I will pass for the moment. I have solved my questions.
> On Apr 14, 2016, at 1:59 PM, Rolf Huehne <rolf.hue...@leibniz-fli.de> wrote:
>
> 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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>
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>
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Philip Bays
Emeritus Professor of Chemistry
Saint Mary's College
Notre Dame, IN 46556
pb...@saintmarys.edu
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