[phenixbb] alternatives to RMSD

Pavel Afonine pafonine at lbl.gov
Mon Jul 7 00:19:45 PDT 2014

Hi Patrick,
supposing models are superposed appropriately (see previous comments on 
phenixbb), step-by-step I see it as following:
- compute density map for model A (or its Fourier synthesis of 
resolution 1A or higher),
- compute density map for model B (or its Fourier synthesis of 
resolution 1A or higher),
- compute map CC per residue or per atom between maps corresponding to A 
and B.

I would think that "superposed appropriately" is a key here.


On 7/5/14, 7:22 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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