Hi Carsten,
This sounds like a non-trivial problem, my understanding is that it's still
an ongoing challenge to best align dissimilar structures. Other ways of
aligning structures involves using the vectors from secondary structure
elements, or feeding in (multiple) sequence alignments. All have their
benefits and drawbacks. Which you use will depend on what you are trying to
do.
Depending on what information you have, the strategy will change and CA-CA
distances may or may not be reasonable to compare. The underlying challenge
is the question of how to know which parts of structures are functionally
equivalent, and the answer gets philosophical once the sequences diverge a
lot. With drift of sequence, geometry and function can drift as well.
I'd have a look into the various algorithms detailed at
http://www.rbvi.ucsf.edu/home/meng/grpmt/structalign.html and see if one
fits your situation. Of course, if you're just looking for a few values,
PyMol's Measurement Wizard is a low-tech way to get a few distances.
Sorry if this isn't too helpful, but without knowing more about your
situation it's difficult to make recommendations.
Cheers,
Shane Caldwell
McGill University
On Sun, Jan 18, 2015 at 9:12 PM, Schubert, Carsten [JRDUS] <
cschu...@its.jnj.com> wrote:
> Hi,
>
>
>
> How can I best determine the distance between matching pairs of atoms in
> two or more aligned structures? Fairly easy to do when the two aligned
> structures are the same, but how does one go about when the structures are
> not the same? The problem is that I cannot figure out how to dependably
> match structurally superimposed CA’s besides a distance criterion, which
> does not seem to be to reliable in the case of large deviations. I tried to
> snoop around in the alignment object created by the align command, but did
> not make much inroads.
>
>
>
> Anyone have any experience with this?
>
>
>
> Thanks
>
>
>
> Carsten
>
>
>
>
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