[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.

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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