VMD-L Mailing List

From: Paweł Kędzierski (pawel.kedzierski_at_pwr.wroc.pl)
Date: Fri Mar 18 2011 - 15:17:31 CDT

On 18.03.2011 18:58, ban arn wrote:
> Dear VMD users
>
> I would like to know is there any script available in vmd or from
> others sources for projection of c-aplha atom coordinates on xy plane.
>
Did you mean filtering out CA atoms and replacing z coordinate with 0
(or whatever)? E.g.:

awk --posix '/^ATOM (.){6} CA /{printf("%.46s%8.3f\n",$0,0);}' your_file.pdb

Or if you filtered out CA previously (within VMD, File->Save
coordinates, selection "protein and name CA") it would be enough to say:

awk '{printf("%.46s%8.3f\n", $0, 0);}' your_file.pdb

This works with gnu awk.
HTH
Pawel
> Any help is greatly appreciated.
>
> Many Thanks
> Balaji
>