Opened 4 years ago

Last modified 4 years ago

#5034 assigned defect

Error in warning message when alias overridden

Reported by: Tristan Croll Owned by: Greg Couch
Priority: normal Milestone:
Component: Command Line Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-3.10.0-1160.25.1.el7.x86_64-x86_64-with-glibc2.17
ChimeraX Version: 1.3.dev202108040454 (2021-08-04 04:54:51 UTC)
Description
Overriding an alias with a new one causes a traceback in the warning message.

Log:
> alias preview_toolshed toolshed url https://cxtoolshed-
> preview.rbvi.ucsf.edu; toolshed reload available

> alias production_toolshed toolshed url https://cxtoolshed.rbvi.ucsf.edu;
> toolshed reload available

> isolde shorthand
    
    
    Initialising ISOLDE-specific command aliases:
    Alias	Equivalent full command
    -------------------------------------------------
    st	isolde step {arguments}
    aw	isolde add water {arguments}
    awsf	isolde add water {arguments} sim false
    al	isolde add ligand {arguments}
    aa	isolde add aa $1 sel {arguments}
    ht	isolde mod his sel {arguments}
    so	setattr sel atoms occupancy {arguments}
    ab	isolde adjust bfactors {arguments}
    ss	isolde sim start sel
    rt	isolde release torsions sel {arguments}
    rd	isolde release distances sel {arguments}
    ra	rd; rt
    pf	isolde pepflip sel
    cf	isolde cisflip sel
    cbb	color bfactor {arguments}
    cbo	color byattr occupancy {arguments}
    cbc	color bychain; color byhet
    cs	clipper set contourSensitivity {arguments}
    

  
UCSF ChimeraX version: 1.3.dev202108040454 (2021-08-04)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open MyD88_20190909_refine_133.pdb

Summary of feedback from opening MyD88_20190909_refine_133.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK Date 2019-09-09 Time 10:43:28 W. Europe Summer Time +0200
(1568018608.44 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 :
C:\Users\macl1978\Dropbox\MyD88\mr_test\MyD88_ALL_20190718_scaled3_C2.mtz  
  
46 messages similar to the above omitted  
  
Chain information for MyD88_20190909_refine_133.pdb #1  
---  
Chain | Description  
A | No description available  
  

> open
> /run/media/tic20/storage/structure_dump/aus/brisbane/kobe/MyD88/reflections.mtz

Summary of feedback from opening
/run/media/tic20/storage/structure_dump/aus/brisbane/kobe/MyD88/reflections.mtz  
---  
note | Reflection data provided as intensities. Performing French & Wilson
scaling to convert to amplitudes...  
  
Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 50,40,38, pixel
0.688,0.646,0.679, shown at level 0.195, step 1, values float32  
Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 50,40,38, pixel
0.688,0.646,0.679, shown at level -0.0737,0.0737, step 1, values float32  
Opened (LIVE) 2mFo-DFc_sharp_29 as #1.1.1.4, grid size 50,40,38, pixel
0.688,0.646,0.679, shown at level 0.306, step 1, values float32  
Chain information for MyD88_20190909_refine_133.pdb  
---  
Chain | Description  
1.2/A | No description available  
  
Opened crystallographic dataset from
/run/media/tic20/storage/structure_dump/aus/brisbane/kobe/MyD88/reflections.mtz  
Found experimental reflection data:  
(dataset) IMEAN, SIGIMEAN  
French and Wilson Amplitudes  
Rwork: 0.3436; Rfree: 0.3985  
Generated maps:  
Reflection Data  
(LIVE) 2mFo-DFc  
(LIVE) mFo-DFc  
(LIVE) 2mFo-DFc_sharp_29  
Any unwanted maps may be safely closed via the Model panel.  

> set bgColor white

> isolde start

> set selectionWidth 4

Opened (LIVE) MDFF potential as #1.1.1.5, grid size 50,40,38, pixel
0.688,0.646,0.679, shown at level 0.172, step 1, values float32  
Done loading forcefield  

> close #1.1

Deleting Crystallographic maps (reflections.mtz)  
Deleting (LIVE) 2mFo-DFc  
Deleting (LIVE) mFo-DFc  
Deleting (LIVE) 2mFo-DFc_sharp_29  
Deleting (LIVE) MDFF potential  
Reflection data provided as intensities. Performing French & Wilson scaling to
convert to amplitudes...  
Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 50,40,38, pixel
0.688,0.646,0.679, shown at level 0.195, step 1, values float32  
Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 50,40,38, pixel
0.688,0.646,0.679, shown at level -0.0737,0.0737, step 1, values float32  
Opened (LIVE) 2mFo-DFc_sharp_29 as #1.1.1.4, grid size 50,40,38, pixel
0.688,0.646,0.679, shown at level 0.306, step 1, values float32  
Opened (LIVE) MDFF potential as #1.1.1.5, grid size 50,40,38, pixel
0.688,0.646,0.679, shown at level 0.172, step 1, values float32  

> select clear

> addh

Summary of feedback from adding hydrogens to MyD88_20190909_refine_133.pdb
#1.2  
---  
notes | No usable SEQRES records for MyD88_20190909_refine_133.pdb (#1.2)
chain A; guessing termini instead  
Chain-initial residues that are actual N termini: /A GLU 159  
Chain-initial residues that are not actual N termini: /A ARG 251  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A LEU 295, /A SER 242  
79 hydrogen bonds  
Adding 'H' to /A ARG 251  
/A LEU 295 is not terminus, removing H atom from 'C'  
1086 hydrogens added  
  
Phi indices max:1088 min: 2  
Psi indices max:1096 min: 17  
ISOLDE: started sim  

> select clear

Updating bulk solvent parameters...  
ISOLDE: stopped sim  

> select #1

2157 atoms, 2179 bonds, 1 pseudobond, 129 residues, 32 models selected  
Phi indices max:2129 min: 2  
Psi indices max:2138 min: 17  
ISOLDE: started sim  

> select clear

> st first

ISOLDE: paused sim  
ISOLDE: resumed sim  
ISOLDE: paused sim  

> stst

Unknown command: stst  

> st

[Repeated 7 time(s)]

> select clear

> st

[Repeated 2 time(s)]

> view /A:282

ISOLDE: resumed sim  

> st

ISOLDE: paused sim  

> st

[Repeated 1 time(s)]ISOLDE: resumed sim  
ISOLDE: paused sim  

> st

[Repeated 3 time(s)]ISOLDE: resumed sim  
ISOLDE: paused sim  

> st

[Repeated 1 time(s)]ISOLDE: resumed sim  
ISOLDE: paused sim  

> st

[Repeated 4 time(s)]ISOLDE: resumed sim  
ISOLDE: paused sim  
ISOLDE: resumed sim  
ISOLDE: paused sim  

> st

[Repeated 2 time(s)]ISOLDE: resumed sim  
ISOLDE: paused sim  
ISOLDE: resumed sim  

> select clear

[Repeated 1 time(s)]ISOLDE: paused sim  

> st

[Repeated 1 time(s)]

> select clear

ISOLDE: resumed sim  
ISOLDE: paused sim  

> st

[Repeated 1 time(s)]

> select clear

> st

[Repeated 2 time(s)]ISOLDE: resumed sim  
ISOLDE: paused sim  

> st

[Repeated 3 time(s)]ISOLDE: resumed sim  
ISOLDE: paused sim  

> st

[Repeated 8 time(s)]ISOLDE: resumed sim  
ISOLDE: paused sim  

> st

[Repeated 2 time(s)]ISOLDE: resumed sim  
ISOLDE: paused sim  

> st

[Repeated 1 time(s)]ISOLDE: resumed sim  
ISOLDE: paused sim  

> st

[Repeated 7 time(s)]ISOLDE: resumed sim  
ISOLDE: paused sim  

> st

[Repeated 16 time(s)]ISOLDE: resumed sim  
ISOLDE: paused sim  

> st

[Repeated 4 time(s)]ISOLDE: resumed sim  
ISOLDE: paused sim  

> st

ISOLDE: resumed sim  
ISOLDE: paused sim  

> st

[Repeated 6 time(s)]ISOLDE: resumed sim  
ISOLDE: paused sim  

> st

[Repeated 3 time(s)]ISOLDE: resumed sim  
ISOLDE: paused sim  

> st

[Repeated 4 time(s)]ISOLDE: resumed sim  
ISOLDE: paused sim  

> st

[Repeated 4 time(s)]ISOLDE: resumed sim  
ISOLDE: paused sim  

> st

[Repeated 7 time(s)]ISOLDE: resumed sim  
ISOLDE: paused sim  

> st

[Repeated 7 time(s)]ISOLDE: resumed sim  
ISOLDE: paused sim  

> st

[Repeated 6 time(s)]Updating bulk solvent parameters...  
ISOLDE: stopped sim  

> cd demo

Current working directory is:
/run/media/tic20/storage/structure_dump/aus/brisbane/kobe/MyD88/demo  

> isolde write phenixRefineInput #1 numProcessors 12

> save MyD88_20190909_refine_133.pdb_for_phenix.cif #1.2 selectedOnly true

Not saving entity_poly_seq for non-authoritative sequences  

> save MyD88_20190909_refine_133.pdb_for_phenix.mtz #1.1.1

Writing data to: '/*/*/[FOBS, SIGFOBS]'  
A phenix.refine input file refine.eff with settings recommended for ISOLDE
models has been written to
/run/media/tic20/storage/structure_dump/aus/brisbane/kobe/MyD88/demo along
with a current snapshot of your model
(MyD88_20190909_refine_133.pdb_for_phenix.cif) and reflections
(MyD88_20190909_refine_133.pdb_for_phenix.mtz). Note that the reflections file
only contains amplitudes - if you have a MTZ file with intensities you may
wish to edit refine.eff to substitute that. You can start a refinement job by
running the following command in the working directory:  
phenix.refine refine.eff.  

