Peak sliders -- DNA

[foster.281]

Hi Bruce et al.,

I'm interested in generating Slider Peaks for a B-DNA model.

I have chemical shifts loaded, and get the tcl error bellow. I also tried using the Generate RNA Peaks function but it doesn't seem to like DNA.

Help!

-M

invalid atom
    while executing
"nv_atom elem symbol $pAtom"
    invoked from within
"set pSymbol [nv_atom elem symbol $pAtom]"
    ("foreach" body line 5)
    invoked from within
"foreach iAtom $tAtoms {
                    set symbol [nv_atom elem symbol $iAtom]
                    if {$symbol ne "H"} {continue}
               ..."
    ("if" then script line 5)
    invoked from within
"if {[info exists pLists(noesy)]} {
                set structures [mol structures $molName active]
                set nStructures [llength $structure..."
    ("foreach" body line 21)
    invoked from within
"foreach "rNum rName" $residuePairs {
            set sgl [to1Letter $rName]
            mol select atoms $entity:$rNum.H*
            set atoms [mol l..."
    ("foreach" body line 3)
    invoked from within
"foreach entity $entities {
        set residuePairs [mol listresidue $molName $entity]
        foreach "rNum rName" $residuePairs {
            set sg..."
    (procedure "::nv::peak::genMoleculePeaks" line 24)
    invoked from within
"::nv::peak::genMoleculePeaks"
    ("binding" script)

[brucej]

Hi Mark

I'll take a look at why this error  is appearing, but all new development of the slider tool is happening in NMRFx Analyst.  It's working pretty well.

Quick overview here: https://nmrfx.org/tutorials/analyst

Longer version here: https://vimeo.com/314587088

I just uploaded new version of NMRFx Analyst today.  I haven't tested it for use with DNA, but this new version at least has BMRB shifts for DNA.  I'll look into training a predictor for DNA (at least to get sequence dependent shifts for helices).

Bruce