Hi Daniel,
Thank! That fixed it- I had thought the &(. atom selection) would override
that part, but good to know.
Best,
Kenneth
On Thu, Jul 9, 2020 at 10:06 PM Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> <: means “residues within” so if _any_ part of the residue meets the
> distance cutoff the whole residue is selected. Try <@ (atoms within)
> instead.
>
> -Dan
>
> On Thu, Jul 9, 2020 at 8:05 PM Kenneth Huang <kennethneltharion.gmail.com>
> wrote:
>
> > Hi all,
> >
> > I'm running into an odd situation where the behavior of the mask command
> > doesn't seem to be lining up exactly with the actual measured distance,
> ie
> > if I have
> >
> > mask "(:35.N4<:5.5)&:47-135&( :LYS.NZ | :ARG.NH1,NH2 | :GLU.OE1,OE2 |
> > > :ASP.OD1,OD2 )" maskout maskout_N4.dat
> > >
> >
> > To measure any charged groups of the protein within 5.5 A of the N4 group
> > on a DNA base, it says frame 1 has both NH groups on an ARG within the
> > raidus,
> >
> > #Frame AtomNum Atom ResNum Res MolNum
> > > 1 2527 NH1 108 ARG 3
> > > 1 2530 NH2 108 ARG 3
> > >
> >
> > But when I try to fetch the distance via
> >
> > distance dN4 :35.N4 :108.NH1 out dist.m35N4-108.dat noimage
> > > distance dN4b :35.N4 :108.NH2 out dist.m35N4b-108.dat noimage
> > >
> >
> > The distance I get for both sets say that it's mugh further than the 5.5
> > radius of mask?
> >
> > 1 6.4996
> > >
> > >
> > 1 5.7482
> > >
> > >
> > My first thought is I've somehow messed up the selection algebra in the
> > mask portion, but I can't seem to find an actual error in it?
> >
> > Best,
> >
> > Kenneth
> >
> > --
> > Ask yourselves, all of you, what power would hell have if those
> imprisoned
> > here could not dream of heaven?
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Received on Fri Jul 10 2020 - 11:00:03 PDT
