VMD-L Mailing List

From: matteo.pennestri_at_virgilio.it
Date: Sat Feb 12 2005 - 12:30:51 CST

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.