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#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 pett, 6 years ago

Component:	Unassigned → Documentation
Owner:	set to Greg Couch
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → 'usage' on an alias fails

comment:2 by Greg Couch, 6 years ago

Status:	assigned → feedback

Did you put ~rama in the bundle_info.xml file? If not, that would explain this behavior.

in reply to: 3 ; follow-up: 3 comment:3 by Tristan Croll, 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 Tristan Croll, 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.

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