Fix some remaining uses of invalid atom coordinates
Fix some remaining uses of invalid atom coordinates

jkonecny12/kakoune,occivink/kakoune,jjthrash/kakoune,casimir/kakoune,danr/kakoune,alexherbo2/kakoune,occivink/kakoune,occivink/kakoune,Somasis/kakoune,casimir/kakoune,Somasis/kakoune,danr/kakoune,lenormf/kakoune,lenormf/kakoune,danr/kakoune,mawww/kakoune,mawww/kakoune,jjthrash/kakoune,jkonecny12/kakoune,alexherbo2/kakoune,casimir/kakoune,jjthrash/kakoune,alexherbo2/kakoune,alexherbo2/kakoune,danr/kakoune,jkonecny12/kakoune,Somasis/kakoune,occivink/kakoune,casimir/kakoune,jkonecny12/kakoune,jjthrash/kakoune,mawww/kakoune,lenormf/kakoune,Somasis/kakoune,mawww/kakoune,lenormf/kakoune