Thanks David,
I worked on the two systems. But the latter one didn't work.
Can you please suggest what is the reason.
rms first out rna_run.rms .P,O3',O5',C3',C4',C5' time 0.50
rms first out rna_test.rms .!P,O3',O5',C3',C4',C5' time 0.50 nofit
Thanks.
Jac
On Tue, Mar 17, 2015 at 5:22 PM, David A Case <case.biomaps.rutgers.edu>
wrote:
> On Mon, Mar 16, 2015, jacob wick wrote:
> >
> > rms first out rna_run.rms .P,O3',O5',C3',C4',C5' time 0.50
> >
> > Is this script helping in comparing backbone of reference with the
> backbone
> > of frames (without taking residues deviations in account) or it is
> > superimposing the reference backbone with the backbones of frame and
> giving
> > the deviations with respect to the residues?
>
> The former. A command like this superimposes frames on the backbone atom,
> and reports the RMS value computed over the same set of atoms.
>
> If you want to fit on one set of atoms, but calculate the deviations for a
> second set of atoms, you need two rms commands. The first is like that
> above,
> which will do the superposition. The second one would have a different
> atom
> mask, and the keyword "nofit", so that no additional fitting would be
> performed.
>
> Play with this a bit on some very simple system to see what is going on.
>
> ....dac
>
>
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Received on Fri Mar 20 2015 - 03:30:03 PDT
