[phenixbb] rmsd:

Mayer, Mark (NIH/NICHD) [E] mayerm at mail.nih.gov
Sun Jan 25 11:28:14 PST 2009

Hi Pavel,

It would be nice if the PDB would include phenix as one of the choices for reporting
program used to calculate rmsd values in a deposition; at the moment we have to report as 'other'.
Not your job I know - perhaps Paul could twist arms?

Best, Mark

-----Original Message-----
From: Pavel Afonine [mailto:PAfonine at lbl.gov]
Sent: Sun 1/25/2009 1:02 AM
To: PHENIX user mailing list
Cc: Mariusz Jaskolski
Subject: Re: [phenixbb] rmsd: phenix vs refmac
Hi Karolina,

> Hi,
> Has anyone solved this problem? I am also fighting with extremly low
> rmsd values.
> For 1.7A structure I get rmsd 0.004A (bond) 0.733 (angles)
> (R/Rfree=0.1884/0.2216) with automatic weight calculation. When I want
> to loose restraints to get more reasonable rmsd I get R/Rfree
> 0.1814/0.2240). However,  at the moment I do not know what "reasonable"
> means while using phenix.refine. Is seems to me that the program include
> hydrogen atoms in rmsd calculations. 

Put hydrogen atoms issue aside (see my previous email), and even put 
particular program use aside too, I would still be uncertain about "what 
reasonable means". There was enough of discussion on this matter in 
CCP4BB and relatively recent Acta D papers.

I'm sure it can be easily criticized, but I would use that X-ray target 
weight that gives you the best Rfree (this is what "optimize_wxc=true" 
option in phenix.refine does, and similar for B-factors).

And yes, for the moment you can use phenix.model_vs_data to report the 
final geometry rmsd statistics for a model containing hydrogen atoms:

phenix.model_vs_data model.pdb data.mtz

Please let me know if you have any questions!


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