VMD-L Mailing List

From: Luis Gracia (lgraval_at_gmail.com)
Date: Tue Feb 22 2005 - 00:20:10 CST

Hi!

if both peptides have different sequence you have to reduce the
selection to the backbone or the trace, try:

set sel1 [atomselect 0 "resid 1 to 25 and backbone"]
set sel2 [atomselect 1 "resid 824 to 878 and backbone"]

hope this helps,

Luis

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.
>
>
>
>
>