[phenixbb] Very low rmsd bond length

[oleg at quantumbioinc.com]

Is the structure overfitted? What is the gap between Rfree and Rwork?

Oleg Borbulevych, Ph.D.
Staff Scientist
QuantumBio, Inc.
2790 W. College Ave.
State College, PA 16801
E-mail: oborbulevych at yahoo.com, oleg at quantumbioinc.com
Linkedin Professional Profile: http://www.linkedin.com/pub/oleg-borbulevych/22/454/b80



-----Original Message-----
From: "Mark Saper" <saper at umich.edu>
Sent: Tuesday, July 25, 2017 8:56pm
To: "Nigel Moriarty" <nwmoriarty at lbl.gov>
Cc: "PHENIX user mailing list" <phenixbb at phenix-online.org>, "Raymond C Trievel" <rtrievel at umich.edu>
Subject: Re: [phenixbb] Very low rmsd bond length

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Unsubscribe: phenixbb-leave at phenix-online.orgTwo of the lower resolution structures have rmsd of 0.002 Å. 

_____________________
Mark A. Saper, Ph.D.
Associate Professor of Biological Chemistry, U-M Medical School
Room 3220B, MSRB III   |  saper at umich.edu  |  +1 (734) 764-3353 

> On Jul 25, 2017, at 7:03 PM, Nigel Moriarty <nwmoriarty at lbl.gov> wrote:
> 
> Mark
> 
> Can you verify the RMSD range for bonds? Is it, "0.005-0.002" as stated or "0.005-0.02"?
> 
> Cheers
> 
> Nigel
> 
> ---
> Nigel W. Moriarty
> Building 33R0349, Molecular Biophysics and Integrated Bioimaging
> Lawrence Berkeley National Laboratory
> Berkeley, CA 94720-8235
> Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
> Fax   : 510-486-5909       Web  : CCI.LBL.gov
> 
>> On Tue, Jul 25, 2017 at 3:52 PM, Mark Saper <saper at umich.edu> wrote:
>> Hi all,
>> 
>> A reviewer points out that my refined structures (which have already been deposited in PDB) have very small RMSD values for bond lengths (0.005–0.002) (refinement resolutions are 2.0–2.8 Å), and that my weights should be decreased.  The weights were calculated with “Optimize XYZ Weight” option turned ON.  This seems to be the case with all of the structures that I have refined during the past 5 years.  My impression from previous discussions is that deriving explicit weights from these optimized ones is not straightforward and so I have never tried to relax the weights.  Moreover inspecting the optimization results in the log file, suggest that changing the weights to increase the RMSD would increase the Rfree. (I can post this if its helpful).
>> 
>> How do I address the reviewer’s concerns?
>> 
>> Thanks,
>> Mark
>> _______________________________________________
>> Mark A. Saper, Ph.D.
>> Associate Professor of Biological Chemistry, U-M Medical School
>> Room 3220B, MSRB III   saper at umich.edu   +1 (734) 764-3353
>> 
>> 
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