Opened 6 years ago

Closed 5 years ago

#1930 closed enhancement (fixed)

RFE: Blast Protein ability to use sequence from Sequence Viewer as query

Reported by: Elaine Meng Owned by: pett
Priority: major Milestone:
Component: Sequence Version:
Keywords: Cc: pett
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description

At least for the command, we already have ways to specify an individual sequence in Sequence Viewer (see "modeller" and "sequence associate" commands).

Change History (6)

comment:1 by pett, 6 years ago

FYI, you can import SeqArg from chimerax.seqalign

comment:2 by Conrad Huang, 6 years ago

Shouldn't this be an addition to the Sequence Viewer? What UI would Blast Protein offer to select a sequence? Do I query the Sequence Manager?

comment:3 by pett, 6 years ago

It can be added to the sequence viewer, but only once the blast _command_ supports a sequence argument.

comment:4 by Conrad Huang, 6 years ago

Owner: changed from Conrad Huang to pett

1fdb46b74 adds support for alignment:seq as alternative to atomspec.

in reply to:  5 ; comment:5 by Elaine Meng, 6 years ago 

Results structure fetch will have to contend with the possibility of not having a query-chain structure to superimpose with matchmaker.  Maybe you already dealt with that.

comment:6 by pett, 5 years ago

Resolution: → fixed
Status: assigned → closed

Sequence viewer's context menu now has an Info category from which the sequences can be blasted

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