[phenixbb] alternatives to RMSD

[Tim Gruene]

Hi Pavel,

if the B-value would correspond to a cloud of possible locations, one
should be able to move an atom within the cloud without altering the
R-value and other quality indicators and without a refinement program
moving the atom back to where it came from.

In my experience this is not the case, why I prefer the (original)
scientific interpretation of the B-value as to model of harmonic motion
rather than its statistical. That is also the reason why I am not a
friend of exorbital B-values in PDB-files. I think they tend to fudge
poor modelling.

Cheers,
Tim

On 07/07/2014 10:02 PM, Pavel Afonine wrote:
> Hi Tim,
> 
> consider two atoms located at say 1A distance apart. In one case their
> B-factors are 1A**2 and in the second case their B-factors are 100A**2.
> In the first case these are two individual atoms and measuring distance
> between them makes sense, while in the second case atoms virtually
> coincide (within the cloud of their possible locations, given their
> B-factor) and therefore measuring distance between them isn't very
> meaningful. Using the map would differentiate these two scenarios, while
> usual way of computing RMSD would not. I guess this is what I was trying
> to say in my previous post.
> 
> Whether the values of a metric of choice are intuitive or not is a
> separate question. After all you can always calibrate your expectations
> using examples with known answer.
> 
> Pavel
> 
> 
> On 7/7/14, 3:47 AM, Tim Gruene wrote:
>> Hi Patrick,
>>
>> why don't you superimpose only the matching segments and report their
>> RMSD? It is the common procedure for RMSD's from superpositions to
>> report the aligned residues together with the RMSD.
>>
>> The advantage compared to a map CC is similar to that of R_sym over
>> R_meas: readers have a better concept (from experience) of what the
>> numbers mean.
>>
>> Best,
>> Tim
>>
>> On 07/02/2014 05:15 PM, Patrick. C wrote:
>>> 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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>>
>>
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-- 
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

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