[Chimera-users] H-bonds - molecules selection questions

Marek Maly marek.maly at ujep.cz
Wed Oct 17 09:47:18 PDT 2012

Hello all,

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  
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)

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  
picture only of all and WHOLE molecules which are in the defined  
neighbourhood of the
initially selected "primary" molecule.

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 ?

   Thanks in advance !

       Best wishes,


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