[phenixbb] alternatives to RMSD

Pavel Afonine pafonine at lbl.gov
Mon Jul 7 13:02:21 PDT 2014

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.


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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