3 atoms, 2 bonds, 1 model selected
> delete sel
> isolde add water
> color sel bychain
> color sel byhetero
> isolde sim start sel
Updating bulk solvent parameters...
Updating bulk solvent parameters...
> isolde add water
> color sel bychain
> color sel byhetero
> isolde sim start sel
Updating bulk solvent parameters...
> select up
3 atoms, 2 bonds, 1 model selected
> delete sel
> isolde add water
> color sel bychain
> color sel byhetero
> isolde sim start sel
Updating bulk solvent parameters...
> isolde add water
> color sel bychain
> color sel byhetero
> isolde sim start sel
Updating bulk solvent parameters...
> isolde add water
> color sel bychain
> color sel byhetero
> isolde sim start sel
Updating bulk solvent parameters...
> select up
3 atoms, 2 bonds, 1 model selected
> delete sel
> delete sel
> isolde add water
> color sel bychain
> color sel byhetero
> isolde sim start sel
Updating bulk solvent parameters...
Updating bulk solvent parameters...
> isolde add water
> color sel bychain
> color sel byhetero
> isolde sim start sel
Updating bulk solvent parameters...
> isolde add water
> color sel bychain
> color sel byhetero
> isolde sim start sel
Updating bulk solvent parameters...
> isolde add water
> color sel bychain
> color sel byhetero
> isolde sim start sel
Updating bulk solvent parameters...
> isolde add water
> color sel bychain
> color sel byhetero
> isolde sim start sel
Updating bulk solvent parameters...
> select up
3 atoms, 2 bonds, 1 model selected
> delete sel
> isolde add water
> color sel bychain
> color sel byhetero
> isolde sim start sel
Updating bulk solvent parameters...
> isolde add water
> color sel bychain
> color sel byhetero
> isolde sim start sel
Updating bulk solvent parameters...
> isolde add water
> color sel bychain
> color sel byhetero
> isolde sim start sel
Updating bulk solvent parameters...
Updating bulk solvent parameters...
> isolde add water
> color sel bychain
> color sel byhetero
> isolde sim start sel
Updating bulk solvent parameters...
> select up
3 atoms, 2 bonds, 1 model selected
> delete sel
> isolde add water
> color sel bychain
> color sel byhetero
> isolde sim start sel
Updating bulk solvent parameters...
> select up
3 atoms, 2 bonds, 1 model selected
> delete sel
Updating bulk solvent parameters...
Updating bulk solvent parameters...
> select clear
Updating bulk solvent parameters...
Updating bulk solvent parameters...
> isolde add water
> color sel bychain
> color sel byhetero
> isolde sim start sel
Updating bulk solvent parameters...
Updating bulk solvent parameters...
> select clear
OpenGL version: 3.3.0 NVIDIA 440.33.01
OpenGL renderer: TITAN Xp/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: Precision T5600
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
CPU: 32 Intel(R) Xeon(R) CPU E5-2687W 0 @ 3.10GHz
Cache Size: 20480 KB
Graphics:
03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP102 [TITAN Xp] [10de:1b02] (rev a1)
Subsystem: NVIDIA Corporation Device [10de:11df]
Kernel driver in use: nvidia
Change History (9)
comment:1 by , 5 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Command Line |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → auto-wipe some commands? |
| Type: | defect → enhancement |
comment:2 by , 5 years ago
| Status: | accepted → feedback |
|---|
follow-up: 3 comment:3 by , 5 years ago
Yes, I am. As for why? Because I started doing so before the Actions menu existed, and didn't realise that option had been added! On 2020-04-23 16:45, ChimeraX wrote:
comment:4 by , 5 years ago
| Resolution: | → wontfix |
|---|---|
| Status: | feedback → closed |
Yeah, actually neither the Actions menu nor the toolbar icons use the 'selAtoms' selector anymore because it's dangerous and confusing and we don't want people to be using it -- which would happen as people saw it in the corresponding logged commands. Though still legal, it has been removed from the documentation. I would recommend "del sel" rather than "del selAtoms" now.
--Eric
follow-up: 5 comment:5 by , 5 years ago
Actually, what I do type is "del sel"... but I thought that was just shorthand for "delete selAtoms". Is it not? There's still the same problem, though: if "del sel" is sitting in the command line, it can be a bit of a bomb waiting to go off when the user selects some atoms and absent-mindedly bumps the enter key. I've done it to myself a couple of times. On 2020-04-23 17:12, ChimeraX wrote:
comment:6 by , 5 years ago
No "sel" is not short for "selAtoms". They are different. "del sel" with nothing selected will do nothing. "del selAtoms" with nothing selected will delete all atoms.
follow-up: 7 comment:7 by , 5 years ago
"sel" means current atom selection, period. Much more dangerous is "selAtoms" which means current atom selection, or if none, all atoms. It stil works but has been expunged from documentation.
comment:8 by , 5 years ago
| Resolution: | wontfix |
|---|---|
| Status: | closed → reopened |
Yeah, we're not fans of this particular paternalistic behavior. I mean the converse scenario is that you select some residues, type "del sel", select some other residues, go to the command line and the command you wanted to repeat is mysteriously gone.
I _suppose_ I could make it a preference to not enter some commands into the command history.
follow-up: 9 comment:9 by , 5 years ago
Fair call. It's of course minor in the grand scheme of things. Possibly better to just advise people not to do irreversible things via the command line unless they're *really* sure of themselves. On 2020-04-23 17:28, ChimeraX wrote:
Note:
See TracTickets
for help on using tickets.
You are not actually typing the command "del selAtoms", are you? If so, why?
Typically you would only get that command in the command line if you used Actions→Atoms/Bonds→Delete and had changed your command line "Typed Commands Only" setting to false (it defaults true).