From 561fd62de568d6669f70c3eb22078d94cc0fb902 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Andr=C3=A1s=20Szil=C3=A1gyi?= Date: Tue, 20 Jun 2023 15:09:50 +0200 Subject: [PATCH] Update README.md to include the -s 4 option and info about hydrogen atoms --- README.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 6453135..85f4b81 100644 --- a/README.md +++ b/README.md @@ -27,7 +27,7 @@ EDTSurf -i inputfile ... Specific options: - -o prefix of output files (default is the prefix of inputfile) - -t triangulation type, 1-MC 2-VCMC (default is 2) -- -s surface type, 1-VWS 2-SAS 3-MS 0-DEPTH (default is 3) +- -s surface type, 1-VWS 2-SAS 3-MS 4-SES 0-DEPTH (default is 3) - -c color mode, 1-pure 2-atom 3-chain (default is 2) - -p probe radius, float point in [0,2.0] (default is 1.4) - -h inner or outer surface for output, 1-inner and outer 2-outer 3-inner (default is 1) @@ -35,6 +35,8 @@ Specific options: Molecule is scaled by this factor to fit in a bounding box. Scale factor is the larger the better, but will increase the memory use. Our strategy is first enlarging the molecule to check if it exceeds the maximum bounding box. If yes, then reset a proper scale factor to fit the molecule in the maximum bounding box. +NOTE: Option -s 3 (MS, i.e. molecular surface calculation) ignores hydrogen atoms, while option -s 4 (SES, solvent excluded surface) takes them into account. + ## Outputs: 1. outname.ply triangulated mesh surface (viewable by meshlab software)