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Opened 6 years ago
Closed 6 years ago
#2574 closed defect (not a bug)
'usage' on an alias fails
| Reported by: | Tristan Croll | Owned by: | Greg Couch |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Documentation | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-3.10.0-957.12.2.el7.x86_64-x86_64-with-centos-7.6.1810-Core
ChimeraX Version: 0.91 (2019-11-13)
Description
The command ~rama is registered as an alias of "rama stop". The command "usage ~rama" fails on first call, but succeeds after I actually use the command.
Log:
Startup Messages
---
warning | 'clip' is a prefix of an existing command 'clipper'
UCSF ChimeraX version: 0.91 (2019-11-13)
© 2016-2019 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
Successfully installed
'ChimeraX_ISOLDE-1.0b3.dev7-cp37-cp37m-linux_x86_64.whl'
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/
Processing
./.cache/ChimeraX/0.91/installers/ChimeraX_ISOLDE-1.0b3.dev7-cp37-cp37m-linux_x86_64.whl
Requirement already satisfied, skipping upgrade: ChimeraX-Core==0.91 in
/opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages (from ChimeraX-
ISOLDE==1.0b3.dev7) (0.91)
Requirement already satisfied, skipping upgrade: ChimeraX-Clipper>=0.9.11 in
./.local/share/ChimeraX/0.91/site-packages (from ChimeraX-ISOLDE==1.0b3.dev7)
(0.9.11)
Requirement already satisfied, skipping upgrade: ChimeraX-Atomic>=1.0 in
/opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages (from ChimeraX-
ISOLDE==1.0b3.dev7) (1.0)
Installing collected packages: ChimeraX-ISOLDE
Found existing installation: ChimeraX-ISOLDE 1.0b3.dev7
Uninstalling ChimeraX-ISOLDE-1.0b3.dev7:
Successfully uninstalled ChimeraX-ISOLDE-1.0b3.dev7
Successfully installed ChimeraX-ISOLDE-1.0b3.dev7
Lock 140571348812176 acquired on
/home/tic20/.cache/ChimeraX/0.91/toolshed/bundle_info.cache.lock
Lock 140571348812176 released on
/home/tic20/.cache/ChimeraX/0.91/toolshed/bundle_info.cache.lock
WARNING: You are using pip version 19.2.3, however version 19.3.1 is
available.
You should consider upgrading via the 'pip install --upgrade pip' command.
> open 3io0 format mmCIF fromDatabase pdb structureFactors true overSampling
3.0
Summary of feedback from opening 3io0 fetched from pdb
---
warning | WARNING: multiple experimental reflection datasets found:
F_meas_au, F_meas_sigma_au,
pdbx_F_plus, pdbx_F_plus_sigma, pdbx_F_minus, pdbx_F_minus_sigma,
pdbx_anom_difference, pdbx_anom_difference_sigma,
intensity_meas, intensity_sigma,
pdbx_I_plus, pdbx_I_plus_sigma, pdbx_I_minus, pdbx_I_minus_sigma
Automatically choosing "intensity_meas, intensity_sigma".
notes | Resolution: 3.003
Reflection data provided as intensities. Performing French & Wilson scaling to
convert to amplitudes...
3io0 title:
Crystal structure of EtuB from Clostridium kluyveri [more info...]
