[Chimera-users] Re: Difference between command line and menus

Thank you for your answer (sorry for the delay, I was not working for 3 days) I am using chimera (not chimeraX), but I could change if needed The command I use is this one : open 1 fic.mol2 ; findhbond intramodel false saveFile LHfic ; findclash #0 test #1 overlapCutoff 0.0 saveFile contact_fic; close 1 when I use the menu: - Find clashes/contact Atoms to check : second set of designed atoms Clash/contact parameters : Find atoms with vDw overlap 0.0 angsrom substract 0.0 from overlap .... I supposed it should do the same, but maybe not.... Edith