Re: [AMBER] NAB superimpose issue

From: Mandar Kulkarni <>
Date: Thu, 10 Jun 2021 11:07:38 +0200

Dear Prof. David Case,

Thanks for the suggestion about the alignframe and setframe.

I tried this approach, without the common base "C" to connect two RNA
duplexes. but the alignment issue is not solved. Please see attached NAB
script and image.

I tried alignframe+setframe on individual nucleotides, it works on them.
But, for RNA duplexes, I am facing issues. Two RNA duplexes get entangled
with this approach (please see attached image, bases used for
alignframe+setframe are shown in licorice).

Do I need to try different atom expressions to define origin and X, Y axes
to make it work? Please let me know your thoughts.

Best Regards,
Mandar Kulkarni

On Tue, Jun 8, 2021 at 7:07 PM David A Case <> wrote:

> On Mon, Jun 07, 2021, Mandar Kulkarni wrote:
> >
> >superimpose( m_align,"1,10" , m_ref, "5,6");
> The second and fourth arguments to superimpose should be atom expressions,
> not just strings. Atom expressions have three subsections, separated by
> colons. The superimpose command requires that the two atom expressions
> return the same number of atoms, and that the two atom lists should be
> matched in an ordered fashion. If the two molecules are not chemically
> identical, one has to be very careful in choosing atom expressions that
> have
> the correct number of atoms in the correct order.
> I think what you are looking for is a setframe/alignframe pair: that will
> align two molecules together in a way that can work even when they have
> different chemistries.
> ...hope this helps...dac
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(image/png attachment: align.png)

Received on Thu Jun 10 2021 - 02:30:02 PDT
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