VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Thu Mar 15 2007 - 14:39:21 CDT

Hi Per,

the easiest way is probably just to average the coordinates after
aligning them, which seems to be what you're doing.

Per Jr. Greisen wrote:
> for i in range(k):
> cas = sel.AtomSel('protein')
> cas.frame(i)
> cas.align()
>
> one gets the coordinates with the least difference?
>
>
Yes, you do. Note that it will by default fit only the atoms contained
in the atom selection, but move the whole molecule. This can also be
done a bit more easily as

for i in range(k):
    cas.align(frame=i)
  
> I have a last question regarding the use of BigDCD - I would like to get
> my coordinates out from a MD simulation where the size of the DCD-file
> exceeds my physical RAM:
>
> import Molecule as mol
>
> m = mol.Molecule()
> m.load('protein.psf')
> m.load('min_prot.dcd')
>
> is it possible to include the bigDCD into the python mode?
>
>
>
Bigdcd is just a tcl script that acts on a frame, deletes it, and reads
the next one; there isn't currently a python equivalent, but you could
probably do the exact same thing in python without too much trouble
using the original bigdcd as a guide.

Peter