Phil, you should check out DSSR. It is amazing! Sorry this is not
documented yet:
new feature: select shortcuts for nucleic acid structures
-- for example: select junctions; select kissingloops
-- activated after load =xxxx/dssr or calculate structure dssr
-- includes:
"@bulges within(dssr,'bulges')",
"@coaxStacks within(dssr,'coaxStacks')",
"@hairpins within(dssr,'hairpins')",
"@hbonds within(dssr,'hbonds')",
"@helices within(dssr,'helices')",
"@iloops within(dssr,'iloops')",
"@isoCanonPairs within(dssr,'isoCanonPairs')",
"@junctions within(dssr,'junctions')",
"@kissingLoops within(dssr,'kissingLoops')",
"@multiplets within(dssr,'multiplets')",
"@nonStack within(dssr,'nonStack')",
"@nts within(dssr,'nts')",
"@naChains within(dssr,'naChains')",
"@pairs within(dssr,'pairs')",
"@ssSegments within(dssr,'ssSegments')",
"@stacks within(dssr,'stacks')",
"@stems within(dssr,'stems')",
load =1d66/dssr
$ print _M.dssr.pairs.select("(nt*) where bp='C-G' or bp='G-C'")
|1|E|DG|38||||
|1|D|DC|1||||
|1|E|DG|37||||
|1|D|DC|2||||
...
|1|D|DG|19||||
$ x= _M.dssr.pairs.select("(nt*) where bp='C-G' or bp='G-C'")
$ select x
Works for RNA and DNA
On Thu, Apr 14, 2016 at 9:07 AM, Philip Bays <pb...@saintmarys.edu> wrote:
> This is for the biomolecular people:
>
> How does one use the term “Selected”? Seems to me that it is redundant.
>
> In the Nucleic Acid area: How does one use CG and AT to select base
> pairing?
>
> Perhaps these are not implemented in Jmol?
>
> PS I am finding today’s version to work well for my purposes, which are
> limited. And HEM now works:-)
>
> Philip Bays
> Emeritus Professor of Chemistry
> Saint Mary's College
> Notre Dame, IN 46556
> pb...@saintmarys.edu
>
>
>
>
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--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
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
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