Improve File→Save when multiple alignments open

[Elaine Meng]

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.4.dev202112290158 (2021-12-29 01:58:43 UTC)
Description
Using File... Save to save an alignment format when more than one alignment is open gives an error.   
Possible improvements 
(1) put an alignment-chooser in the Save dialog
(2) remove alignment formats from Save dialog to avoid the problem

However,  maybe having more than one alignment is relatively rare so doing nothing is another option.

Log:
> open /Users/meng/Desktop/startup.cxc

> alias reset view orient; view initial

> alias start tool show $1

> alias whereprefs info path user unversioned config

> alias captut open help:user/tutorials/binding-sites.html#cap-example

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

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

> alias btut open
> https://www.cgl.ucsf.edu/home/meng/chimerax/vdocs/user/tutorials/binding-
> sites.html

> alias stut open https://www.rbvi.ucsf.edu/chimerax/data/conservation-
> coloring/conservation-coloring.html

> alias ltut open https://www.rbvi.ucsf.edu/chimerax/data/loop-modeling/loop-
> modeling.html; ui dockable false "Help Viewer"

executed startup.cxc  
UCSF ChimeraX version: 1.4.dev202112290158 (2021-12-29)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/meng/Desktop/startup.cxc format cmd

> alias reset view orient; view initial

> alias start tool show $1

> alias whereprefs info path user unversioned config

> alias captut open help:user/tutorials/binding-sites.html#cap-example

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

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

> alias btut open
> https://www.cgl.ucsf.edu/home/meng/chimerax/vdocs/user/tutorials/binding-
> sites.html

> alias stut open https://www.rbvi.ucsf.edu/chimerax/data/conservation-
> coloring/conservation-coloring.html

> alias ltut open https://www.rbvi.ucsf.edu/chimerax/data/loop-modeling/loop-
> modeling.html; ui dockable false "Help Viewer"

executed startup.cxc  

> open 2mnr

2mnr title:  
Mechanism of the reaction catalyzed by mandelate racemase. 2. Crystal
structure of mandelate racemase At 2.5 angstroms resolution: identification of
the active site and possible catalytic residues [more info...]  
  
Chain information for 2mnr #1  
---  
Chain | Description | UniProt  
A | mandelate racemase | MANR_PSEPU  
  
Non-standard residues in 2mnr #1  
---  
MN — manganese (II) ion  
SO4 — sulfate ion  
  
2mnr mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  

> open 4enl

4enl title:  
Crystal structure of holoenzyme refined At 1.9 angstroms resolution: trigonal-
bipyramidal geometry of the cation binding site [more info...]  
  
Chain information for 4enl #2  
---  
Chain | Description | UniProt  
A | enolase | ENO1_YEAST  
  
Non-standard residues in 4enl #2  
---  
SO4 — sulfate ion  
ZN — zinc ion  
  
4enl mmCIF Assemblies  
---  
1| author_defined_assembly  
  

> open 1muc

1muc title:  
Structure of muconate lactonizing enzyme At 1.85 angstroms resolution [more
info...]  
  
Chain information for 1muc #3  
---  
Chain | Description | UniProt  
A B | muconate lactonizing enzyme | CATB_PSEPU  
  
Non-standard residues in 1muc #3  
---  
MN — manganese (II) ion  
  
1muc mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  

> close #3

> mmaker #2 to #1 show true

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 2mnr, chain A (#1) with 4enl, chain A (#2), sequence alignment
score = 219.9  
Alignment identifier is 1  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Hiding conservation header for alignment 1  
Chains used in RMSD evaluation for alignment 1: 2mnr #1/A, 4enl #2/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1  
RMSD between 73 pruned atom pairs is 1.307 angstroms; (across all 312 pairs:
12.638)  
  
Traceback (most recent call last):  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 297, in execute  
cmd.run(cmd_text)  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2853, in run  
prev_annos = self._process_positional_arguments()  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2629, in
_process_positional_arguments  
value, text = self._parse_arg(anno, text, session, False)  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2488, in _parse_arg  
value, replacement, rest = annotation.parse(text, session)  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 890, in parse  
return anno.parse(text, session)  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/args.py", line 159, in parse  
token, used, rest = next_token(text)  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 1816, in next_token  
assert text and not text[0].isspace()  
AssertionError  
  
AssertionError  
  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 1816, in next_token  
assert text and not text[0].isspace()  
  
See log for complete Python traceback.  
  

> sequence align 1

Web Service: CLUSTAL-OMEGA (v1.1.0) is a general purpose multiple sequence
alignment program for protein and DNA/RNA.  
Alignment identifier is 2  
Associated 2mnr chain A to 2mnr, chain A with 0 mismatches  
Associated 4enl chain A to 4enl, chain A with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2  

> usage seq align

sequence align seqSource [program program]  
— align sequences  
seqSource: alignment-id or sequences  
program: one of clustal, clustalOmega, muscle, or omega  

> sequence align 1 muscle

Expected a keyword  

> sequence align 1 program muscle

Web Service: MUSCLE (v3.8.31) stands for MUltiple Sequence Comparison by Log-
Expectation.  
Alignment identifier is 3  
Associated 2mnr chain A to 2mnr, chain A with 0 mismatches  
Associated 4enl chain A to 4enl, chain A with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 3  

> save /Users/meng/Desktop/nerf.fa

More than one alignment open; use 'alignment' keyword to specify one  




OpenGL version: 4.1 Metal - 76.1
OpenGL renderer: Apple M1 Pro
OpenGL vendor: AppleHardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,1
      Processor Name: Unknown
      Processor Speed: 2.4 GHz
      Number of Processors: 1
      Total Number of Cores: 10
      L2 Cache: 20 MB
      Memory: 16 GB

Software:

    System Software Overview:

      System Version: macOS 12.0.1 (21A559)
      Kernel Version: Darwin 21.1.0
      Time since boot: 3:03

Graphics/Displays:

    Apple G13X:

      Chipset Model: Apple G13X
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 16
      Vendor: Apple (0x106b)
      Metal Family: Supported, Metal GPUFamily Apple 7
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3456 x 2234 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal

Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
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    appdirs: 1.4.4
    appnope: 0.1.2
    Babel: 2.9.1
    backcall: 0.2.0
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    certifi: 2021.5.30
    cftime: 1.5.1.1
    charset-normalizer: 2.0.9
    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.11
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    ChimeraX-AtomicLibrary: 5.0
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    ChimeraX-BasicActions: 1.1
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    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.2
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4.dev202112290158
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
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    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: 2.1.2
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    ChimeraX-HKCage: 1.3
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    ChimeraX-Toolbar: 1.1
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    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
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    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
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