[phenixbb] alternatives to RMSD

Morten Grøftehauge mortengroftehauge.work at gmail.com
Tue Jul 29 05:11:26 PDT 2014


Hi Patrick,

The quick and easy way of doing this would be to use Rob Nicholls' ProSMART
in CCP4. It does a local structure alignment and gives you a value for the
superposition of main chain atoms.
I don't know of any tool in Phenix that does this.

Cheers,
Morten




On 8 July 2014 14:56, MARTYN SYMMONS <martainn_oshiomains at btinternet.com>
wrote:

> 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 at shelx.uni-ac.gwdg.de
> Date : 07/07/2014 - 11:47 (GMTDT)
> To : phenixbb at 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
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-- 
Morten K Grøftehauge, PhD
Pohl Group
Durham University
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