Thanks Rolf!
PM
Forwarded per Rolf's request
On 01/28/2016 07:08 PM, Pshemak Maslak wrote:
>
> The new DSSR has base pairs and nucleotide indexed by numbers, For
> example (the 9th base-pair):
>
> auxiliaryinfo.models[1].dssr.pairs[9].bp "A-T"
> auxiliaryinfo.models[1].dssr.pairs[9].nt1 "|1|D|A|10||||"
> auxiliaryinfo.models[1].dssr.pairs[9].nt2 "|1|E|T|29||||"
>
> What is the proper syntax to select any one of these"
>
From the example I showed in the previous thread regarding the DSSR
change I would suspect that the first base would be residue "A" number
"10" from chain "D". And I would suspect the "1" being the model number.
But because it wasn't included in the former residue selection
expression I am not really sure.
The syntax for the selection expression is the same as before:
select [A]10:D
select [T]29:E
Or if you would add the (suspected) model number it would look like this:
select [A]10:D/1
select [T]29:E/1
You can split the 'nt1' and 'nt2' strings by "|" into an array and then
build the selection expression as a string:
----- Jmol commands ----------
nt1 = auxiliaryinfo.models[1].dssr.pairs[9].nt1.split("|");
nt2 = auxiliaryinfo.models[1].dssr.pairs[9].nt2.split("|");
res_nt1 = "[" + nt1[4] + "]" + nt1[5] + ":" + nt1[3] + "/" + nt1[2];
res_nt2 = "[" + nt2[4] + "]" + nt2[5] + ":" + nt2[3] + "/" + nt2[2];
select @res_nt1;
select @res_nt2;
------------------------------
I currently cannot post to the 'jmol-users' list because my recent email
address change wasn't confirmed there yet. Please forward my answer to
the list so that others can also see it.
Regards,
Rolf
--
Rolf Huehne
Postdoc
Leibniz Institute on Aging - Fritz Lipmann Institute (FLI)
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