VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Sat Feb 12 2005 - 13:23:01 CST

Dear Matteo,

unless the identities of every single amino acid in each helix are
identical, you're still going to have a different number of atoms in
each selection. If that's the case, you should be able to just add the
alpha or backbone keyword to your selection, so that you're only doing
alpha carbons or backbone. This should have the same number of atoms
regardless of identity. So if you do

set sel1 [atomselect 0 "alpha and resid 1 to 25"]

set sel2 [atomselect 1 "alpha and resid 824 to 878"]

It should work right.

Hope this helps.
Cheers,
Peter
matteo.pennestri_at_virgilio.it wrote:

>Thanks for the rapid replying but it still dosen't work.
>I try to explain better my problem.
>I have a peptide "0" of 25 aminoacids and a protein "1" of 149 aa bound
>to a 25 aa peptides.
>I try to align the 0 peptide to the peptide of protein 1.
>
>set sel1 [atomselect 0 "resid 1 to 25"]
>
>set sel2 [atomselect 1 "resid 824 to 878"] (!the 25 aminoacids of the peptides
>bound to the protein 1!)
>
>set transformation_matrix [measure fit $sel1 $sel2]
>
>At this point the reply is: measure fit: selections must have the same number
>of atoms
>
>but want align the same number of aminoacid (and both of them are in same
>type of alpha-helix)
>
>is It possible that is I try to align a x-plor peptide stucture with a pdb
>cristal structure?
>
>Please help me.
>
>Best wishes
>
>Matteo.
>
>
>
>