Hi Vincent Don't be concerned about asking, this is the place for that. We all learn from each other.
> 1. I'm trying to select residue of the protein within a given cutoff > distance from a previously selected set of atoms.Currently I'm using : > > select amino and within(5.0, STP2) ; > color red ; > > which select atoms within 5A from atoms of the residue named STP2. But > I want to select residue within 5A, and not only atoms. Is it possible > to do so? "within" is very powerful and I'm quite sure it should allow you to do that. http://chemapps.stolaf.edu/jmol/docs/#atomexpressions WITHIN(setName,atomExpression) "The setName can be any one of the words BOUNDBOX, CHAIN, ELEMENT, GROUP, MODEL, MOLECULE, SITE, or STRUCTURE" Of these, "group" should do it, when combined with distance. I have not used this often, but something like Do you want (a) that the whole residue is within 5A, or (b) that any of its atoms is within 5A? select amino and within(group, within(5.0, STP2) ); # will do (b) Also, consider if you need "amino" or "protein". They are slightly different when nonstandard residues are involved. > 2. I want to allow the user to display/hide severl selections. To do > so, I use a checkbox in the applet: > > jmolCheckbox('select pockets and resNo=2; hide none; select none;', > 'hide pockets and resNo=2;', > 'Show alpha spheres for site 3', true) 'select pockets and resNo=2; hide none; select none;' is cancelling itself. No point doing it so: you select and unselect. > The problem is that the hide none apply to the whole system, not to > the selection I made before. Of course. So maybe you want display displayed,selected ? Anyway, any new selection cancels the previous one, so may you don't need this. You cannot keep several selections in memory, If you want to control several atoms sets, it's better to use user-named atom sets. The command is "define". > display pockets and resNo=2 > > But this command results in displaying only the selection. Is it > possible to turn hiding off for a given selection only ? Both display and hide are global. You must combine them like in display displayed, myNewSet hide hidden, myNewSet meaning "add atoms in myNewSet to whatever is already displayed, or hidden" Let us know if you find the cure. ------------------------------------------------------------------------------ Return on Information: Google Enterprise Search pays you back Get the facts. http://p.sf.net/sfu/google-dev2dev _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
