On 04/14/2016 07:19 PM, Robert Hanson wrote:
> 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
>
I tried 'select within(dssr,"basePairs")' and 'select
within(basepair,"GCAT")' for PDB entry '3cro' at
http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm (see examples below) and
didn't get the expected results.
In example 1 also about 300 protein atoms were selected, and in example
2 also about 900 protein atoms were selected.
In example 3 two basepairs were not recognized, but at least no protein
atoms were selected. Adding 'calculate structure dssr' didn't make a
difference.
----- Example 1 ----------------
load =3cro
calculate structure dssr
cartoon only
selectionhalos on
select within(dssr,"basePairs")
----- Example 2 ----------------
load =3cro/dssr
cartoon only
selectionhalos on
select within(dssr,"basePairs")
----- Example 3 ----------------
load =3cro
cartoon only
selectionhalos on
select within(basepair,"GCAT")
--------------------------------
Regards,
Rolf
--
Rolf Huehne
Postdoc
Leibniz Institute on Aging - Fritz Lipmann Institute (FLI)
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07745 Jena, Germany
Phone: +49 3641 65 6205
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E-Mail: rolf.hue...@leibniz-fli.de
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