Hi Patrick, supposing models are superposed appropriately (see previous comments on phenixbb), step-by-step I see it as following: - compute density map for model A (or its Fourier synthesis of resolution 1A or higher), - compute density map for model B (or its Fourier synthesis of resolution 1A or higher), - compute map CC per residue or per atom between maps corresponding to A and B. I would think that "superposed appropriately" is a key here. Pavel On 7/5/14, 7:22 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:* [email protected] *Sent:* Fri, 04 Jul 2014 20:34:33 -0700 *To:* [email protected], [email protected] *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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