> ui tool show Shell

> isolde write phenixRefineInput #1 numProcessors 12

> save MyD88_20190909_refine_133.pdb_for_phenix.cif #1.2 selectedOnly true

Not saving entity_poly_seq for non-authoritative sequences  

> save MyD88_20190909_refine_133.pdb_for_phenix.mtz #1.1.1

Writing data to: '/*/*/[FOBS, SIGFOBS]'  
A phenix.refine input file refine.eff with settings recommended for ISOLDE
models has been written to
/run/media/tic20/storage/structure_dump/aus/brisbane/kobe/MyD88/demo along
with a current snapshot of your model
(MyD88_20190909_refine_133.pdb_for_phenix.cif) and reflections
(MyD88_20190909_refine_133.pdb_for_phenix.mtz). Note that the reflections file
only contains amplitudes - if you have a MTZ file with intensities you may
wish to edit refine.eff to substitute that. You can start a refinement job by
running the following command in the working directory:  
phenix.refine refine.eff.  

> close #1

Deleting Crystallographic maps (reflections.mtz)  
Deleting (LIVE) 2mFo-DFc  
Deleting (LIVE) mFo-DFc  
Deleting (LIVE) 2mFo-DFc_sharp_29  
Deleting (LIVE) MDFF potential  

> open
> /run/media/tic20/storage/structure_dump/aus/brisbane/kobe/MyD88/demo/MyD88_20190909_refine_133.pdb_for_phenix_refine_001.cif

Summary of feedback from opening
/run/media/tic20/storage/structure_dump/aus/brisbane/kobe/MyD88/demo/MyD88_20190909_refine_133.pdb_for_phenix_refine_001.cif  
---  
warnings | Skipping chem_comp category: Missing column 'type' near line 176  
Missing entity information. Treating each chain as a separate entity.  
Bad residue range for struct_conf "1" near line 125  
Bad residue range for struct_conf "2" near line 126  
Bad residue range for struct_conf "3" near line 127  
Bad residue range for struct_conf "4" near line 128  
Bad residue range for struct_conf "5" near line 129  
3 messages similar to the above omitted  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
  
Chain information for MyD88_20190909_refine_133.pdb_for_phenix_refine_001.cif
#1  
---  
Chain | Description  
A | No description available  
  
Chain information for MyD88_20190909_refine_133.pdb_for_phenix_refine_001.cif  
---  
Chain | Description  
1.2/A | No description available  
  

> dssp

Reflection data provided as intensities. Performing French & Wilson scaling to
convert to amplitudes...  
Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 50,40,38, pixel
0.688,0.646,0.679, shown at level 0.403, step 1, values float32  
Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 50,40,38, pixel
0.688,0.646,0.679, shown at level -0.164,0.164, step 1, values float32  
Opened (LIVE) 2mFo-DFc_sharp_29 as #1.1.1.4, grid size 50,40,38, pixel
0.688,0.646,0.679, shown at level 0.744, step 1, values float32  
Opened (LIVE) MDFF potential as #1.1.1.5, grid size 50,40,38, pixel
0.688,0.646,0.679, shown at level 0.401, step 1, values float32  

> open
> /run/media/tic20/storage/structure_dump/aus/brisbane/kobe/MyD88/demo/MyD88_20190909_refine_133.pdb_for_phenix.cif

Summary of feedback from opening
/run/media/tic20/storage/structure_dump/aus/brisbane/kobe/MyD88/demo/MyD88_20190909_refine_133.pdb_for_phenix.cif  
---  
warnings | Unknown polymer entity '1' near line 123  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
  
Chain information for MyD88_20190909_refine_133.pdb_for_phenix.cif #2  
---  
Chain | Description  
A | ?  
  

> show #2

> close #2

> select clear

> addh

Summary of feedback from adding hydrogens to
MyD88_20190909_refine_133.pdb_for_phenix_refine_001.cif #1.2  
---  
notes | No usable SEQRES records for
MyD88_20190909_refine_133.pdb_for_phenix_refine_001.cif (#1.2) chain A;
guessing termini instead  
Chain-initial residues that are actual N termini: /A GLU 159  
Chain-initial residues that are not actual N termini: /A ARG 251  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A LEU 295, /A SER 242  
117 hydrogen bonds  
Adding 'H' to /A ARG 251  
/A LEU 295 is not terminus, removing H atom from 'C'  
1089 hydrogens added  
  

> select clear

Phi indices max:1813 min: 68  
Psi indices max:1830 min: 86  
ISOLDE: started sim  

> select clear

Updating bulk solvent parameters...  
ISOLDE: stopped sim  
Phi indices max:1939 min: 85  
Psi indices max:1956 min: 103  
ISOLDE: started sim  
Updating bulk solvent parameters...  
ISOLDE: stopped sim  

> st first

> st

[Repeated 5 time(s)]

> select #1

2157 atoms, 2179 bonds, 1 pseudobond, 129 residues, 32 models selected  
Phi indices max:2129 min: 2  
Psi indices max:2138 min: 17  
ISOLDE: started sim  

> select clear

ISOLDE: paused sim  

> st

[Repeated 7 time(s)]ISOLDE: resumed sim  
ISOLDE: paused sim  

> st

[Repeated 6 time(s)]ISOLDE: resumed sim  

> select clear

ISOLDE: paused sim  

> st

[Repeated 6 time(s)]ISOLDE: resumed sim  
ISOLDE: paused sim  
ISOLDE: resumed sim  

> select clear

ISOLDE: paused sim  

> st

[Repeated 8 time(s)]ISOLDE: resumed sim  

> select clear

ISOLDE: paused sim  

> st

[Repeated 5 time(s)]ISOLDE: resumed sim  
ISOLDE: paused sim  

> st

[Repeated 7 time(s)]ISOLDE: resumed sim  

> st

ISOLDE: paused sim  

> st

[Repeated 2 time(s)]ISOLDE: resumed sim  
ISOLDE: paused sim  

> st

ISOLDE: resumed sim  
ISOLDE: paused sim  

> st

[Repeated 13 time(s)]ISOLDE: resumed sim  
ISOLDE: paused sim  

> st

[Repeated 1 time(s)]

> hide #!1.1.1.2 models

> show #!1.1.1.5 models

> hide #!1.1.1.5 models

> show #!1.1.1.2 models

> hide #!1.1.1.4 models

> show #!1.1.1.5 models

> select clear

[Repeated 1 time(s)]ISOLDE: resumed sim  
ISOLDE: paused sim  

> st

[Repeated 9 time(s)]ISOLDE: resumed sim  
ISOLDE: paused sim  

> select clear

> st

ISOLDE: resumed sim  

> select clear

ISOLDE: paused sim  

> st

[Repeated 9 time(s)]

> show #!1.1.1.4 models

> hide #!1.1.1.5 models

ISOLDE: resumed sim  
ISOLDE: paused sim  

> st

[Repeated 5 time(s)]ISOLDE: resumed sim  
ISOLDE: paused sim  

> st

[Repeated 3 time(s)]ISOLDE: resumed sim  
ISOLDE: paused sim  

> st

ISOLDE: resumed sim  
ISOLDE: paused sim  

> st

[Repeated 1 time(s)]ISOLDE: resumed sim  
ISOLDE: paused sim  

> st

[Repeated 2 time(s)]ISOLDE: resumed sim  

> st

ISOLDE: paused sim  
ISOLDE: resumed sim  
ISOLDE: paused sim  

> st

ISOLDE: resumed sim  
ISOLDE: paused sim  

> st

[Repeated 3 time(s)]ISOLDE: resumed sim  
ISOLDE: paused sim  

> st

[Repeated 4 time(s)]ISOLDE: resumed sim  
ISOLDE: paused sim  

> st

ISOLDE: resumed sim  
ISOLDE: paused sim  

> st

[Repeated 6 time(s)]Updating bulk solvent parameters...  
ISOLDE: stopped sim  

> open
> /run/media/tic20/storage/structure_dump/aus/brisbane/kobe/MyD88/demo/myd88.fa

