From 9a0e474e892cfd6978931854572965bbf88f8a31 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Mon, 14 Feb 2022 22:58:01 +0000 Subject: [PATCH] JAL-3551 --- src/jalview/ext/pymol/PymolCommands.java | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/src/jalview/ext/pymol/PymolCommands.java b/src/jalview/ext/pymol/PymolCommands.java index 36957f5..652682a 100644 --- a/src/jalview/ext/pymol/PymolCommands.java +++ b/src/jalview/ext/pymol/PymolCommands.java @@ -110,10 +110,11 @@ public class PymolCommands extends StructureCommandsBase { // https://pymolwiki.org/index.php/Super List commands = new ArrayList<>(); - String refAtomsAlphaOnly = getAtomSpec(refAtoms, true); - String atomSpec2AlphaOnly = getAtomSpec(atomSpec, true); - commands.add(new StructureCommand("super", refAtomsAlphaOnly, - atomSpec2AlphaOnly)); + String refAtomsAlphaOnly = "("+getAtomSpec(refAtoms, true)+" and (altloc '' or altloc 'a'))"; + String atomSpec2AlphaOnly = "("+getAtomSpec(atomSpec, true)+" and (altloc '' or altloc 'a'))"; + // pair_fit mobile -> reference + commands.add(new StructureCommand("pair_fit", + atomSpec2AlphaOnly, refAtomsAlphaOnly)); /* * and show superposed residues as cartoon -- 1.7.10.2