Option to number based on reference sequence

[olibclarke@…]

The following bug report has been submitted:
Platform:        Darwin-18.5.0-x86_64-i386-64bit
ChimeraX Version: 0.9 (2019-04-28)
Description
Sequence viewer numbering (feature request)

Hi,

Would it be possible at some point to add a preference for the upper scale of a sequence alignment loaded in ChimeraX to reflect the numbering of a selected reference sequence, rather than the alignment position? The numbering of the reference sequence is much more useful when cross referencing with a structure, I think.

Cheers
Oli

Log:
UCSF ChimeraX version: 0.9 (2019-04-28)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
/Users/olibclarke/Dropbox/Downloads/muscle-I20190426-161819-0369-68254776-p2m.fasta.txt

Unrecognized file suffix '.txt'  

> open
/Users/olibclarke/Dropbox/Downloads/muscle-I20190426-161819-0369-68254776-p2m.fasta

Summary of feedback from opening
/Users/olibclarke/Dropbox/Downloads/muscle-I20190426-161819-0369-68254776-p2m.fasta  
---  
note | Alignment identifier is muscle-I20190426-161819-0369-68254776-p2m.fasta  
  
Opened 7 sequences from muscle-I20190426-161819-0369-68254776-p2m.fasta  




OpenGL version: 4.1 INTEL-12.8.38
OpenGL renderer: Intel(R) Iris(TM) Graphics 6100
OpenGL vendor: Intel Inc.

[pett]

Many of the features of the Chimera 1 sequence viewer don't yet exist in the ChimeraX viewer, but will once I have time to implement them. One of those features is to put sequence-specific numberings to the left (and/or right) of each sequence. Would the be sufficient? It isn't *quite* as good as having the numbering on top, but on the other hand is unambiguous as to what sequence the numbering refers to.

[olibclarke@…]

Hi Eric

If there are going to be numbers on top, I would much rather have those numbers correspond to a user-settable reference sequence, rather than the alignment position, which I don’t find useful in this context - it doesn’t convey any information that I can relate to whatever structure I’m looking at. Having said that, sequence specific numberings on the left/right would be a great improvement, and I know you all have a lot on your to-do list!

Cheers
Oli

[pett]

Okay, I went ahead and implemented your suggestion rather than the variant I had suggested. In tomorrow's daily build there will be a "Numberings" entry in the sequence viewer context menu that allows you to control what sequence to use as the reference for the overall numbering (until a reference sequence is specified, the top numbering behaves as it always has), as well as control over whether the left and right side numberings are shown or not.