On Oct 17, 2012, at 9:47 AM, Marek Maly wrote:

Hello all,

#1
I am just curious if it is in Chimera implemented possibility
to select all the molecules which are connected via H-bonds with previously
selected ("primary") molecule.

If it is not implemented I would vote for putting it in the developers queue
as it would allow to show easily and clearly (after action command "show selected only") just
all the molecules from the given solution directly interacting
with previously selected "primary" molecule and it would be a nice and useful feature I think.

Perhaps the optimal solution would be to add into "H-bond Parameters" table an additional "clik choice" which would ensure (if marked) that together with visualizing of all H-bonds (defined in the table) will be also selected all molecules which are connected by that H-bonds.

(as the supplementary option might be eventually selection of end residues only (not whole molecules) which might be also useful in some cases)

Hi Marek,
This is sort of possible now, depending on whether your molecules are single residues or separate models.  Here's the recipe:

1) Find the H-bonds
2) Go to Tools->General Controls and open the Pseudobond Panel
3) Select the hydrogen bonds group in the panel
4) Click the panel's Select Bonded button
5) Use the up arrow key to increase the selection to residues (if your molecules are residues, e.g. water), or use up arrow a few more times if your molecules are models.

If your molecules aren't single residues / chains / models then you are kind of stuck, since the selection increase/decrease mechanism doesn't have a "molecule" level per se.  Perhaps I could make it so that if you hold the shift key down with up-arrow, the selection changes

atom -> residue -> connected fragment (molecule) -> model

instead of

atom -> residue -> chain (by chain ID) -> model

I'll think about it.

#2
Similarly would be cool to have in menu-table "Select -> Zone..." except

"Select all atoms/bonds of any residue in selection zone" also
possibility like:

"Select all atoms/bonds of any MOLECULE having at least one atom in selection zone".

Then again using the action "show selected only" one might have quick and nice
picture only of all and WHOLE molecules which are in the defined neighbourhood of the
initially selected "primary" molecule.

Again, up-arrow could possibly be helpful here.  Nonetheless, a useful suggestion.


#3
Perhaps  is it shame :)) but until now I was not able to find the right button to clear/delete
previously visualized H-bonds.

So my solution (probably not so much elegant) is that I simply select one atom (which is
really not the candidate for H-bond ) like C atom and then I ask to visualize all H-bonds
which has this atom as the one end. So naturally no H-bond is found and if
I do not mark "Retain currently displayed H-bonds" also the previously visualized H-bonds
are deleted. But perhaps there is more elegant solution, if not button so at least some command ?

The command "~hb" will remove H-bonds.  Also, in the Pseudobond Panel you can close the "hydrogen bonds" group.

--Eric

                        Eric Pettersen

                        UCSF Computer Graphics Lab

                        http://www.cgl.ucsf.edu