From a146a6e4655a2aebda35e272fdd6ddb4dfef4434 Mon Sep 17 00:00:00 2001 From: Andrew Jewett Date: Wed, 2 Feb 2022 12:15:13 -0800 Subject: [PATCH] updated README and tests --- README.md | 7 ++++--- tests/test_align2msf.sh | 1 + 2 files changed, 5 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index a65eb00..cdeab7b 100644 --- a/README.md +++ b/README.md @@ -8,8 +8,9 @@ minrms ## Background -Similarity in the amino acid sequence of proteins can be difficult -to detect if they are evolutionarily distant. +Proteins from evolutionarily distant ancestors can have amino acid sequences +which are so different that traditional sequence alignment methods can +fail to detect any similarity. However similarity in the 3D structure of proteins often persists long [after the sequences have diverged.](https://doi.org/10.1006/jmbi.1993.1489) It is possible to detect evolutionary similarity between proteins from @@ -75,7 +76,7 @@ and all of "myoglobin.pdb", with the following constraints: You can relax these constraints by ignoring the optional arguments above: ``` -minrms -fm 4 hemoglobin.pdb,"*.A" myoglobin.pdb +minrms -fm 4 -ir -r hemoglobin.pdb,"*.A" myoglobin.pdb ``` *(This will run much more slowly and is not recommended.)* diff --git a/tests/test_align2msf.sh b/tests/test_align2msf.sh index 3638bc6..29749a8 100644 --- a/tests/test_align2msf.sh +++ b/tests/test_align2msf.sh @@ -13,6 +13,7 @@ test_align2msf() { mv myoglobin.pdb 1a6m.pdb python3 ../bin/align2msf/align2msf.py align_server_output/1a6m+4hhbA.txt 1a6m.pdb 4hhb.pdb > align2msf_output.msf FILE_SIZE=`wc -c align2msf_output.msf | awk '{print $1}'` + echo $FILE_SIZE assertTrue "align2msf.py failed" "[ $FILE_SIZE -eq 1578 ]" #rm -f align2msf_output.msf cd ../