Re: [AMBER] NAB superimpose issue

From: David A Case <>
Date: Thu, 10 Jun 2021 08:56:38 -0400

On Thu, Jun 10, 2021, Mandar Kulkarni wrote:
>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.

m = getpdb("rna_1.pdb");
setframe( 2, m, // aligning U4 from m1
":4,U3:C5", ":4,U3:N1",
":4,U3:C6", ":4,U3:N3" );
alignframe( m, NULL );
putpdb( "std_m1.pdb", m );

m = getpdb("rna_2.pdb");
setframe( 2, m, // aligning A1 from m2
":1,A5:C5", ":1,A5:N3",
":1,A5:C4", ":1,A5:N1" );
alignframe( m, NULL );
putpdb( "std_m2.pdb", m );

The script above will put C6 of residue 4 of rna_1 at the origin, and it
will also put C4 of residue 1 of rna_2 at the origin (i.e. these two atoms
will be right on top of each other.) That is surely not what you want.

It's hard to tell from what you've written what the desired outcome is.
Are you trying to make a co-linear stack of two duplexes? Once you get the
helix axes along a desired direction, you would probably want to shift one
of the two helices along its helical axis, in order to displace them by a
certain amount.

...hope this helps....dac

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Received on Thu Jun 10 2021 - 06:00:03 PDT
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