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
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> ****************************************************************
>
>
>
>
> 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
>>
>
