VMD-L Mailing List

From: Nicolas SAPAY (nicolas.sapay_at_cermav.cnrs.fr)
Date: Mon Jul 27 2009 - 03:36:38 CDT

> Dear Vmd users,
>
> greetings.

Hello

>
>
> I would like to remove all proton in a protein download in Protein Data
> Bank.
>
> Someone can tell me how to proceed?

First, select all but the hydrogens:
     set sel [atomselect top "not hydrogen"]

I think this assumes that the protons name start with a H. Then save your
selection:
     animate write pdb no_hydrogen.pdb sel $sel top

Your're done

Cheers,
Nicolas

>
> Warm regard to all
>
> albert
> 

-- 
[ Nicolas Sapay - Post-Doctoral Fellow ]
CERMAV - www.cermav.cnrs.fr
BP53, 38041 Grenoble cedex 9, France
Phone: +33 (0)4 76 03 76 44