VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Aug 02 2011 - 17:09:34 CDT

Hi,
  The "sugar" selection keyword is actually a macro. You can see
what the macro expands to like this:
  vmd > atomselect macro sugar
  resname AGLC

You can delete the existing macro and replace it with your own like this:
  atomselect delmacro sugar
  atomselect macro sugar {resname FOO BAR BAX}

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Aug 02, 2011 at 03:11:49PM -0400, Molybdos Kirkimpolakis wrote:
> Dear VMD Masters,
>
> I want to select the sugars in my protein using VMD but it seems that VMD
> does not recognize them. I am using Amber force field because my protein
> has important sugars that I cannot delete. Can you help me to select the
> sugars?
>
> Let's say I want to set zero the beta factor of the sugars I do the
> following
>
> set allatoms [atomselect top all]
> $allatoms set beta 0
> set atomsugar [atomselect top sugar]
> $atomsugar set beta 1
> $allatoms writepdb new.pdb
>
> However when I see in the pdb the beta factor of the sugars; they are
> still zero.
>
> can anyone help me out.
>
> Thanks so much
>
>
>
> --
> cheers
>
> D-aiaad-eooTH`iei D-aonthi
>
> OIC,IA AEIEIAEAO
> Molybdos Kirkimpolakis 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
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