On 6/17/10 9:34 AM, "Tim Stevens" <[log in to unmask]> wrote:
>> Maybe longer term a rather more comprehensive RMSD calculation routine with
>> greater flexibility for choosing residues/atoms could be included?
>
> Ah. The way that I have done things is to try to eliminate any need to do
> any fiddling with residue or atom selections. The superposition from the
> inbuilt method should be very good indeed, and aims to give a solution
> fairly close to global more probabilistic methods.
>
> Unless there is a problem with the current method I would rather not have
> to extend the GUI to allow arbitrary residue/atom comparison.
Just to weigh in with my unsolicited opinion, I don't see a huge problem
with having limitations on the RMSD routines, since as you say elsewhere
Analysis isn't really a structure calculation program. However, I can see a
very useful and probably trivially implemented compromise.
We often have disordered tails (or other regions) in NMR structures. For
example, excluding the long and completely disordered N terminus (no long
range restraints) in a current project of mine drops the backbone RMSD for
25 structures from low double digit values to <1 A.
Something as simple as adding code to align over a single specified (and
continuous) range of residues, something like "if res.num >= X and res.num
<= Y" and defaulting to the full range, would probably suffice to focus on
the desired structural "core" in better than 90% of cases. For the rest,
there are indeed multiple programs available that allow exquisite control
over selections, and I would guess anyone doing structure calculations has
at least one already installed.
Cheers,
Andrew
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