Hi Francois, here are the pieces we have... There is a command phenix.fobs_minus_fobs_map that takes two Fobs datasets (say one collected from a structure with ligand and another one collected from the same structure without ligand) and a PDB file with a model (as a sources of phases) and computes the map {Fobs1-Fobs2, model_phases}. To compute this map, internally each dataset, Fobs1 and Fobs2, gets scaled against Fcalc computed from the input model (well, to be precise, against Fmodel = scale * exp(-h*U_overall*ht) * (Fcalc + k_sol * exp(-B_sol*s^2) * Fmask) ). Then the overall scale gets applied back to Fobs1 and Fobs2, making them scaled relative to structure factors computed from input model. So having all these pieces, I can put together a script or a command line tool, that will take multiple datasets (several Fobs), and input PDB file with a model, and will scale all Fobs against input model. Of course, it is assumed that all datasets have the same crystal symmetry (unit cell and space group). Is this what you would like to do? Pavel. On 4/8/10 10:10 PM, Francois Berenger wrote:

Ok, sorry for not having been enough informative then. My goal is to put 2 MTZ on absolute scale.

Currently, the ones I have are all calculated from some PDBs (using CCP4's sfall) so they have FC and PHIC (and hopefully are already on absolute scale). Maybe soon I will have an MTZ containing experimental data so this one will only have FP and SIGFP.

I was thinking I should do a wilson plot, then apply to the corresponding MTZ the B-factor and scale correction that was found.

I don't want to scale one to the other because the calculated one is always in P1 and in a big unit cell, unlike the real data MTZ.

Regards, Francois.

Pavel Afonine wrote:

...

Hi Francois,

in PHENIX there are many tools that do this or similar task, internally or exposed to the user-level in some sense (may be not exactly what you ask).

If you explain what exactly and why you are trying to do then I might be able to suggest a right tool or help with a custom script.

From your question it is not clear to me what you mean by "to apply both the scale and overall B-factor correction found by the wilson plot to a given MTZ file". A "given MTZ file" may contain Fobs, Fcalc, or Fourier map coefficients or HL coefficients, or whatever else I or a program decide to store in it.

Pavel.

On 4/8/10 8:54 PM, Francois Berenger wrote:

...

Hello,

Is there a tool to apply both the scale and overall B-factor correction found by the wilson plot to a given MTZ file?

After applying these corrections, is there another way than redoing wilson to check that the output MTZ is on absolute scale?

Thanks a lot, Francois. _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

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