Summary of feedback from opening
/run/media/tic20/storage/structure_dump/aus/brisbane/kobe/MyD88/demo/myd88.fa  
---  
notes | Alignment identifier is myd88.fa  
Associated MyD88_20190909_refine_133.pdb_for_phenix_refine_001.cif (1.2) chain
A to 7BEQ_1|Chain A|Myeloid differentiation primary response protein
MyD88|Homo sapiens (9606) with 0 mismatches  
  
Opened 1 sequences from myd88.fa  

> aa LYS

Phi indices max:1843 min: 63  
Psi indices max:1860 min: 73  
ISOLDE: started sim  
Updating bulk solvent parameters...  
ISOLDE: stopped sim  

> aa LEU

Phi indices max:1245 min: 401  
Psi indices max:1262 min: 418  
ISOLDE: started sim  
Updating bulk solvent parameters...  
ISOLDE: stopped sim  

> aa SER

Phi indices max:1139 min: 317  
Psi indices max:1156 min: 334  
ISOLDE: started sim  
Updating bulk solvent parameters...  
ISOLDE: stopped sim  

> aa PRO approx helix

Phi indices max:1087 min: 258  
Psi indices max:1104 min: 266  
ISOLDE: started sim  
Updating bulk solvent parameters...  
ISOLDE: stopped sim  

> aa GLY

Phi indices max:1073 min: 237  
Psi indices max:1090 min: 245  
ISOLDE: started sim  
Updating bulk solvent parameters...  
ISOLDE: stopped sim  

> aa ALA

Phi indices max:965 min: 537  
Psi indices max:977 min: 557  
ISOLDE: started sim  
Updating bulk solvent parameters...  
ISOLDE: stopped sim  

> aa HIS

Phi indices max:895 min: 510  
Psi indices max:912 min: 518  
ISOLDE: started sim  
Updating bulk solvent parameters...  
ISOLDE: stopped sim  
Phi indices max:1922 min: 63  
Psi indices max:1939 min: 73  
ISOLDE: started sim  
Updating bulk solvent parameters...  
ISOLDE: stopped sim  

> aa GLN

> select up

18 atoms, 18 bonds, 1 residue, 1 model selected  

> isolde ignore sel

ISOLDE: currently ignoring 1 residues in model 1.2  
Phi indices max:1476 min: 536  
Psi indices max:1493 min: 549  
ISOLDE: started sim  
Updating bulk solvent parameters...  
ISOLDE: stopped sim  

> isolde ~ignore

Must have exactly two atoms selected!  
Phi indices max:1326 min: 497  
Psi indices max:1343 min: 510  
ISOLDE: started sim  
Updating bulk solvent parameters...  
ISOLDE: stopped sim  
Phi indices max:2076 min: 63  
Psi indices max:2093 min: 73  
ISOLDE: started sim  

> select clear

Updating bulk solvent parameters...  
ISOLDE: stopped sim  

> isolde write phenixRefineInput #1 numProcessors 12

> save MyD88_20190909_refine_133.pdb_for_phenix_refine_001.cif_for_phenix.cif
> #1.2 selectedOnly true

Not saving entity_poly_seq for non-authoritative sequences  

> save MyD88_20190909_refine_133.pdb_for_phenix_refine_001.cif_for_phenix.mtz
> #1.1.1

Writing data to: '/*/*/[FOBS, SIGFOBS]'  
A phenix.refine input file refine.eff with settings recommended for ISOLDE
models has been written to
/run/media/tic20/storage/structure_dump/aus/brisbane/kobe/MyD88/demo along
with a current snapshot of your model
(MyD88_20190909_refine_133.pdb_for_phenix_refine_001.cif_for_phenix.cif) and
reflections
(MyD88_20190909_refine_133.pdb_for_phenix_refine_001.cif_for_phenix.mtz). Note
that the reflections file only contains amplitudes - if you have a MTZ file
with intensities you may wish to edit refine.eff to substitute that. You can
start a refinement job by running the following command in the working
directory:  
phenix.refine refine.eff.  

> isolde write phenixRefineInput #1 numProcessors 12

> save round_2_for_phenix.cif #1.2 selectedOnly true

Not saving entity_poly_seq for non-authoritative sequences  

> save round_2_for_phenix.mtz #1.1.1

Writing data to: '/*/*/[FOBS, SIGFOBS]'  
A phenix.refine input file refine.eff with settings recommended for ISOLDE
models has been written to
/run/media/tic20/storage/structure_dump/aus/brisbane/kobe/MyD88/demo along
with a current snapshot of your model (round_2_for_phenix.cif) and reflections
(round_2_for_phenix.mtz). Note that the reflections file only contains
amplitudes - if you have a MTZ file with intensities you may wish to edit
refine.eff to substitute that. You can start a refinement job by running the
following command in the working directory:  
phenix.refine refine.eff.  

> close #1

Deleting Crystallographic maps (reflections.mtz)  
Deleting (LIVE) 2mFo-DFc  
Deleting (LIVE) mFo-DFc  
Deleting (LIVE) 2mFo-DFc_sharp_29  
Deleting (LIVE) MDFF potential  

> open
> /run/media/tic20/storage/structure_dump/aus/brisbane/kobe/MyD88/demo/round_2_for_phenix_refine_001.cif

Summary of feedback from opening
/run/media/tic20/storage/structure_dump/aus/brisbane/kobe/MyD88/demo/round_2_for_phenix_refine_001.cif  
---  
warnings | Skipping chem_comp category: Missing column 'type' near line 176  
Missing entity information. Treating each chain as a separate entity.  
Bad residue range for struct_conf "1" near line 125  
Bad residue range for struct_conf "2" near line 126  
Bad residue range for struct_conf "3" near line 127  
Bad residue range for struct_conf "4" near line 128  
Bad residue range for struct_conf "5" near line 129  
3 messages similar to the above omitted  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
  
Chain information for round_2_for_phenix_refine_001.cif #1  
---  
Chain | Description  
A | No description available  
  
Chain information for round_2_for_phenix_refine_001.cif  
---  
Chain | Description  
1.2/A | No description available  
  
Reflection data provided as intensities. Performing French & Wilson scaling to
convert to amplitudes...  
Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 50,40,38, pixel
0.688,0.646,0.679, shown at level 0.396, step 1, values float32  
Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 50,40,38, pixel
0.688,0.646,0.679, shown at level -0.139,0.139, step 1, values float32  
Opened (LIVE) 2mFo-DFc_sharp_29 as #1.1.1.4, grid size 50,40,38, pixel
0.688,0.646,0.679, shown at level 0.723, step 1, values float32  
Opened (LIVE) MDFF potential as #1.1.1.5, grid size 50,40,38, pixel
0.688,0.646,0.679, shown at level 0.379, step 1, values float32  

> addh

Summary of feedback from adding hydrogens to round_2_for_phenix_refine_001.cif
#1.2  
---  
notes | No usable SEQRES records for round_2_for_phenix_refine_001.cif (#1.2)
chain A; guessing termini instead  
Chain-initial residues that are actual N termini: /A GLU 159  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A LEU 295  
121 hydrogen bonds  
/A LEU 295 is not terminus, removing H atom from 'C'  
1148 hydrogens added  
  

> select clear

> open
> /run/media/tic20/storage/structure_dump/aus/brisbane/kobe/MyD88/demo/MyD88_20190909_refine_133.pdb_for_phenix.cif

Summary of feedback from opening
/run/media/tic20/storage/structure_dump/aus/brisbane/kobe/MyD88/demo/MyD88_20190909_refine_133.pdb_for_phenix.cif  
---  
warnings | Unknown polymer entity '1' near line 123  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
  
Chain information for MyD88_20190909_refine_133.pdb_for_phenix.cif #2  
---  
Chain | Description  
A | ?  
  

> hide #!2 models

> close #2

> cbb

2274 atoms, 137 residues, atom bfactor range 30.4 to 86.9  

> cbc

> cbb

2274 atoms, 137 residues, atom bfactor range 30.4 to 86.9  

> cbc

> open 7ber

7ber title:  
SFX structure of the MyD88 TIR domain higher-order assembly (solved, rebuilt
and refined using an identical protocol to the MicroED structure of the MyD88
TIR domain higher-order assembly) [more info...]  
  
