[phenixbb] alternatives to RMSD
pafonine at lbl.gov
Mon Jul 7 00:19:45 PDT 2014
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
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
> Thank you,
> -----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,
>> 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
>> 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,
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