From 8bd52017fd5da2da5f9423365e0cb85d6d48c37b Mon Sep 17 00:00:00 2001 From: Martin Steinegger Date: Sat, 9 Jul 2022 01:28:19 +0900 Subject: [PATCH] Update README.md --- README.md | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index b852f32e..2be0dbae 100644 --- a/README.md +++ b/README.md @@ -78,7 +78,12 @@ In case of the alignment type (`--alignment-type 1`) tmalign we sort the results ### Rescore aligments using TMscore -It is possible to compute TMscores for the kind of alignment output (e.g. 3Di/AA) using the following commands: +Easiest way to get the alignment TMscore normalized by min(alnLen,qLen,targetLen) as well as a rotation matrix is through the following command: +``` +foldseek easy-search example/ example/ aln tmp --format-output query,target,alntmscore,u,t +``` + +Alternative, it is possible to compute TMscores for the kind of alignment output (e.g. 3Di/AA) using the following commands: ``` foldseek createdb example/ targetDB foldseek createdb example/ queryDB