Chain information for 7ber #2  
---  
Chain | Description | UniProt  
A | Myeloid differentiation primary response protein MyD88 | MYD88_HUMAN  
  

> matchmaker #2 to #1

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 round_2_for_phenix_refine_001.cif, chain A (#1.2) with 7ber, chain
A (#2), sequence alignment score = 685.1  
RMSD between 137 pruned atom pairs is 0.468 angstroms; (across all 137 pairs:
0.468)  
  

> show

> hide HC

> hide #2 models

> color #2 green

> color #2 byhetero

> show #2

> cbb

3407 atoms, 275 residues, atom bfactor range 13.7 to 102  

> cbb #1

2274 atoms, 137 residues, atom bfactor range 30.4 to 86.9  

> #1

Expected fewer arguments  

> alias cbc color bychain $1; color byhet $1

Traceback (most recent call last):  
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 280, in execute  
cmd.run(cmd_text)  
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/chimerax/std_commands/alias.py", line 35, in alias  
cli.create_alias(name, text, user=True, logger=logger)  
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 3477, in create_alias  
register(name, alias.cmd_desc(synopsis='alias of "%s"' % text, url=url),  
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2297, in register  
_parent_info.add_subcommand(words[-1], name, cmd_desc, logger=logger)  
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2210, in add_subcommand  
logger.info("FYI: alias is hiding existing command" %  
TypeError: not all arguments converted during string formatting  
  
TypeError: not all arguments converted during string formatting  
  
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2210, in add_subcommand  
logger.info("FYI: alias is hiding existing command" %  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 465.19.01
OpenGL renderer: NVIDIA TITAN Xp/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: Precision T5600
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
Virutal Machine: none
CPU: 32 Intel(R) Xeon(R) CPU E5-2687W 0 @ 3.10GHz
Cache Size: 20480 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:            62G        9.4G         36G        233M         17G         52G
	Swap:          4.9G          0B        4.9G

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
Locale: ('en_GB', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.5.30
    cftime: 1.5.0
    chardet: 4.0.0
    ChimeraX-AddCharge: 1.1.4
    ChimeraX-AddH: 2.1.10
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.28
    ChimeraX-AtomicLibrary: 4.1
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.3
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-Clipper: 0.17.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.3.2
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3.dev202108040454
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.4
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1
    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-ISOLDE: 1.3.dev32
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    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: 1.2.1
    ChimeraX-MDcrds: 2.4
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0.2
    ChimeraX-ModelPanel: 1.1
    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: 1.7
    ChimeraX-PDB: 2.5.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.1
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-Phenix: 0.3
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-Sample: 0.1
    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: 2.4.1
    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: 1.6
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.11
    ChimeraX-uniprot: 2.1
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-Voyager: 0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    comtypes: 1.1.10
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.23
    decorator: 5.0.9
    distlib: 0.3.1
    distro: 1.5.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.3.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.20
    imagecodecs: 2021.4.28
    imagesize: 1.2.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 2.11.3
    jupyter-client: 6.1.12
    jupyter-core: 4.7.1
    kiwisolver: 1.3.1
    line-profiler: 3.3.0
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 1.1.1
    matplotlib: 3.4.2
    matplotlib-inline: 0.1.2
    msgpack: 1.0.2
    netCDF4: 1.5.6
    networkx: 2.6.2
    numexpr: 2.7.3
    numpy: 1.21.0
    numpydoc: 1.1.0
    OpenMM: 7.6.0
    openvr: 1.16.801
    packaging: 21.0
    ParmEd: 3.2.0
    parso: 0.8.2
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 8.2.0
    pip: 21.1.1
    pkginfo: 1.7.0
    prompt-toolkit: 3.0.19
    psutil: 5.8.0
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.9.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.1
    pytz: 2021.1
    pyzmq: 22.1.0
    qtconsole: 5.1.0
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.25.1
    scipy: 1.6.3
    setuptools: 57.0.0
    sfftk-rw: 0.7.0.post1
    six: 1.16.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.4.0
    Sphinx: 4.0.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    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-jurko: 0.6
    tables: 3.6.1
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.0.5
    urllib3: 1.26.6
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.2
    wheel-filename: 1.3.0

Change History (2)

in reply to:  1 ; comment:1 by Tristan Croll, 4 years ago 

For what it's worth, ever since I discovered Python's new(ish - Python 3.6) f-string formatting I've never looked back. Just sooo much nicer:

                    logger.info(f"FYI: alias is hiding existing command: {dq_repr(name)}")
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: 10 August 2021 16:01
To: Tristan Croll <tic20@cam.ac.uk>
Subject: [ChimeraX] #5034: ChimeraX bug report submission

#5034: ChimeraX bug report submission
---------------------------+-----------------------------
 Reporter:  Tristan Croll  |                Type:  defect
   Status:  new            |            Priority:  normal
Component:  Unassigned     |          Blocked By:
 Blocking:                 |  Notify when closed:
---------------------------+-----------------------------
 {{{
 The following bug report has been submitted:
 Platform:        Linux-3.10.0-1160.25.1.el7.x86_64-x86_64-with-glibc2.17
 ChimeraX Version: 1.3.dev202108040454 (2021-08-04 04:54:51 UTC)
 Description
 Overriding an alias with a new one causes a traceback in the warning
 message.

 Log:
 > alias preview_toolshed toolshed url https://cxtoolshed-
 > preview.rbvi.ucsf.edu; toolshed reload available

 > alias production_toolshed toolshed url https://cxtoolshed.rbvi.ucsf.edu;
 > toolshed reload available

 > isolde shorthand


     Initialising ISOLDE-specific command aliases:
     Alias       Equivalent full command
     -------------------------------------------------
     st  isolde step {arguments}
     aw  isolde add water {arguments}
     awsf        isolde add water {arguments} sim false
     al  isolde add ligand {arguments}
     aa  isolde add aa $1 sel {arguments}
     ht  isolde mod his sel {arguments}
     so  setattr sel atoms occupancy {arguments}
     ab  isolde adjust bfactors {arguments}
     ss  isolde sim start sel
     rt  isolde release torsions sel {arguments}
     rd  isolde release distances sel {arguments}
     ra  rd; rt
     pf  isolde pepflip sel
     cf  isolde cisflip sel
     cbb color bfactor {arguments}
     cbo color byattr occupancy {arguments}
     cbc color bychain; color byhet
     cs  clipper set contourSensitivity {arguments}



 UCSF ChimeraX version: 1.3.dev202108040454 (2021-08-04)
 © 2016-2021 Regents of the University of California. All rights reserved.
 How to cite UCSF ChimeraX

 > open MyD88_20190909_refine_133.pdb

 Summary of feedback from opening MyD88_20190909_refine_133.pdb
 ---
 warnings | Ignored bad PDB record found on line 1
 REMARK Date 2019-09-09 Time 10:43:28 W. Europe Summer Time +0200
 (1568018608.44 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 :
 C:\Users\macl1978\Dropbox\MyD88\mr_test\MyD88_ALL_20190718_scaled3_C2.mtz

 46 messages similar to the above omitted

 Chain information for MyD88_20190909_refine_133.pdb #1
 ---
 Chain | Description
 A | No description available


 > open
 >
 /run/media/tic20/storage/structure_dump/aus/brisbane/kobe/MyD88/reflections.mtz

 Summary of feedback from opening
 /run/media/tic20/storage/structure_dump/aus/brisbane/kobe/MyD88/reflections.mtz
 ---
 note | Reflection data provided as intensities. Performing French & Wilson
 scaling to convert to amplitudes...

 Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 50,40,38, pixel
 0.688,0.646,0.679, shown at level 0.195, step 1, values float32
 Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 50,40,38, pixel
 0.688,0.646,0.679, shown at level -0.0737,0.0737, step 1, values float32
 Opened (LIVE) 2mFo-DFc_sharp_29 as #1.1.1.4, grid size 50,40,38, pixel
 0.688,0.646,0.679, shown at level 0.306, step 1, values float32
 Chain information for MyD88_20190909_refine_133.pdb
 ---
 Chain | Description
 1.2/A | No description available

 Opened crystallographic dataset from
 /run/media/tic20/storage/structure_dump/aus/brisbane/kobe/MyD88/reflections.mtz
 Found experimental reflection data:
 (dataset) IMEAN, SIGIMEAN
 French and Wilson Amplitudes
 Rwork: 0.3436; Rfree: 0.3985
 Generated maps:
 Reflection Data
 (LIVE) 2mFo-DFc
 (LIVE) mFo-DFc
 (LIVE) 2mFo-DFc_sharp_29
 Any unwanted maps may be safely closed via the Model panel.

