Two ways you can do this:
You should be able to do this:
*calculate hbondsx = {*}.find("~d~G:C", true);*
*select on group @{x[1]}*
However, there is a bug there. (Now fixed.)
Alternatively, you could load DSSR annotations, which gives you detailed
RNA or DNA base information:
*load =1d66/dssr*
and then use the Jmol SQL syntax to find the base pairs you want:
*pairs = getProperty("auxiliaryinfo.models[1].dssr.basepairs[select
res1,res2 where bp='C-G' or bp='G-C']"*
You can see more what is available using:
*getproperty auxiliaryinfo.models[1].dssr*
Now you can select on those:
*select on @{pairs[1].res1},@{pairs[1].res2}*
Jmol.___JmolVersion="14.3.12_2015.02.28"
bug fix: {*}.find("~d~G:C") broken (find with bioSMARTS)
On Sat, Feb 28, 2015 at 11:02 AM, Pshemak Maslak <n...@psu.edu> wrote:
> I can select GC base pairs within a DNA stretch using: within(BASEPAIR,"GC").
> Let's say I have 10 such pairs. Is there a way to select any specific pair
> from that set?
>
> Thanks,
>
> PM
>
>
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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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Dive into the World of Parallel Programming The Go Parallel Website, sponsored
by Intel and developed in partnership with Slashdot Media, is your hub for all
things parallel software development, from weekly thought leadership blogs to
news, videos, case studies, tutorials and more. Take a look and join the
conversation now. http://goparallel.sourceforge.net/
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