VMD-L Mailing List

From: Justin Gullingsrud (justin_at_ks.uiuc.edu)
Date: Sun Dec 29 2002 - 19:22:03 CST

Hi,

VMD determines secondary structure from a program called Stride, which
doesn't always come up with exactly the same assignment as what is listed
in the PDB file. You can override the secondary structure using the
Tcl text interface. For example, if you want to change residues 13-18
to Turn, enter the following at the VMD text console:

mol ssrecalc top
set sel [atomselect top "resid 13 to 18"]
$sel set structure turn

The ssrecalc line is done to make sure VMD computes secondary structure for
the entire molecule before overriding the selected range if residues.

Let us know if you need any more help with this.

Thanks,
Justin

On Sun, Dec 29, 2002 at 01:16:32PM -0800, Sichun Yang wrote:
> Dear all VMD users,
>
> Addition to my last email:
> The drawing method of the representation I am using is Cartoon.
>
> I have a naive question about the Representation.
> Because VMD shows me a Turn as 3-10 Helix. It has a mess about the Turn
> and 3-10 helix in my case.
> So I wonder what the logic is here and how I can improve it.
> Thanks for your attention.
>
> Enjoy the Holidays!
> Sichun
> 

-- 
  Justin Gullingsrud        3111 Beckman Institute        217-244-8946
  I been dropping the new science, and I be kicking the new knowledge,
  and I'm seeing to a degree that you can't get in college.  -- b.boys