 > set bgColor white

 > isolde start

 > set selectionWidth 4

 Opened (LIVE) MDFF potential as #1.1.1.5, grid size 50,40,38, pixel
 0.688,0.646,0.679, shown at level 0.172, step 1, values float32
 Done loading forcefield

 > close #1.1

 Deleting Crystallographic maps (reflections.mtz)
 Deleting (LIVE) 2mFo-DFc
 Deleting (LIVE) mFo-DFc
 Deleting (LIVE) 2mFo-DFc_sharp_29
 Deleting (LIVE) MDFF potential
 Reflection data provided as intensities. Performing French & Wilson
 scaling to
 convert to amplitudes...
 Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 50,40,38, pixel
 0.688,0.646,0.679, shown at level 0.195, step 1, values float32
 Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 50,40,38, pixel
 0.688,0.646,0.679, shown at level -0.0737,0.0737, step 1, values float32
 Opened (LIVE) 2mFo-DFc_sharp_29 as #1.1.1.4, grid size 50,40,38, pixel
 0.688,0.646,0.679, shown at level 0.306, step 1, values float32
 Opened (LIVE) MDFF potential as #1.1.1.5, grid size 50,40,38, pixel
 0.688,0.646,0.679, shown at level 0.172, step 1, values float32

 > select clear

 > addh

 Summary of feedback from adding hydrogens to MyD88_20190909_refine_133.pdb
 #1.2
 ---
 notes | No usable SEQRES records for MyD88_20190909_refine_133.pdb (#1.2)
 chain A; guessing termini instead
 Chain-initial residues that are actual N termini: /A GLU 159
 Chain-initial residues that are not actual N termini: /A ARG 251
 Chain-final residues that are actual C termini:
 Chain-final residues that are not actual C termini: /A LEU 295, /A SER 242
 79 hydrogen bonds
 Adding 'H' to /A ARG 251
 /A LEU 295 is not terminus, removing H atom from 'C'
 1086 hydrogens added

 Phi indices max:1088 min: 2
 Psi indices max:1096 min: 17
 ISOLDE: started sim

 > select clear

 Updating bulk solvent parameters...
 ISOLDE: stopped sim

 > select #1

 2157 atoms, 2179 bonds, 1 pseudobond, 129 residues, 32 models selected
 Phi indices max:2129 min: 2
 Psi indices max:2138 min: 17
 ISOLDE: started sim

 > select clear

 > st first

 ISOLDE: paused sim
 ISOLDE: resumed sim
 ISOLDE: paused sim

 > stst

 Unknown command: stst

 > st

 [Repeated 7 time(s)]

 > select clear

 > st

 [Repeated 2 time(s)]

 > view /A:282

 ISOLDE: resumed sim

 > st

 ISOLDE: paused sim

 > st

 [Repeated 1 time(s)]ISOLDE: resumed sim
 ISOLDE: paused sim

 > st

 [Repeated 3 time(s)]ISOLDE: resumed sim
 ISOLDE: paused sim

 > st

 [Repeated 1 time(s)]ISOLDE: resumed sim
 ISOLDE: paused sim

 > st

 [Repeated 4 time(s)]ISOLDE: resumed sim
 ISOLDE: paused sim
 ISOLDE: resumed sim
 ISOLDE: paused sim

 > st

 [Repeated 2 time(s)]ISOLDE: resumed sim
 ISOLDE: paused sim
 ISOLDE: resumed sim

 > select clear

 [Repeated 1 time(s)]ISOLDE: paused sim

 > st

 [Repeated 1 time(s)]

 > select clear

 ISOLDE: resumed sim
 ISOLDE: paused sim

 > st

 [Repeated 1 time(s)]

 > select clear

 > st

 [Repeated 2 time(s)]ISOLDE: resumed sim
 ISOLDE: paused sim

 > st

 [Repeated 3 time(s)]ISOLDE: resumed sim
 ISOLDE: paused sim

 > st

 [Repeated 8 time(s)]ISOLDE: resumed sim
 ISOLDE: paused sim

 > st

 [Repeated 2 time(s)]ISOLDE: resumed sim
 ISOLDE: paused sim

 > st

 [Repeated 1 time(s)]ISOLDE: resumed sim
 ISOLDE: paused sim

 > st

 [Repeated 7 time(s)]ISOLDE: resumed sim
 ISOLDE: paused sim

 > st

 [Repeated 16 time(s)]ISOLDE: resumed sim
 ISOLDE: paused sim

 > st

 [Repeated 4 time(s)]ISOLDE: resumed sim
 ISOLDE: paused sim

 > st

 ISOLDE: resumed sim
 ISOLDE: paused sim

 > st

 [Repeated 6 time(s)]ISOLDE: resumed sim
 ISOLDE: paused sim

 > st

 [Repeated 3 time(s)]ISOLDE: resumed sim
 ISOLDE: paused sim

 > st

 [Repeated 4 time(s)]ISOLDE: resumed sim
 ISOLDE: paused sim

 > st

 [Repeated 4 time(s)]ISOLDE: resumed sim
 ISOLDE: paused sim

 > st

 [Repeated 7 time(s)]ISOLDE: resumed sim
 ISOLDE: paused sim

 > st

 [Repeated 7 time(s)]ISOLDE: resumed sim
 ISOLDE: paused sim

 > st

 [Repeated 6 time(s)]Updating bulk solvent parameters...
 ISOLDE: stopped sim

 > cd demo

 Current working directory is:
 /run/media/tic20/storage/structure_dump/aus/brisbane/kobe/MyD88/demo

 > isolde write phenixRefineInput #1 numProcessors 12

 > save MyD88_20190909_refine_133.pdb_for_phenix.cif #1.2 selectedOnly true

 Not saving entity_poly_seq for non-authoritative sequences

 > save MyD88_20190909_refine_133.pdb_for_phenix.mtz #1.1.1

 Writing data to: '/*/*/[FOBS, SIGFOBS]'
 A phenix.refine input file refine.eff with settings recommended for ISOLDE
 models has been written to
 /run/media/tic20/storage/structure_dump/aus/brisbane/kobe/MyD88/demo along
 with a current snapshot of your model
 (MyD88_20190909_refine_133.pdb_for_phenix.cif) and reflections
 (MyD88_20190909_refine_133.pdb_for_phenix.mtz). Note that the reflections
 file
 only contains amplitudes - if you have a MTZ file with intensities you may
 wish to edit refine.eff to substitute that. You can start a refinement job
 by
 running the following command in the working directory:
 phenix.refine refine.eff.

 > ui tool show Shell

 > isolde write phenixRefineInput #1 numProcessors 12

 > save MyD88_20190909_refine_133.pdb_for_phenix.cif #1.2 selectedOnly true

 Not saving entity_poly_seq for non-authoritative sequences

 > save MyD88_20190909_refine_133.pdb_for_phenix.mtz #1.1.1

 Writing data to: '/*/*/[FOBS, SIGFOBS]'
 A phenix.refine input file refine.eff with settings recommended for ISOLDE
 models has been written to
 /run/media/tic20/storage/structure_dump/aus/brisbane/kobe/MyD88/demo along
 with a current snapshot of your model
 (MyD88_20190909_refine_133.pdb_for_phenix.cif) and reflections
 (MyD88_20190909_refine_133.pdb_for_phenix.mtz). Note that the reflections
 file
 only contains amplitudes - if you have a MTZ file with intensities you may
 wish to edit refine.eff to substitute that. You can start a refinement job
 by
 running the following command in the working directory:
 phenix.refine refine.eff.

 > close #1

 Deleting Crystallographic maps (reflections.mtz)
 Deleting (LIVE) 2mFo-DFc
 Deleting (LIVE) mFo-DFc
 Deleting (LIVE) 2mFo-DFc_sharp_29
 Deleting (LIVE) MDFF potential

 > open
 >
 /run/media/tic20/storage/structure_dump/aus/brisbane/kobe/MyD88/demo/MyD88_20190909_refine_133.pdb_for_phenix_refine_001.cif

 Summary of feedback from opening
 /run/media/tic20/storage/structure_dump/aus/brisbane/kobe/MyD88/demo/MyD88_20190909_refine_133.pdb_for_phenix_refine_001.cif
 ---
 warnings | Skipping chem_comp category: Missing column 'type' near line
 176
 Missing entity information. Treating each chain as a separate entity.
 Bad residue range for struct_conf "1" near line 125
 Bad residue range for struct_conf "2" near line 126
 Bad residue range for struct_conf "3" near line 127
 Bad residue range for struct_conf "4" near line 128
 Bad residue range for struct_conf "5" near line 129
 3 messages similar to the above omitted
 Missing or incomplete entity_poly_seq table. Inferred polymer
 connectivity.

