AMBER Archive (2005)

Subject: Re: AMBER: Adding residues to a DNA sequence

From: Kara Di Giorgio (kdigiorgio_at_sbcglobal.net)
Date: Fri Jul 29 2005 - 11:39:43 CDT

I've looked at the NAB documentation and I'm not sure I'm up to it.
I've tried the following:

1. making a cgc residue that adds a cg and overlaps the first c in my
sequence using nucgen. Loading this into xLeap and making it a
residue. Re-naming the atoms in the overlap c the same, unique,
numbers as I rename the overlap c in my pdb file. Change the residue
name in the pdb file to match the cgc residue in xLeap and then load
the pdb in xLeap. This doesn't work. It creates a structure that's
all over the place.

2. Try to visually align the molecules in VMD with the hope of saving
the coordinates of the both structures together once I get it
organized. I'm having trouble with the alignment. It's hard using the
mouse to translate and rotate one structure on top of another.

Is there a command to choose atoms of each molecule and "'superimpose"
them in VMD? (I saw that that's available in NAB and it's possible in
Spartan, but I can't figure out how to merge the structures in
Spartan.)

Thanks,

Kara Di Giorgio

On Jul 27, 2005, at 2:31 PM, David A. Case wrote:

> On Mon, Jul 25, 2005, Kara Di Giorgio wrote:
>
>> How do you suggest superimposing the residues? What program would you
>> suggest using? How do I replace the two residues with the longer
>> regular helix. I had thought of this but didn't know how to do it.
>
> Well, *I* would use NAB (http://www.scripps.edu/case), but there are
> lots
> of programs that can superimpose parts of molecules on top of one
> another,
> often in a visual fashion (e.g. in VMD) so that you can see
> immediately if
> it did what you want or not.
>
> ...dac
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu