Allow alphafold sequences argument to handle subsequences from a sequence viewer panel

[Tom Goddard]

The SequencesArg in the atomic bundle can be specified with a alignment-id and sequence id like "1:1". But it cannot handle a subregion of such a sequence that was desired in ticket #6001 where the Martti was trying to run alphafold on a subsequence of an open structure. The modeller command handles such subsequences with specifiers like "1:1:18-450" where the last part is a sequence region in gapped sequence viewer numbering. Might be nice to allow that. It may be very error prone because the user will quite possibly think the associated structure residue numbering is being used. Still it might be useful to someone some day as an alternative to pasting in an explicit trimmed sequence in the alphafold command.

Begin forwarded message:

From: Elaine Meng
Subject: specifying a sub-sequence in a command
Date: January 26, 2022 at 2:22:32 PM PST
To: Tom Goddard

Eric reminded me that there is actually a mechanism to specify part of a sequence in the Sequence Viewer but that you would have to use a different parsing routine. See for example "modeller loops" syntax:

<​https://www.cgl.ucsf.edu/home/meng/chimerax/vdocs/user/commands/modeller.html>
<​https://www.cgl.ucsf.edu/home/meng/chimerax/vdocs/user/commands/modeller.html#loops-details>