Sorry for jumping into the post, but I would like the community’s opinion about
completeness, once this topic was raised here. What could be considered
reasonable? Recently I have seen a 65% completeness Crystal structure and,
surprisingly, the electron density map was not that bad for a > 3.2 A
structure. How such a nice map could have been calculated with such poor
parameters? I could only think of anisotropy.
Best
Rafael Marques da Silva
PhD Student – Structural Biology
University of Leicester
Mestre em Física Biomolecular
Universidade de São Paulo
Bacharel em Ciências Biológicas
Universidade Federal de São Carlos
phone: +55 16 99766-0021
"A sorte acompanha uma mente bem treinada"
________________________________________________
________________________________
De: CCP4 bulletin board <[email protected]> em nome de Paul Adams
<[email protected]>
Enviado: Wednesday, February 28, 2024 2:58:16 PM
Para: [email protected] <[email protected]>
Assunto: Re: [ccp4bb] Rwork and Rfree the same?
By setting wxc (weight of the X-ray term) to 0.1 there is good chance that the
refinement is dominated by the geometry term and the model isn’t really seeing
the effect of the X-ray data. I suspect this would result in R-factors that are
similar. Why they are so low is less clear, but as others have pointed out 38%
completeness is a problem. It would be good to check if that is 38% overall, or
just very incomplete in the higher resolution shells. If it is complete at
lower resolution you might be able to do something with the dataset, but not
using the default parameterization in refinement programs - you’ll need to
apply constraints and additional restraints if you can, and look at the
weighting (by modifying wxc_scale, not wxc).
There is a Phenix mailing list you might want to use as well (I assume you are
using phenix.refine): https://phenix-online.org/mailman/listinfo/phenixbb
On Feb 28, 2024, at 8:21 AM, Justin Cruite <[email protected]> wrote:
Thanks everyone,
I agree, 18.4% Rwork and Rfree is too good to be true for a 3.4 Å dataset. The
data was processed using autoProc and the staranisano mtz was used for MR. The
completeness is only 38%. It could be that the Rfree and Rwork reflection sets
are small because of this? What is the best way to check the number of
reflections used for Rwork and Rfree? Is this dataset usable at all?
Thanks!
Justin
On Wed, Feb 28, 2024 at 10:21 AM nicfoos
<[email protected]<mailto:[email protected]>> wrote:
Hello Justin,
There is something weird in your results. You mention Rwork/Rfree of
0.1837.
This means a pretty good refinement and also is very unusual to be
obtain for a resolution of 3.37.
Additionally you should not have Rfree = Rwork.
I suspect something wrong with you Rfree reflections sets. What size is
it ? Is your dataset complet ?
How did you cut the res. ?
I hope this may help you.
Nicolas
On 2024-02-28 16:10, Justin Cruite wrote:
> Hi everyone,
>
> What does it mean if your Rwork and Rfree are exactly the same?
>
> I solved a 3.37 Å structure with Phaser-MR and immediately ran 10
> cycles of refinement with wxc = 0.1. Everything else at default. The
> Rwork and Rfree are both 0.1837. Is this bad?
>
> Thank you!
>
> Justin
>
> -------------------------
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
________________________________
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
--
Paul Adams (he/him/his)
Associate Laboratory Director for Biosciences, LBL (https://biosciences.lbl.gov)
Principal Investigator, Computational Crystallography Initiative, LBL
(http://cci.lbl.gov)
Vice President for Technology, the Joint BioEnergy Institute
(http://www.jbei.org)
Principal Investigator, ALS-ENABLE, Advanced Light Source
(http://als-enable.lbl.gov)
Laboratory Research Manager, ENIGMA Science Focus Area (http://enigma.lbl.gov)
Adjunct Professor, Department of Bioengineering, UC Berkeley
(http://bioeng.berkeley.edu)
Member of the Graduate Group in Comparative Biochemistry, UC Berkeley
(http://compbiochem.berkeley.edu)
Building 91, Room 410
Building 978, Room 4126
Tel: 1-510-486-4225
http://cci.lbl.gov/paul
ORCID: 0000-0001-9333-8219
Lawrence Berkeley Laboratory
1 Cyclotron Road
BLDG 91R0183
Berkeley, CA 94720, USA.
Executive Assistant: Michael Espinosa [ [email protected] ][ 1-510-333-6788 ]
Phenix Consortium: Ashley Dawn [ [email protected] ][ 1-510-486-5455 ]
--
________________________________
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
########################################################################
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list
hosted by www.jiscmail.ac.uk, terms & conditions are available at
https://www.jiscmail.ac.uk/policyandsecurity/
