id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
14976	Make blastprotein command load structures and alignment without GUI	Tom Goddard	Zach Pearson	"I'd like 3 new options to the blastprotein command

   blastprotein ... gui false loadStructures true showSequenceAlignment true

that allow loading all the atomic structures found and showing the sequence alignment without doing these steps through the GUI and without showing the GUI.  The use is that I am making a tool to explore the differences between tens or hundreds or thousands of homolog structures that come from PDB or the AlphaFold database, looking at kinases with Klim Verba as an example system.  Currently I have to run Blast then select all the lines in the gui and press the buttons.  We'll be doing this for many different Blast searches, so being able to do it by command is much easier than all the mouse clicking.  In general in ChimeraX we have tried to make command equivalents for all GUI tools to allow scripting, and heavy repeated use where the GUI is not needed.

Besides these 3 new options I also want the loaded structures to be associated with their sequences in the sequence alignment.  Currently when using the BLAST GUI the structures get associated automatically and that causes them to be associated with the wrong sequence alignment lines, probably because their are identical sequences in the alignment.  So structure 4xv9_A should associate with the alignment sequence named 4xv9_A.  In my current kinase example with 211 sequence (4xv9 chain A sequcence, 1e-100 evalue cutoff) almost every structure is associated with a different sequence in the alignment."	enhancement	closed	high		Sequence		fixed		Elaine Meng Eric Pettersen				all	ChimeraX