 Chain information for
 MyD88_20190909_refine_133.pdb_for_phenix_refine_001.cif
 #1
 ---
 Chain | Description
 A | No description available

 Chain information for
 MyD88_20190909_refine_133.pdb_for_phenix_refine_001.cif
 ---
 Chain | Description
 1.2/A | No description available


 > dssp

 Reflection data provided as intensities. Performing French & Wilson
 scaling to
 convert to amplitudes...
 Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 50,40,38, pixel
 0.688,0.646,0.679, shown at level 0.403, step 1, values float32
 Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 50,40,38, pixel
 0.688,0.646,0.679, shown at level -0.164,0.164, step 1, values float32
 Opened (LIVE) 2mFo-DFc_sharp_29 as #1.1.1.4, grid size 50,40,38, pixel
 0.688,0.646,0.679, shown at level 0.744, step 1, values float32
 Opened (LIVE) MDFF potential as #1.1.1.5, grid size 50,40,38, pixel
 0.688,0.646,0.679, shown at level 0.401, step 1, values float32

 > open
 >
 /run/media/tic20/storage/structure_dump/aus/brisbane/kobe/MyD88/demo/MyD88_20190909_refine_133.pdb_for_phenix.cif

 Summary of feedback from opening
 /run/media/tic20/storage/structure_dump/aus/brisbane/kobe/MyD88/demo/MyD88_20190909_refine_133.pdb_for_phenix.cif
 ---
 warnings | Unknown polymer entity '1' near line 123
 Missing or incomplete entity_poly_seq table. Inferred polymer
 connectivity.

 Chain information for MyD88_20190909_refine_133.pdb_for_phenix.cif #2
 ---
 Chain | Description
 A | ?


 > show #2

 > close #2

 > select clear

 > addh

 Summary of feedback from adding hydrogens to
 MyD88_20190909_refine_133.pdb_for_phenix_refine_001.cif #1.2
 ---
 notes | No usable SEQRES records for
 MyD88_20190909_refine_133.pdb_for_phenix_refine_001.cif (#1.2) chain A;
 guessing termini instead
 Chain-initial residues that are actual N termini: /A GLU 159
 Chain-initial residues that are not actual N termini: /A ARG 251
 Chain-final residues that are actual C termini:
 Chain-final residues that are not actual C termini: /A LEU 295, /A SER 242
 117 hydrogen bonds
 Adding 'H' to /A ARG 251
 /A LEU 295 is not terminus, removing H atom from 'C'
 1089 hydrogens added


 > select clear

 Phi indices max:1813 min: 68
 Psi indices max:1830 min: 86
 ISOLDE: started sim

 > select clear

 Updating bulk solvent parameters...
 ISOLDE: stopped sim
 Phi indices max:1939 min: 85
 Psi indices max:1956 min: 103
 ISOLDE: started sim
 Updating bulk solvent parameters...
 ISOLDE: stopped sim

 > st first

 > st

 [Repeated 5 time(s)]

 > select #1

 2157 atoms, 2179 bonds, 1 pseudobond, 129 residues, 32 models selected
 Phi indices max:2129 min: 2
 Psi indices max:2138 min: 17
 ISOLDE: started sim

 > select clear

 ISOLDE: paused sim

 > st

 [Repeated 7 time(s)]ISOLDE: resumed sim
 ISOLDE: paused sim

 > st

 [Repeated 6 time(s)]ISOLDE: resumed sim

 > select clear

 ISOLDE: paused sim

 > st

 [Repeated 6 time(s)]ISOLDE: resumed sim
 ISOLDE: paused sim
 ISOLDE: resumed sim

 > select clear

 ISOLDE: paused sim

 > st

 [Repeated 8 time(s)]ISOLDE: resumed sim

 > select clear

 ISOLDE: paused sim

 > st

 [Repeated 5 time(s)]ISOLDE: resumed sim
 ISOLDE: paused sim

 > st

 [Repeated 7 time(s)]ISOLDE: resumed sim

 > st

 ISOLDE: paused sim

 > st

 [Repeated 2 time(s)]ISOLDE: resumed sim
 ISOLDE: paused sim

 > st

 ISOLDE: resumed sim
 ISOLDE: paused sim

 > st

 [Repeated 13 time(s)]ISOLDE: resumed sim
 ISOLDE: paused sim

 > st

 [Repeated 1 time(s)]

 > hide #!1.1.1.2 models

 > show #!1.1.1.5 models

 > hide #!1.1.1.5 models

 > show #!1.1.1.2 models

 > hide #!1.1.1.4 models

 > show #!1.1.1.5 models

 > select clear

 [Repeated 1 time(s)]ISOLDE: resumed sim
 ISOLDE: paused sim

 > st

 [Repeated 9 time(s)]ISOLDE: resumed sim
 ISOLDE: paused sim

 > select clear

 > st

 ISOLDE: resumed sim

 > select clear

 ISOLDE: paused sim

 > st

 [Repeated 9 time(s)]

 > show #!1.1.1.4 models

 > hide #!1.1.1.5 models

 ISOLDE: resumed sim
 ISOLDE: paused sim

 > st

 [Repeated 5 time(s)]ISOLDE: resumed sim
 ISOLDE: paused sim

 > st

 [Repeated 3 time(s)]ISOLDE: resumed sim
 ISOLDE: paused sim

 > st

 ISOLDE: resumed sim
 ISOLDE: paused sim

 > st

 [Repeated 1 time(s)]ISOLDE: resumed sim
 ISOLDE: paused sim

 > st

 [Repeated 2 time(s)]ISOLDE: resumed sim

 > st

 ISOLDE: paused sim
 ISOLDE: resumed sim
 ISOLDE: paused sim

 > st

 ISOLDE: resumed sim
 ISOLDE: paused sim

 > st

 [Repeated 3 time(s)]ISOLDE: resumed sim
 ISOLDE: paused sim

 > st

 [Repeated 4 time(s)]ISOLDE: resumed sim
 ISOLDE: paused sim

 > st

 ISOLDE: resumed sim
 ISOLDE: paused sim

 > st

 [Repeated 6 time(s)]Updating bulk solvent parameters...
 ISOLDE: stopped sim

 > open
 >
 /run/media/tic20/storage/structure_dump/aus/brisbane/kobe/MyD88/demo/myd88.fa

 Summary of feedback from opening
 /run/media/tic20/storage/structure_dump/aus/brisbane/kobe/MyD88/demo/myd88.fa
 ---
 notes | Alignment identifier is myd88.fa
 Associated MyD88_20190909_refine_133.pdb_for_phenix_refine_001.cif (1.2)
 chain
 A to 7BEQ_1|Chain A|Myeloid differentiation primary response protein
 MyD88|Homo sapiens (9606) with 0 mismatches

 Opened 1 sequences from myd88.fa

 > aa LYS

 Phi indices max:1843 min: 63
 Psi indices max:1860 min: 73
 ISOLDE: started sim
 Updating bulk solvent parameters...
 ISOLDE: stopped sim

 > aa LEU

 Phi indices max:1245 min: 401
 Psi indices max:1262 min: 418
 ISOLDE: started sim
 Updating bulk solvent parameters...
 ISOLDE: stopped sim

 > aa SER

 Phi indices max:1139 min: 317
 Psi indices max:1156 min: 334
 ISOLDE: started sim
 Updating bulk solvent parameters...
 ISOLDE: stopped sim

 > aa PRO approx helix

 Phi indices max:1087 min: 258
 Psi indices max:1104 min: 266
 ISOLDE: started sim
 Updating bulk solvent parameters...
 ISOLDE: stopped sim

 > aa GLY

 Phi indices max:1073 min: 237
 Psi indices max:1090 min: 245
 ISOLDE: started sim
 Updating bulk solvent parameters...
 ISOLDE: stopped sim

 > aa ALA

 Phi indices max:965 min: 537
 Psi indices max:977 min: 557
 ISOLDE: started sim
 Updating bulk solvent parameters...
 ISOLDE: stopped sim

 > aa HIS

 Phi indices max:895 min: 510
 Psi indices max:912 min: 518
 ISOLDE: started sim
 Updating bulk solvent parameters...
 ISOLDE: stopped sim
 Phi indices max:1922 min: 63
 Psi indices max:1939 min: 73
 ISOLDE: started sim
 Updating bulk solvent parameters...
 ISOLDE: stopped sim

 > aa GLN

 > select up

 18 atoms, 18 bonds, 1 residue, 1 model selected

 > isolde ignore sel

 ISOLDE: currently ignoring 1 residues in model 1.2
 Phi indices max:1476 min: 536
 Psi indices max:1493 min: 549
 ISOLDE: started sim
 Updating bulk solvent parameters...
 ISOLDE: stopped sim

 > isolde ~ignore

 Must have exactly two atoms selected!
 Phi indices max:1326 min: 497
 Psi indices max:1343 min: 510
 ISOLDE: started sim
 Updating bulk solvent parameters...
 ISOLDE: stopped sim
 Phi indices max:2076 min: 63
 Psi indices max:2093 min: 73
 ISOLDE: started sim

 > select clear

 Updating bulk solvent parameters...
 ISOLDE: stopped sim

 > isolde write phenixRefineInput #1 numProcessors 12

 > save
 MyD88_20190909_refine_133.pdb_for_phenix_refine_001.cif_for_phenix.cif
 > #1.2 selectedOnly true

 Not saving entity_poly_seq for non-authoritative sequences

 > save
 MyD88_20190909_refine_133.pdb_for_phenix_refine_001.cif_for_phenix.mtz
 > #1.1.1

 Writing data to: '/*/*/[FOBS, SIGFOBS]'
 A phenix.refine input file refine.eff with settings recommended for ISOLDE
 models has been written to
 /run/media/tic20/storage/structure_dump/aus/brisbane/kobe/MyD88/demo along
 with a current snapshot of your model
 (MyD88_20190909_refine_133.pdb_for_phenix_refine_001.cif_for_phenix.cif)
 and
 reflections
 (MyD88_20190909_refine_133.pdb_for_phenix_refine_001.cif_for_phenix.mtz).
 Note
 that the reflections file only contains amplitudes - if you have a MTZ
 file
 with intensities you may wish to edit refine.eff to substitute that. You
 can
 start a refinement job by running the following command in the working
 directory:
 phenix.refine refine.eff.

