[phenixbb] alternatives to RMSD

[Edward A. Berry]

I agree that would be useful as an alternative to RMSD,
but if I understand the original post, the problem
with RMSD is that the two secondary structure elements
are connected by a variable turn so that they cannot be superimposed
simultaneously. That could still be a problem, comparing maps.

What you can do is report the change in angle between them,
and the residues making up the hinge.
A program called dyndom (dynamic domains) is good for this,
Or you can superimpose each "domain" separately, view the
superimposed molecules, and see haw far into the turn
from each side thesuperposition is good

To get the change in angle between the two parts,
first superimpose model A on model B using only residues
in domain 1 (say, the helix).
Save that reoriented model A, and now superimpose it on model B
using only residues in domain 2 (the strand).
The angle involved in this second rotation is the chang in interdomain angle.

(You could also report RMSD for superposition of the individual domain,
but helix-on-helix or strand-on-strand are likely to be pretty good fits
and not very informative.)
eab

On 07/05/2014 10:22 AM, PC wrote:
> Hi Pavel,
>
> Thank you very much, this sounds very interesting.
>
> I have used ccp4, coot and phenix but I am no expert but I am definitely interested in trying this method if you could give more information.
>
> Thank you,
> Patrick.
>
>
>     -----Original Message-----
>     *From:* pafonine at lbl.gov
>     *Sent:* Fri, 04 Jul 2014 20:34:33 -0700
>     *To:* patrick.cossins at inbox.com, phenixbb at phenix-online.org
>     *Subject:* Re: [phenixbb] alternatives to RMSD
>
>     Hi Patrick,
>
>     RMSD is a poor measure in this case as it does not account for B-factors, occupancies, alternative conformations and so on information a crystal structure model may make available. Macromolecules are not a bunch of points in space.
>
>     While I'm sure more thorough methods exist, I would vote for the simplest, most direct and obvious one. You can calculate electron density map using a Gaussian approximation from model A and B (yes, electron density map - not a Fourier image of it!). That will naturally account for all: B-factors, occupancies, other disorder. Then you can calculate a map similarity measure, such as map correlation, for instance. After all, why use a cannon to kill a fly?!
>
>     If you are interested to follow this route I can explain the details.
>
>     All the best,
>     Pavel
>
>>     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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