VMD-L Mailing List

From: Maik Götte (maik.goette_at_uni-kassel.de)
Date: Mon Mar 08 2004 - 09:20:56 CST

I'm trying to fit the alignment of two C-subunits of PKA, which have different
conformational states (btw. they differ in aminoacid counts).
Now, if I'm telling the RMSD-tool to fit 13 residues from the A-Helix with
"top"-option (which are the same aminoacids in each molecule), and just fit
the backbone, the result is junk (the molecules obviously doesn't fit). If I
try to fit all atoms of the residues (that should fit much better), the
following message is displayed: measure fit: selections must have the same
number of atoms (while using "align". "RMSD" worked
When I use the "average" or "selected" option the error sounds:
vecsub: two vectors don't have the same size.

What did I do wrong? 

-- 
Maik Götte
University of Kassel, Germany
Student, Dipl. Biology
 
Email: maik.goette_at_uni-kassel.de
Webpage: http://http://www.biologie.uni-kassel.de/