 > isolde write phenixRefineInput #1 numProcessors 12

 > save round_2_for_phenix.cif #1.2 selectedOnly true

 Not saving entity_poly_seq for non-authoritative sequences

 > save round_2_for_phenix.mtz #1.1.1

 Writing data to: '/*/*/[FOBS, SIGFOBS]'
 A phenix.refine input file refine.eff with settings recommended for ISOLDE
 models has been written to
 /run/media/tic20/storage/structure_dump/aus/brisbane/kobe/MyD88/demo along
 with a current snapshot of your model (round_2_for_phenix.cif) and
 reflections
 (round_2_for_phenix.mtz). Note that the reflections file only contains
 amplitudes - if you have a MTZ file with intensities you may wish to edit
 refine.eff to substitute that. You can start a refinement job by running
 the
 following command in the working directory:
 phenix.refine refine.eff.

 > close #1

 Deleting Crystallographic maps (reflections.mtz)
 Deleting (LIVE) 2mFo-DFc
 Deleting (LIVE) mFo-DFc
 Deleting (LIVE) 2mFo-DFc_sharp_29
 Deleting (LIVE) MDFF potential

 > open
 >
 /run/media/tic20/storage/structure_dump/aus/brisbane/kobe/MyD88/demo/round_2_for_phenix_refine_001.cif

 Summary of feedback from opening
 /run/media/tic20/storage/structure_dump/aus/brisbane/kobe/MyD88/demo/round_2_for_phenix_refine_001.cif
 ---
 warnings | Skipping chem_comp category: Missing column 'type' near line
 176
 Missing entity information. Treating each chain as a separate entity.
 Bad residue range for struct_conf "1" near line 125
 Bad residue range for struct_conf "2" near line 126
 Bad residue range for struct_conf "3" near line 127
 Bad residue range for struct_conf "4" near line 128
 Bad residue range for struct_conf "5" near line 129
 3 messages similar to the above omitted
 Missing or incomplete entity_poly_seq table. Inferred polymer
 connectivity.

 Chain information for round_2_for_phenix_refine_001.cif #1
 ---
 Chain | Description
 A | No description available

 Chain information for round_2_for_phenix_refine_001.cif
 ---
 Chain | Description
 1.2/A | No description available

 Reflection data provided as intensities. Performing French & Wilson
 scaling to
 convert to amplitudes...
 Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 50,40,38, pixel
 0.688,0.646,0.679, shown at level 0.396, step 1, values float32
 Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 50,40,38, pixel
 0.688,0.646,0.679, shown at level -0.139,0.139, step 1, values float32
 Opened (LIVE) 2mFo-DFc_sharp_29 as #1.1.1.4, grid size 50,40,38, pixel
 0.688,0.646,0.679, shown at level 0.723, step 1, values float32
 Opened (LIVE) MDFF potential as #1.1.1.5, grid size 50,40,38, pixel
 0.688,0.646,0.679, shown at level 0.379, step 1, values float32

 > addh

 Summary of feedback from adding hydrogens to
 round_2_for_phenix_refine_001.cif
 #1.2
 ---
 notes | No usable SEQRES records for round_2_for_phenix_refine_001.cif
 (#1.2)
 chain A; guessing termini instead
 Chain-initial residues that are actual N termini: /A GLU 159
 Chain-initial residues that are not actual N termini:
 Chain-final residues that are actual C termini:
 Chain-final residues that are not actual C termini: /A LEU 295
 121 hydrogen bonds
 /A LEU 295 is not terminus, removing H atom from 'C'
 1148 hydrogens added


 > select clear

 > open
 >
 /run/media/tic20/storage/structure_dump/aus/brisbane/kobe/MyD88/demo/MyD88_20190909_refine_133.pdb_for_phenix.cif

 Summary of feedback from opening
 /run/media/tic20/storage/structure_dump/aus/brisbane/kobe/MyD88/demo/MyD88_20190909_refine_133.pdb_for_phenix.cif
 ---
 warnings | Unknown polymer entity '1' near line 123
 Missing or incomplete entity_poly_seq table. Inferred polymer
 connectivity.

 Chain information for MyD88_20190909_refine_133.pdb_for_phenix.cif #2
 ---
 Chain | Description
 A | ?


 > hide #!2 models

 > close #2

 > cbb

 2274 atoms, 137 residues, atom bfactor range 30.4 to 86.9

 > cbc

 > cbb

 2274 atoms, 137 residues, atom bfactor range 30.4 to 86.9

 > cbc

 > open 7ber

 7ber title:
 SFX structure of the MyD88 TIR domain higher-order assembly (solved,
 rebuilt
 and refined using an identical protocol to the MicroED structure of the
 MyD88
 TIR domain higher-order assembly) [more info...]

 Chain information for 7ber #2
 ---
 Chain | Description | UniProt
 A | Myeloid differentiation primary response protein MyD88 | MYD88_HUMAN


 > matchmaker #2 to #1

 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 round_2_for_phenix_refine_001.cif, chain A (#1.2) with 7ber,
 chain
 A (#2), sequence alignment score = 685.1
 RMSD between 137 pruned atom pairs is 0.468 angstroms; (across all 137
 pairs:
 0.468)


 > show

 > hide HC

 > hide #2 models

 > color #2 green

 > color #2 byhetero

 > show #2

 > cbb

 3407 atoms, 275 residues, atom bfactor range 13.7 to 102

 > cbb #1

 2274 atoms, 137 residues, atom bfactor range 30.4 to 86.9

 > #1

 Expected fewer arguments

 > alias cbc color bychain $1; color byhet $1

 Traceback (most recent call last):
 File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
 packages/chimerax/cmd_line/tool.py", line 280, in execute
 cmd.run(cmd_text)
 File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
 packages/chimerax/core/commands/cli.py", line 2856, in run
 result = ci.function(session, **kw_args)
 File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
 packages/chimerax/std_commands/alias.py", line 35, in alias
 cli.create_alias(name, text, user=True, logger=logger)
 File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
 packages/chimerax/core/commands/cli.py", line 3477, in create_alias
 register(name, alias.cmd_desc(synopsis='alias of "%s"' % text, url=url),
 File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
 packages/chimerax/core/commands/cli.py", line 2297, in register
 _parent_info.add_subcommand(words[-1], name, cmd_desc, logger=logger)
 File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
 packages/chimerax/core/commands/cli.py", line 2210, in add_subcommand
 logger.info("FYI: alias is hiding existing command" %
 TypeError: not all arguments converted during string formatting

 TypeError: not all arguments converted during string formatting

 File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
 packages/chimerax/core/commands/cli.py", line 2210, in add_subcommand
 logger.info("FYI: alias is hiding existing command" %

 See log for complete Python traceback.





