That's a reasonable approach and I think that it is similar to the one used by FATCAT - which I notice is the basis for structural comparison at the RCSB site.
Motivation and some results in the paper ( http://www.ncbi.nlm.nih.gov/pubmed/14534198)
It's not clear to me, though, how to fairly compare the resulting RMSD of fragments with twists between. If I introduce an arbitrary number of twists then I can improve the rmsd artificially. In sequence matching there is a penalty for introducing a gap and that is scaled compared with the amino acid substitution scoring to split the match into a 'reasonable' number of sub-alignments. Obviously in 3D case there should also be a penalty for introducing a split in the structure to do a twist re-orientation - but how to quantify it compared with RMSD and get a global score?
Seems to me better would be to express the whole problem in torsional space - so the twists would be large displacements while the matched sections should have close fit in torsional angles. And a global score could be calculated. Someone must have tried this?
All the best
Martyn
Cambridge
----Original message----
>From : tg@shelx.uni-ac.gwdg.de
Date : 07/07/2014 - 11:47 (GMTDT)
To : phenixbb@phenix-online.org
Subject : Re: [phenixbb] alternatives to RMSD
Hi Patrick,
why don't you superimpose only the matching segments and report their
RMSD? It is the common procedure for RMSD's from superpositions to
report the aligned residues together with the RMSD.
The advantage compared to a map CC is similar to that of R_sym over
R_meas: readers have a better concept (from experience) of what the
numbers mean.
Best,
Tim
On 07/02/2014 05:15 PM, Patrick. C wrote:
> Hi Phenix users,
>
> I am not a crystallographer but I though you guys might be a good place to ask
> this question.
>
> I have 2 super secondary structures, A and B and they consist of Helix-turn-Strand
>
> Due to the turn the two structures have a poor RMSD because the two flanking
> fragments of Helix and Strand are far from each other but when I superimpose the
> two fragments individually(helixA with helix B and standA with strandB in Pymol
> they align very well).
>
> Now, is there a way to express this instead of using the RMSD?
> When the two structures align well the RMSD is very good but a slight movement
> and the RMSD is awful.
> But looking at the two structures I can see they follow the same path through space.
>
> Thank you,
> Patrick
>
>
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--
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
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