Chain information for 3io0
---
Chain | Description
1.3/A | EtuB protein
3io0 mmCIF Assemblies
---
1| author_and_software_defined_assembly
> usage rota
rota [structures] [report true or false]
— Add rotamer validator markup to models and optionally report current
outliers
rota stop [structures]
— Close the rotamer annotators for the given models (or all if no models
given)
> rota #1 report true
NON-FAVOURED ROTAMERS:
#1.3 A: THR 77 (P=0.0144)
#1.3 A: MET 78 (P=0.0065)
#1.3 A: THR 79 (P=0.0003)
#1.3 A: VAL 82 (P=0.0044)
#1.3 A: THR 89 (P=0.0000)
#1.3 A: VAL 90 (P=0.0000)
#1.3 A: VAL 93 (P=0.0196)
#1.3 A: ASN 96 (P=0.0007)
#1.3 A: LYS 103 (P=0.0005)
#1.3 A: ASP 108 (P=0.0145)
#1.3 A: ASN 109 (P=0.0030)
#1.3 A: THR 110 (P=0.0189)
#1.3 A: ARG 112 (P=0.0000)
#1.3 A: ILE 114 (P=0.0002)
#1.3 A: GLU 132 (P=0.0092)
#1.3 A: VAL 134 (P=0.0074)
#1.3 A: LEU 146 (P=0.0001)
#1.3 A: ARG 148 (P=0.0035)
#1.3 A: THR 150 (P=0.0014)
#1.3 A: LYS 151 (P=0.0117)
#1.3 A: VAL 167 (P=0.0008)
#1.3 A: GLU 175 (P=0.0085)
#1.3 A: LYS 179 (P=0.0000)
#1.3 A: LYS 183 (P=0.0071)
#1.3 A: THR 201 (P=0.0035)
#1.3 A: ARG 203 (P=0.0187)
#1.3 A: SER 205 (P=0.0044)
#1.3 A: LYS 210 (P=0.0059)
#1.3 A: MET 232 (P=0.0174)
#1.3 A: THR 237 (P=0.0120)
#1.3 A: LYS 240 (P=0.0063)
#1.3 A: LEU 246 (P=0.0000)
#1.3 A: THR 253 (P=0.0003)
#1.3 A: LEU 264 (P=0.0136)
#1.3 A: ILE 265 (P=0.0001)
#1.3 A: THR 266 (P=0.0002)
#1.3 A: ILE 267 (P=0.0000)
#1.3 A: GLN 276 (P=0.0082)
#1.3 A: LEU 278 (P=0.0000)
#1.3 A: ARG 282 (P=0.0066)
#1.3 A: LEU 289 (P=0.0000)
#1.3 A: SER 298 (P=0.0021)
#1.3 A: MET 299 (P=0.0001)
#1.3 A: SER 300 (P=0.0159)
#1.3 A: LYS 301 (P=0.0000)
> close #1
Deleting (LIVE) 2mFo-DFc_sharp_29
Deleting (LIVE) mFo-DFc
Deleting (LIVE) 2mFo-DFc
Deleting Crystallographic maps (3io0-sf.cif)
> open 3io0 structureFactors true
Summary of feedback from opening 3io0 fetched from pdb
---
warning | WARNING: multiple experimental reflection datasets found:
F_meas_au, F_meas_sigma_au,
pdbx_F_plus, pdbx_F_plus_sigma, pdbx_F_minus, pdbx_F_minus_sigma,
pdbx_anom_difference, pdbx_anom_difference_sigma,
intensity_meas, intensity_sigma,
pdbx_I_plus, pdbx_I_plus_sigma, pdbx_I_minus, pdbx_I_minus_sigma
Automatically choosing "intensity_meas, intensity_sigma".
notes | Resolution: 3.003
Reflection data provided as intensities. Performing French & Wilson scaling to
convert to amplitudes...
3io0 title:
Crystal structure of EtuB from Clostridium kluyveri [more info...]
