Ignore non-protein sequences for some operations

[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
minor RFE: maybe realignment should discard nonprotein sequences when specified by chain-spec that includes both protein and nucleic.

For example,

open 1an4
seq align #1

... gives a multiple alignment of 2 protein chains and 2 nucleic acid chains

Maybe this also applies to alphafold when a chain-spec is used to specify input sequence(s).   

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 4enl format mmcif fromDatabase pdb

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 #1  
---  
Chain | Description | UniProt  
A | enolase | ENO1_YEAST  
  
Non-standard residues in 4enl #1  
---  
SO4 — sulfate ion  
ZN — zinc ion  
  
4enl mmCIF Assemblies  
---  
1| author_defined_assembly  
  

> close

> open 1an4 format mmcif fromDatabase pdb

1an4 title:  
Structure and function of the B/HLH/Z domain of usf [more info...]  
  
Chain information for 1an4 #1  
---  
Chain | Description | UniProt  
A B | protein (upstream stimulatory factor) | USF1_HUMAN  
C | DNA (5'-D(*CP*ap*CP*CP*CP*GP*GP*TP*CP*ap*CP*GP*TP*GP*GP*CP*C
P*TP*ap*CP*A)-3') |  
D | DNA (5'-D(*GP*TP*GP*TP*ap*GP*GP*CP*CP*ap*CP*GP*TP*GP*ap*CP*C
P*GP*GP*GP*T)-3') |  
  

> 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 1  
Associated 1an4 chain A to chain B with 0 mismatches  
Associated 1an4 chain B to chain B with 0 mismatches  
Associated 1an4 chain C to chain C with 0 mismatches  
Associated 1an4 chain D to chain D with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  




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: 6:40

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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    ChimeraX-SaveCommand: 1.5
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    ChimeraX-SideView: 1.0
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[Eric Pettersen]

Realignment now tosses non-protein sequences. Reassigning to T.G. for possible alphafold remediation.