Joel,
> align 1kjg & i. 1-99 & n. ca, 1kjh & i. 1-99 & n. ca
pair_fit 1kjg///1-99/ca, 1kjh///1-99/ca
pair_fit will use all atoms, whereas align will only use atoms that are
matched with respect to a dynamic-programming sequence alignment.
Cheers,
Warren
--
Warren L. DeLano, Ph.D.
you can set the number of cycles of refinement on the command line.
change this:
> align 1kjg & i. 1-99 & n. ca, 1kjh & i. 1-99 & n. ca
to this:
> align 1kjg & i. 1-99 & n. ca, 1kjh & i. 1-99 & n. ca, 0, 0
I forget what the first 0 means; the second means "don't refine." It'll
use all matching
So whilst I'm picking your collective brains, how would I set up a
superimposition using say 4 different residues usingthe backbones or ca
atoms? ie two from each separate chain of the homodimer?
Thanks again
J
--
Joel Tyndall, PhD
Lecturer
National School of Pharmacy
University of Otago
PO
Hi folks,
Been sitting here getting a little confused with the seemingly endless
possibilities of the fit and align commands. What I want to do is a
pairwise alignment of the ca atoms of protein portion of some HIV
complexes ie 2 chains of 99 residues).
When I use the command
align 1kjg &