Chain information for 3io0
---
Chain | Description
1.3/A | EtuB protein
3io0 mmCIF Assemblies
---
1| author_and_software_defined_assembly
> select up
Nothing selected
> rota #1 report true
NON-FAVOURED ROTAMERS:
#1.3 A: THR 77 (P=0.0144)
#1.3 A: MET 78 (P=0.0065)
#1.3 A: THR 79 (P=0.0003)
#1.3 A: VAL 82 (P=0.0044)
#1.3 A: THR 89 (P=0.0000)
#1.3 A: VAL 90 (P=0.0000)
#1.3 A: VAL 93 (P=0.0196)
#1.3 A: ASN 96 (P=0.0007)
#1.3 A: LYS 103 (P=0.0005)
#1.3 A: ASP 108 (P=0.0145)
#1.3 A: ASN 109 (P=0.0030)
#1.3 A: THR 110 (P=0.0189)
#1.3 A: ARG 112 (P=0.0000)
#1.3 A: ILE 114 (P=0.0002)
#1.3 A: GLU 132 (P=0.0092)
#1.3 A: VAL 134 (P=0.0074)
#1.3 A: LEU 146 (P=0.0001)
#1.3 A: ARG 148 (P=0.0035)
#1.3 A: THR 150 (P=0.0014)
#1.3 A: LYS 151 (P=0.0117)
#1.3 A: VAL 167 (P=0.0008)
#1.3 A: GLU 175 (P=0.0085)
#1.3 A: LYS 179 (P=0.0000)
#1.3 A: LYS 183 (P=0.0071)
#1.3 A: THR 201 (P=0.0035)
#1.3 A: ARG 203 (P=0.0187)
#1.3 A: SER 205 (P=0.0044)
#1.3 A: LYS 210 (P=0.0059)
#1.3 A: MET 232 (P=0.0174)
#1.3 A: THR 237 (P=0.0120)
#1.3 A: LYS 240 (P=0.0063)
#1.3 A: LEU 246 (P=0.0000)
#1.3 A: THR 253 (P=0.0003)
#1.3 A: LEU 264 (P=0.0136)
#1.3 A: ILE 265 (P=0.0001)
#1.3 A: THR 266 (P=0.0002)
#1.3 A: ILE 267 (P=0.0000)
#1.3 A: GLN 276 (P=0.0082)
#1.3 A: LEU 278 (P=0.0000)
#1.3 A: ARG 282 (P=0.0066)
#1.3 A: LEU 289 (P=0.0000)
#1.3 A: SER 298 (P=0.0021)
#1.3 A: MET 299 (P=0.0001)
#1.3 A: SER 300 (P=0.0159)
#1.3 A: LYS 301 (P=0.0000)
> close #1
Deleting (LIVE) mFo-DFc
Deleting (LIVE) 2mFo-DFc
Deleting (LIVE) 2mFo-DFc_sharp_29
Deleting Crystallographic maps (3io0-sf.cif)
> open 3io0
3io0 title:
Crystal structure of EtuB from Clostridium kluyveri [more info...]
Chain information for 3io0 #1
---
Chain | Description
A | EtuB protein
3io0 mmCIF Assemblies
---
1| author_and_software_defined_assembly
> show
> rota #1 report true
NON-FAVOURED ROTAMERS:
#1 A: THR 77 (P=0.0144)
#1 A: MET 78 (P=0.0065)
#1 A: THR 79 (P=0.0003)
#1 A: VAL 82 (P=0.0044)
#1 A: THR 89 (P=0.0000)
#1 A: VAL 90 (P=0.0000)
#1 A: VAL 93 (P=0.0196)
#1 A: ASN 96 (P=0.0007)
#1 A: LYS 103 (P=0.0005)
#1 A: ASP 108 (P=0.0145)
#1 A: ASN 109 (P=0.0030)
#1 A: THR 110 (P=0.0189)
#1 A: ARG 112 (P=0.0000)
#1 A: ILE 114 (P=0.0002)
#1 A: GLU 132 (P=0.0092)
#1 A: VAL 134 (P=0.0074)
#1 A: LEU 146 (P=0.0001)
#1 A: ARG 148 (P=0.0035)
#1 A: THR 150 (P=0.0014)
#1 A: LYS 151 (P=0.0117)
#1 A: VAL 167 (P=0.0008)
#1 A: GLU 175 (P=0.0085)
#1 A: LYS 179 (P=0.0000)
#1 A: LYS 183 (P=0.0071)
#1 A: THR 201 (P=0.0035)
#1 A: ARG 203 (P=0.0187)
#1 A: SER 205 (P=0.0044)
#1 A: LYS 210 (P=0.0059)
#1 A: MET 232 (P=0.0174)
#1 A: THR 237 (P=0.0120)
#1 A: LYS 240 (P=0.0063)
#1 A: LEU 246 (P=0.0000)
#1 A: THR 253 (P=0.0003)
#1 A: LEU 264 (P=0.0136)
#1 A: ILE 265 (P=0.0001)
#1 A: THR 266 (P=0.0002)
#1 A: ILE 267 (P=0.0000)
#1 A: GLN 276 (P=0.0082)
#1 A: LEU 278 (P=0.0000)
#1 A: ARG 282 (P=0.0066)
#1 A: LEU 289 (P=0.0000)
#1 A: SER 298 (P=0.0021)
#1 A: MET 299 (P=0.0001)
#1 A: SER 300 (P=0.0159)
#1 A: LYS 301 (P=0.0000)
> cofr showPivot false
> toolshed show Shell
/opt/UCSF/ChimeraX-daily/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")
> save rota_markup.jpg
> usage rota