 OpenGL version: 3.3.0 NVIDIA 465.19.01
 OpenGL renderer: NVIDIA TITAN Xp/PCIe/SSE2
 OpenGL vendor: NVIDIA Corporation
 Manufacturer: Dell Inc.
 Model: Precision T5600
 OS: CentOS Linux 7 Core
 Architecture: 64bit ELF
 Virutal Machine: none
 CPU: 32 Intel(R) Xeon(R) CPU E5-2687W 0 @ 3.10GHz
 Cache Size: 20480 KB
 Memory:
                       total        used        free      shared
 buff/cache   available
         Mem:            62G        9.4G         36G        233M
 17G         52G
         Swap:          4.9G          0B        4.9G

 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
 Locale: ('en_GB', 'UTF-8')
 PyQt5 5.15.2, Qt 5.15.2
 Installed Packages:
     alabaster: 0.7.12
     appdirs: 1.4.4
     Babel: 2.9.1
     backcall: 0.2.0
     blockdiag: 2.0.1
     certifi: 2021.5.30
     cftime: 1.5.0
     chardet: 4.0.0
     ChimeraX-AddCharge: 1.1.4
     ChimeraX-AddH: 2.1.10
     ChimeraX-AlignmentAlgorithms: 2.0
     ChimeraX-AlignmentHdrs: 3.2
     ChimeraX-AlignmentMatrices: 2.0
     ChimeraX-Alignments: 2.1
     ChimeraX-AlphaFold: 1.0
     ChimeraX-AltlocExplorer: 1.0
     ChimeraX-AmberInfo: 1.0
     ChimeraX-Arrays: 1.0
     ChimeraX-Atomic: 1.28
     ChimeraX-AtomicLibrary: 4.1
     ChimeraX-AtomSearch: 2.0
     ChimeraX-AtomSearchLibrary: 1.0
     ChimeraX-AxesPlanes: 2.0
     ChimeraX-BasicActions: 1.1
     ChimeraX-BILD: 1.0
     ChimeraX-BlastProtein: 1.1.1
     ChimeraX-BondRot: 2.0
     ChimeraX-BugReporter: 1.0
     ChimeraX-BuildStructure: 2.5.3
     ChimeraX-Bumps: 1.0
     ChimeraX-BundleBuilder: 1.1
     ChimeraX-ButtonPanel: 1.0
     ChimeraX-CageBuilder: 1.0
     ChimeraX-CellPack: 1.0
     ChimeraX-Centroids: 1.1
     ChimeraX-ChemGroup: 2.0
     ChimeraX-Clashes: 2.1
     ChimeraX-Clipper: 0.17.0
     ChimeraX-ColorActions: 1.0
     ChimeraX-ColorGlobe: 1.0
     ChimeraX-ColorKey: 1.3.2
     ChimeraX-CommandLine: 1.1.4
     ChimeraX-ConnectStructure: 2.0
     ChimeraX-Contacts: 1.0
     ChimeraX-Core: 1.3.dev202108040454
     ChimeraX-CoreFormats: 1.1
     ChimeraX-coulombic: 1.3
     ChimeraX-Crosslinks: 1.0
     ChimeraX-Crystal: 1.0
     ChimeraX-CrystalContacts: 1.0
     ChimeraX-DataFormats: 1.2
     ChimeraX-Dicom: 1.0
     ChimeraX-DistMonitor: 1.1.4
     ChimeraX-DistUI: 1.0
     ChimeraX-Dssp: 2.0
     ChimeraX-EMDB-SFF: 1.0
     ChimeraX-ExperimentalCommands: 1.0
     ChimeraX-FileHistory: 1.0
     ChimeraX-FunctionKey: 1.0
     ChimeraX-Geometry: 1.1
     ChimeraX-gltf: 1.0
     ChimeraX-Graphics: 1.1
     ChimeraX-Hbonds: 2.1
     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-ISOLDE: 1.3.dev32
     ChimeraX-ItemsInspection: 1.0
     ChimeraX-Label: 1.1
     ChimeraX-LinuxSupport: 1.0
     ChimeraX-ListInfo: 1.1.1
     ChimeraX-Log: 1.1.4
     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: 1.2.1
     ChimeraX-MDcrds: 2.4
     ChimeraX-MedicalToolbar: 1.0.1
     ChimeraX-Meeting: 1.0
     ChimeraX-MLP: 1.1
     ChimeraX-mmCIF: 2.3
     ChimeraX-MMTF: 2.1
     ChimeraX-Modeller: 1.0.2
     ChimeraX-ModelPanel: 1.1
     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: 1.7
     ChimeraX-PDB: 2.5.1
     ChimeraX-PDBBio: 1.0
     ChimeraX-PDBLibrary: 1.0.1
     ChimeraX-PDBMatrices: 1.0
     ChimeraX-Phenix: 0.3
     ChimeraX-PickBlobs: 1.0
     ChimeraX-Positions: 1.0
     ChimeraX-PresetMgr: 1.0.1
     ChimeraX-PubChem: 2.1
     ChimeraX-ReadPbonds: 1.0
     ChimeraX-Registration: 1.1
     ChimeraX-RemoteControl: 1.0
     ChimeraX-ResidueFit: 1.0
     ChimeraX-RestServer: 1.1
     ChimeraX-RNALayout: 1.0
     ChimeraX-RotamerLibMgr: 2.0
     ChimeraX-RotamerLibsDunbrack: 2.0
     ChimeraX-RotamerLibsDynameomics: 2.0
     ChimeraX-RotamerLibsRichardson: 2.0
     ChimeraX-Sample: 0.1
     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: 2.4.1
     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: 1.6
     ChimeraX-STL: 1.0
     ChimeraX-Storm: 1.0
     ChimeraX-Struts: 1.0
     ChimeraX-Surface: 1.0
     ChimeraX-SwapAA: 2.0
     ChimeraX-SwapRes: 2.1
     ChimeraX-TapeMeasure: 1.0
     ChimeraX-Test: 1.0
     ChimeraX-Toolbar: 1.1
     ChimeraX-ToolshedUtils: 1.2
     ChimeraX-Tug: 1.0
     ChimeraX-UI: 1.11
     ChimeraX-uniprot: 2.1
     ChimeraX-UnitCell: 1.0
     ChimeraX-ViewDockX: 1.0.1
     ChimeraX-Vive: 1.1
     ChimeraX-VolumeMenu: 1.0
     ChimeraX-Voyager: 0.1
     ChimeraX-VTK: 1.0
     ChimeraX-WavefrontOBJ: 1.0
     ChimeraX-WebCam: 1.0
     ChimeraX-WebServices: 1.0
     ChimeraX-Zone: 1.0
     colorama: 0.4.4
     comtypes: 1.1.10
     cxservices: 1.0
     cycler: 0.10.0
     Cython: 0.29.23
     decorator: 5.0.9
     distlib: 0.3.1
     distro: 1.5.0
     docutils: 0.17.1
     filelock: 3.0.12
     funcparserlib: 0.3.6
     grako: 3.16.5
     h5py: 3.3.0
     html2text: 2020.1.16
     idna: 2.10
     ihm: 0.20
     imagecodecs: 2021.4.28
     imagesize: 1.2.0
     ipykernel: 5.5.5
     ipython: 7.23.1
     ipython-genutils: 0.2.0
     jedi: 0.18.0
     Jinja2: 2.11.3
     jupyter-client: 6.1.12
     jupyter-core: 4.7.1
     kiwisolver: 1.3.1
     line-profiler: 3.3.0
     lxml: 4.6.3
     lz4: 3.1.3
     MarkupSafe: 1.1.1
     matplotlib: 3.4.2
     matplotlib-inline: 0.1.2
     msgpack: 1.0.2
     netCDF4: 1.5.6
     networkx: 2.6.2
     numexpr: 2.7.3
     numpy: 1.21.0
     numpydoc: 1.1.0
     OpenMM: 7.6.0
     openvr: 1.16.801
     packaging: 21.0
     ParmEd: 3.2.0
     parso: 0.8.2
     pexpect: 4.8.0
     pickleshare: 0.7.5
     Pillow: 8.2.0
     pip: 21.1.1
     pkginfo: 1.7.0
     prompt-toolkit: 3.0.19
     psutil: 5.8.0
     ptyprocess: 0.7.0
     pycollada: 0.7.1
     pydicom: 2.1.2
     Pygments: 2.9.0
     PyOpenGL: 3.1.5
     PyOpenGL-accelerate: 3.1.5
     pyparsing: 2.4.7
     PyQt5-commercial: 5.15.2
     PyQt5-sip: 12.8.1
     PyQtWebEngine-commercial: 5.15.2
     python-dateutil: 2.8.1
     pytz: 2021.1
     pyzmq: 22.1.0
     qtconsole: 5.1.0
     QtPy: 1.9.0
     RandomWords: 0.3.0
     requests: 2.25.1
     scipy: 1.6.3
     setuptools: 57.0.0
     sfftk-rw: 0.7.0.post1
     six: 1.16.0
     snowballstemmer: 2.1.0
     sortedcontainers: 2.4.0
     Sphinx: 4.0.1
     sphinxcontrib-applehelp: 1.0.2
     sphinxcontrib-blockdiag: 2.0.0
     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-jurko: 0.6
     tables: 3.6.1
     tifffile: 2021.4.8
     tinyarray: 1.2.3
     tornado: 6.1
     traitlets: 5.0.5
     urllib3: 1.26.6
     wcwidth: 0.2.5
     webcolors: 1.11.1
     wheel: 0.36.2
     wheel-filename: 1.3.0

 }}}

--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5034>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

comment:2 by pett, 4 years ago

Component: Unassigned → Command Line
Owner: set to Greg Couch
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Error in warning message when alias overridden
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