[phenixbb] alternatives to RMSD

Tim Gruene tg at shelx.uni-ac.gwdg.de
Mon Jul 7 03:47:37 PDT 2014

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.


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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Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen


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