rota [structures] [report true or false]
— Add rotamer validator markup to models and optionally report current
outliers
rota stop [structures]
— Close the rotamer annotators for the given models (or all if no models
given)
> usage ~rama
"~rama" is not a command name
> usage ~rota
~rota [optional]
— alias of "rota stop $*"
optional: the rest of line
rota stop [structures]
— Close the rotamer annotators for the given models (or all if no models
given)
> usage rama
rama [structures] [showFavored true or false] [report true or false]
— Add Ramachandran validator markup to models and optionally report current
outliers
rama stop [structures]
— Close the Ramachandran annotators for the given models (or all if no models
given)
> ~rama
> usage ~rama
~rama [optional]
— alias of "rama stop $*"
optional: the rest of line
rama stop [structures]
— Close the Ramachandran annotators for the given models (or all if no models
given)
> usage ~cartoon
~cartoon [optional]
— alias of "cartoon hide $*"
optional: the rest of line
cartoon hide [atoms]
— undisplay cartoon for specified residues
OpenGL version: 3.3.0 NVIDIA 415.27
OpenGL renderer: TITAN Xp/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Change History (4)
comment:1 by , 6 years ago
| Component: | Unassigned → Documentation |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → 'usage' on an alias fails |
comment:2 by , 6 years ago
| Status: | assigned → feedback |
|---|
follow-up: 3 comment:3 by , 6 years ago
You're right - I hadn't done that. But I'm still missing something here.
After adding ~rama to bundle_info.xml and rebuilding, "usage ~rama" in a
fresh session just gives me a blank result. But if I do "usage rama" and
*then* "usage ~rama" I get the command description.
In my bundle_info.xml:
<ChimeraXClassifier>ChimeraX :: Command :: rama :: General :: Live
Ramachandran validation of models</ChimeraXClassifier>
<ChimeraXClassifier>ChimeraX :: Command :: ~rama :: General :: Turn
off live Ramachandran validation of models</ChimeraXClassifier>
... and the actual Python command definition:
def register_rama(logger):
from chimerax.core.commands import (
register, CmdDesc, BoolArg, create_alias
)
from chimerax.atomic import StructuresArg
desc = CmdDesc(
optional=[
('structures', StructuresArg),
],
keyword=[
('show_favored', BoolArg),
('report', BoolArg),
],
synopsis='Add Ramachandran validator markup to models and
optionally report current outliers'
)
register('rama', desc, rama, logger=logger)
undesc = CmdDesc(
optional=[('structures', StructuresArg)],
synopsis='Close the Ramachandran annotators for the given models
(or all if no models given)'
)
register('rama stop', undesc, unrama, logger=logger)
create_alias('~rama', 'rama stop $*', logger=logger)
On 2019-11-14 23:12, ChimeraX wrote:
comment:4 by , 6 years ago
| Resolution: | → not a bug |
|---|---|
| Status: | feedback → closed |
My bad. Forgot I needed to add the alias to register_command() in the bundle init.
Note:
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Did you put ~rama in the bundle_info.xml file? If not, that would explain this behavior.