id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2574 'usage' on an alias fails Tristan Croll Greg Couch "{{{ 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 }}} " defect closed normal Documentation not a bug all ChimeraX