Hello Partha, At the moment I was more looking, if it makes a difference what comes out from Refmac, when I feed it different start models; straight from Phaser, reset B-values, after shaking coordinates, after shaking coordinates and SA, and so on.... I assumed, if I put the output from Phenix (with R/Rfree X/X reported by phenix) to be identical to the R/Rfree Refmac reports as START value when it gets directly the output pdb from phenix? I thought the reported R/Rfree values are just something like 'model vs data'? That's what I am confused about... No twinning, no automated water building, just 1mol/asu, no twinning Sabine On 08/12/2011 02:36 PM, Partha Chakrabarti wrote:

Hi Sabine, I believe the comparison should be with same input, not output of one piped into another. How different are the geometry? Different programs use different algorithm and different xray:geometry term by default. Hence, it might only make sense if the RMSD are almost exactly the same. Furthermore, is one program detecting NCS or twining or building waters automatically? Then everything is blown up anyway. In any case, refinemt program A vs. B is an interesting topic! I would not start one.. ;) MFG, Partha

On Fri, Aug 12, 2011 at 5:19 PM, Sabine Schneider mailto:[email protected]> wrote:

Hello,

I am refining a structure at 2.1A solved by MR. For curiosity I'm testing things like 'shaking' coordinates, simulated annealing, refinement Refmac vs Phenix and so on, to see what influence that has on stats, maps etc.

For instance after MR I did a bit of shaking the coordinates with pdbset (noise 0.1), followed by simulated annealing in Phenix. Phenix states after SA:

Start R-work = 0.2671, R-free = 0.2992 Final R-work = 0.2312, R-free = 0.2666

When I use the output pdb of phenix directly in Refmac (with same mtz as input for Phenix) Refmac tells me: Initial R factor 0.2392 R free 0.2887

So I am quite puzzled about the discrepancy. Or can someone tell me if I made an error in reasoning somewhere?

Thanks a lot for the help! Sabine

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Yes, same mtz input file Sabine On 08/12/2011 03:04 PM, Antony Oliver wrote:

Possibly a silly question - but did you use the same R-free reflection subset in both refinements?

Sent from my iPhone

On 12 Aug 2011, at 13:59, "Sabine Schneider" mailto:[email protected]> wrote:

...

Hello Partha,

At the moment I was more looking, if it makes a difference what comes out from Refmac, when I feed it different start models; straight from Phaser, reset B-values, after shaking coordinates, after shaking coordinates and SA, and so on....

I assumed, if I put the output from Phenix (with R/Rfree X/X reported by phenix) to be identical to the R/Rfree Refmac reports as START value when it gets directly the output pdb from phenix? I thought the reported R/Rfree values are just something like 'model vs data'? That's what I am confused about...

No twinning, no automated water building, just 1mol/asu, no twinning

Sabine

On 08/12/2011 02:36 PM, Partha Chakrabarti wrote:

...

Hi Sabine, I believe the comparison should be with same input, not output of one piped into another. How different are the geometry? Different programs use different algorithm and different xray:geometry term by default. Hence, it might only make sense if the RMSD are almost exactly the same. Furthermore, is one program detecting NCS or twining or building waters automatically? Then everything is blown up anyway. In any case, refinemt program A vs. B is an interesting topic! I would not start one.. ;) MFG, Partha

On Fri, Aug 12, 2011 at 5:19 PM, Sabine Schneider mailto:[email protected]> wrote:

Hello,

I am refining a structure at 2.1A solved by MR. For curiosity I'm testing things like 'shaking' coordinates, simulated annealing, refinement Refmac vs Phenix and so on, to see what influence that has on stats, maps etc.

For instance after MR I did a bit of shaking the coordinates with pdbset (noise 0.1), followed by simulated annealing in Phenix. Phenix states after SA:

Start R-work = 0.2671, R-free = 0.2992 Final R-work = 0.2312, R-free = 0.2666

When I use the output pdb of phenix directly in Refmac (with same mtz as input for Phenix) Refmac tells me: Initial R factor 0.2392 R free 0.2887

So I am quite puzzled about the discrepancy. Or can someone tell me if I made an error in reasoning somewhere?

Thanks a lot for the help! Sabine

_______________________________________________ phenixbb mailing list [email protected] mailto:[email protected] http://phenix-online.org/mailman/listinfo/phenixbb

_______________________________________________ phenixbb mailing list [email protected] mailto:[email protected] http://phenix-online.org/mailman/listinfo/phenixbb

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Hi Sabine, I am by no means an expert in such things and I am sure that you will get a comprehensive answer at some point. My understanding is that differences in weightings, and the treatment of the solvent correction means reproducing R-factors across different programs is not really possible. Also in the greater scheme of things they are not too dissimilar. Kind regards David On 12/08/2011 13:57, Sabine Schneider wrote:

Hello Partha,

At the moment I was more looking, if it makes a difference what comes out from Refmac, when I feed it different start models; straight from Phaser, reset B-values, after shaking coordinates, after shaking coordinates and SA, and so on....

I assumed, if I put the output from Phenix (with R/Rfree X/X reported by phenix) to be identical to the R/Rfree Refmac reports as START value when it gets directly the output pdb from phenix? I thought the reported R/Rfree values are just something like 'model vs data'? That's what I am confused about...

No twinning, no automated water building, just 1mol/asu, no twinning

Sabine

On 08/12/2011 02:36 PM, Partha Chakrabarti wrote:

...

Hi Sabine, I believe the comparison should be with same input, not output of one piped into another. How different are the geometry? Different programs use different algorithm and different xray:geometry term by default. Hence, it might only make sense if the RMSD are almost exactly the same. Furthermore, is one program detecting NCS or twining or building waters automatically? Then everything is blown up anyway. In any case, refinemt program A vs. B is an interesting topic! I would not start one.. ;) MFG, Partha

On Fri, Aug 12, 2011 at 5:19 PM, Sabine Schneider mailto:[email protected]> wrote:

Hello,

I am refining a structure at 2.1A solved by MR. For curiosity I'm testing things like 'shaking' coordinates, simulated annealing, refinement Refmac vs Phenix and so on, to see what influence that has on stats, maps etc.

For instance after MR I did a bit of shaking the coordinates with pdbset (noise 0.1), followed by simulated annealing in Phenix. Phenix states after SA:

Start R-work = 0.2671, R-free = 0.2992 Final R-work = 0.2312, R-free = 0.2666

When I use the output pdb of phenix directly in Refmac (with same mtz as input for Phenix) Refmac tells me: Initial R factor 0.2392 R free 0.2887

So I am quite puzzled about the discrepancy. Or can someone tell me if I made an error in reasoning somewhere?

Thanks a lot for the help! Sabine

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_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

-- David Goldstone, PhD National Institute for Medical Research Molecular Structure The Ridgeway Mill Hill London NW7 1AA