On Mon, Mar 29, 2010 at 10:23 PM, Eric Martz <[email protected]>wrote:
> Currently, FirstGlance in Jmol suggests hydrogen bonds whenever a
> nitrogen or oxygen is within 3.5 Angstroms of another nitrogen or
> oxygen. This crude method fails to take into account whether or not
> either atom actually has a hydrogen to donate, and the angle of the
> acceptor to the donor.
>
> If the model contains all hydrogens (or once Jmol can add them), is
> Jmol capable of selecting donor-acceptor pairs using not only
> distance, but angular criteria?
>
>
the currently undocumented measure() function gets you access to the sort of
thing you can do with measure, but in code. or, if you do use the measure
command, then you can use the array information in getProperty measureInfo
to do more with that.
> For example, in 3hyd,
>
> see http://proteopedia.org/wiki/index.php/User:Eric_Martz/Sandbox_10
>
>
java.io.FileNotFoundException:
http://proteopedia.org/wiki/scripts/User:Eric_Martz/Sandbox_10/Hbond_angles_to_n-term/1.spt
> [Leu1]:A.N #1 is donating [Leu1]:A.H3 #11 to HOH8 #135 at 126.4
> degrees (donor to acceptor distance 2.8 Angstroms), or to HOH10 #137
> at 154.9 degrees (D-A distance 3.1 A).
>
> Can I select one or the other (and which would be the stronger
> hbond?) based on these angles? What would the script commands be?
>
> Thanks, -Eric
>
>
>
>
> ------------------------------------------------------------------------------
> Download Intel® Parallel Studio Eval
> Try the new software tools for yourself. Speed compiling, find bugs
> proactively, and fine-tune applications for parallel performance.
> See why Intel Parallel Studio got high marks during beta.
> http://p.sf.net/sfu/intel-sw-dev
> _______________________________________________
> Jmol-users mailing list
> [email protected]
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
--
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
------------------------------------------------------------------------------
Download Intel® Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev
_______________________________________________
Jmol-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-users
