VMD-L Mailing List

From: Justin Gullingsrud (justin_at_ks.uiuc.edu)
Date: Wed Mar 07 2001 - 23:16:30 CST

On Thu, Mar 08, 2001 at 12:50:24PM +0800, Kuen Phon Wu wrote:
>
> Dear VMD-L:
>
> I have 10 DNA molecules with similar 3D struture.
>
> I try to source the rmsd.tcl from VMD 1.6 to align and get the
> rmsd value. When I use the align window to align the 10 DNA,
> what name I can choose?
>
> Using "name C5" or "name P" to align all DNAs is working now,the rmsd
> value is smaller than the value from InsighII caculation. Also ,if I enable
> the backone check box,error message exists.
>
> Is there any command I can align the backbone of DNA without the two
> flexible end.

You could try something like "backbone and resid 2-9" or something like that,
so that you got the same number of base pairs from each molecule. Is that
what you mean?

Cheers,

Justin

>
> Thanks for any help.
>
> Kuenphon Wu. 

-- 
Justin Gullingsrud      3111 Beckman Institute
H: (217) 384-4220       I got a million ideas that I ain't even rocked yet...
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