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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