RNA is a bit tricky because the pairing can be rather loose. But here's a
slick way: Use Jmol bioSMILES.
load =1d66
calculate hbonds # necessary for defining the connections
selectionhalos on
select within(group,within(smiles,"~d~G(C)"))
delay 1
select within(group,within(smiles,"~d~A:T"))
# ~d~ means "DNA" (and not ~r~, RNA, or ~p~, protein)
# G(C) or G:C means "G base-paired with C"
# Note that you can specify two-base sets as well using the SMILES ring
nomenclature:
select within(group,within(smiles,"~d~G:1A:TC:1"))
# The ":" there means "base-paired with" so this is GA paired with TC (going
the other way on the other chain).
# For more details, see
http://jmol.svn.sourceforge.net/viewvc/jmol/trunk/Jmol/src/org/jmol/smiles/package.html
Bob
2011/3/5 Angel Herráez <[email protected]>
> Hi all
>
> I am tryng to write a script that will detect paired bases (A-U, G-C) in a
> RNA molecule.
> Before I start trying, any ideas about how to address it would be welcome.
>
> For now, I am thinking of using WITHIN with distance.
> (I am assuming that in large pdb files maybe the hbonds detection is not
> reliable, so I would
> not depend on that)
>
> Thanks for any ideas
> Angel
>
>
>
>
>
>
> ------------------------------------------------------------------------------
> What You Don't Know About Data Connectivity CAN Hurt You
> This paper provides an overview of data connectivity, details
> its effect on application quality, and explores various alternative
> solutions. http://p.sf.net/sfu/progress-d2d
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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
------------------------------------------------------------------------------
What You Don't Know About Data Connectivity CAN Hurt You
This paper provides an overview of data connectivity, details
its effect on application quality, and explores various alternative
solutions. http://p.sf.net/sfu/progress-d2d
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