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) 353-9334 Email: 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 >
