Re: [Jmol-users] Hydrogen Atoms Shared Between Amino Acids

[Robert H. <ha...@st...>]

Sara,

In answer to your question, hydrogens are assigned to groups by attachment,
not distance.

Do check your version. Could be there was some bug at one point relating to
this, but I don't see it now. Are you saying that with

selectionHalos on

you get that H highlighted both with

select 232

and with

select 227

? I remember at one point we had the problem that Hs were not being added
to groups, but that's been fixed long ago.

Bob Hanson




On Fri, Mar 9, 2012 at 3:50 PM, Sara Bonner <bo...@mi...> wrote:

> HI
>
> Using the set addPdbHydrogens functionality I am finding that sometimes
> the hydrogens are associated with more than one amino acid.  Are you making
> the hydrogen selection based on the label of the hydrogen or based on its
> distance from the surrounding atoms?  Is there any way to have control over
> this?
>
> Example:
> set addPdbHydrogens;
> load=1H6I;
> select [ALA]232:A;
> spacefill 100%;
> select [TYR]227:A;
> spacefill 50%;
>
> Note how the hydrogen atom labeled [ALA]232:A.H #3348 changes in size for
> both selections.
>
> This becomes relevant for me as I am sorting hydrogen bonds according to
> the structures they apply to.  From the example given about, according to
> the label on the hydrogen this should be a tertiary hbond between the
> oxygen in 227 and the hydrogen in 232 and that part works fine.  The
> problem comes in when this same hbond is added to the secondary hbonds.
>  Because both the O and H atoms are considered to be in the same amino acid
> bondMode AND doesn't help.
>
> Thanks
> Sara
>
>
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-- 
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900