[phenixbb] alternatives to RMSD
Pavel Afonine
pafonine at lbl.gov
Mon Jul 7 00:07:10 PDT 2014
Hi Ed,
yes, this makes sense, sure: having models to be superposed
appropriately to begin with certainly is a good idea. My point was that
coordinate-based rmsd does not account for B-factors and occupancy that
is a problem if you are comparing flexible molecules. A possible
solution may be to use a more generous (=more information rich)
representation of atomic model such as electron density map that would
'automatically' take care of disorder.
Pavel
On 7/5/14, 9:37 AM, Edward A. Berry wrote:
> 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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