Angel Herraez wrote: >Hi > >I imagined that "set bondMode or" would affect the behaviour of >"restrict" and "hide", so that a bond between an atom that won't be >hidden and another that will be hidden remains visible. > > not possible, I think. The hiddenness of the atom on one end of the bond makes that bond unviewable.
>It seems that this is not so. The hidden atom goes away together with >its bond. >Example: >I have a ligand with one covalent bond linking it to a protein. I >give "set bondMode or; restrict ligand" or "set bondMode or; hide not >ligand" and I would like the ligand and its bond to the protein to be >seen (without any atom on the protein). >(i.e., the same that happens --regarding bond width instead of >showing/hiding-- if I use >"set bondMode or; select ligand; wireframe 0.4" ) > > > then you probably have to do it that way. >Does this idea make sense to others? >Would it be possible to implement? I would vote as the only option, >or the default, since the use of "set bondMode" is quite purposeful, >not accidental (the default is "set bondMode and"). > > > I don't think it's possible -- hiddenness is a very low-level aspect -- bonds aren't hidden, just atoms. If anything, the bond would have to be "half-hidden", but bonds are drawn from atom to atom, not from atom to half-way to the other atom. Also, hidden means just that -- hidden. If you draw a bond to a hidden atom, you effectively unhide it. So I think if you want to do this what you should do is display ligand or connected(ligand) select connected(ligand); spacefill off;wireframe 0.4 or something like that, and you will get your bond. > >------------------------------------------------------------------------- >Take Surveys. Earn Cash. Influence the Future of IT >Join SourceForge.net's Techsay panel and you'll get the chance to share your >opinions on IT & business topics through brief surveys - and earn cash >http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV >_______________________________________________ >Jmol-users mailing list >Jmol-users@lists.sourceforge.net >https://lists.sourceforge.net/lists/listinfo/jmol-users > > ------------------------------------------------------------------------- Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
