Dear Mike,
I think that the old CCP4 superpose program used to be
able to do this ? (This was a FORTRAN program, based on code from Wayne
Hendrickson's PROLSQ program). With this program you specify one set of
residues to do the alignment with and another set to do the statistics on
(after alignment).
I don't know if this is still in the CCP4 archive somewhere, but I do have a
copy of the source code that I could let you have.
Best wishes,
Andrew
On 13 May 2014, at 14:59, R. M. Garavito rmgarav...@gmail.com wrote:
Dear Eugene and other CCP4ers
The recent discussion about superposition has prompted me to ask about a
different kind of superposition problem. We are working on a small dimeric
protein that is entirely made up of helices. Instead of large, concerted
domain movements, which I am quite familiar with, we have 3 structures for
the dimer that display slightly, but significantly different helical
conformations. I have been able to find the minimal substructure that allows
the best superposition (lowest RSMD and maximum number of
aligned/superimposed C-alphas).
The problem is that none of the superposition programs available outputs a
list of residue by residue deviations OUTSIDE of the alignment set (for good
reason as there may not be 1 to 1 correspondence outside of this set). I can
do some of this in a piecemeal fashion with Moleman2, but not everything I
want. My question is, after creating an optimal structural alignment, are
there newer programs that:
(1) Create a list of residue by residue deviations over different subsets of
the structure, particularly OUTSIDE of an alignment set?
(2) Localize and measure movement of secondary structure (helix tilt or
bending)?
I can't seem to find what I need, but I may not be searching with the right
key words.
Thanks,
Michael
R. Michael Garavito, Ph.D.
Professor of Biochemistry Molecular Biology
603 Wilson Rd., Rm. 513
Michigan State University
East Lansing, MI 48824-1319
Office: (517) 355-9724 Lab: (517) 353-9125
FAX: (517) 353-9334Email: rmgarav...@gmail.com
On May 11, 2014, at 7:14 AM, Eugene Krissinel eugene.krissi...@stfc.ac.uk
wrote:
My guess is that only atom pairs that are superposed to some measure of
distance between them, are output. Can't say that I checked lsqkab code this
weekend, but documentation does not suggest anything like that.
Is this a problem for you? note that you can use other aligners/superposers
in CCP4, ssm or Gesamt which will output all coordinates.
Eugene
