Re: [ccp4bb] Rwork and Rfree the same?

What type of Rfree flags do you have? The CCP4 flags will be a random integer between 0 and 19, with 0 being used for the free set. Reminding myself: "Phenix uses the CNS/XPLOR convention for R-free flags, where 1 marks the test set and 0 the "working" set." Shelx is different, too, but that pro

Re: [ccp4bb] Rwork and Rfree the same?

Dear Justin, Be careful of the reported “fill-in” effect of unobserved data by some refinement programs (not sure if this is your case or even if it was, whether it may cause the Rfactor to be identical) when using anisotropic cut-off. It is documentated here: https://staraniso.globalphasing.

Re: [ccp4bb] Rwork and Rfree the same?

Dear All, In addition to Paul Adams point, I would note that people have sometimes been confused by different definitions of completeness and resolution when looking at Staraniso data, particularly if there is significant anisotropy. It would be worth checking not only which shell but which d

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

Re: [ccp4bb] Superimposition save as PDB for ccp4 refmac question

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[ccp4bb] mixture

Dear All, can someone quickly update me with a way to refine a mixture of structures in refmac or phenix. For example, the mixture consists of 80 % structure 1 and 20 % structure 2. It is important that structure 1 is kept fixed (is not refined) and only structure 2 is varied. Best Marius Marius

Re: [ccp4bb] Superimposition save as PDB for ccp4 refmac question

Hi Marco You could always try the CCP4 tools (since this is the CCP4 BB…) “superpose” or “gesamt” to superpose (or is it “superimpose”? discuss…). Harry > On 28 Feb 2024, at 00:53, Marco Bravo wrote: > > Hello all, > Does anyone know how to save a superimposed pymol or chimerax session as a

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Re: [ccp4bb] Rwork and Rfree the same?

Well REFMAC tells you how many reflections are used.. And if you do mtzdmp data.mtz that will tell you too.. With such low completeness R factors are pretty meaningless - you must have many more parameters than observations so that does often give low Rfactors.. On Wed, 28 Feb 2024 at 16:21, Jus

Re: [ccp4bb] Rwork and Rfree the same?

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

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Re: [ccp4bb] Superimposition save as PDB for ccp4 refmac question

Dear Marco, > Refmac: Input coordinate file is not complete Probably the CRYST1 record (unit cell and space group information) is missing in your pdb file. You could copy this from another pdb file (and may need to correct it). Best regards, Keitaro On Wed, 28 Feb 2024 at 09:54, Marco Bravo wr

Re: [ccp4bb] Rwork and Rfree the same?

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 se

Re: [ccp4bb] Rwork and Rfree the same?

Well - it is extremely surprising! How many reflections are there in the "work" set (Rwork) and the "free" set (Rfree)? I suspect that somehow all the reflections are in both sets?? Eleanor On Wed, 28 Feb 2024 at 15:11, Justin Cruite wrote: > Hi everyone, > > > > What does it mean if your Rwork

[ccp4bb] Rwork and Rfree the same?

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 ##

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