Well, the problem seems to occur when Intensities are input to PHENIX
instead of structure factors. I repeated a run using Fobs, SigFobs as
input instead of IMEAN, SIGIMEAN and the Density Fit Analysis graph
looks "normal".
At 16:57 17-01-2013, Nathaniel Echols wrote:
Actually, after some experimenting, I have just discovered that the
map coefficients produced by the very latest code are actually on the
same scale now, regardless of the scale of the input F(obs). This was
not what I expected at all. However, I should add that I still don't
know whether this scale will be what Coot expects. It is very
difficult for me to tell what is happening internally, but when the
"isotropize" option is selected (it's on by default) the map
coefficient amplitudes are being multiplied by the overall anisotropic
scale matrix. I'm not sure how this is calculated.
On Thu, Jan 17, 2013 at 8:29 AM, Nathaniel Echols <nech...@lbl.gov> wrote:
> On Thu, Jan 17, 2013 at 8:21 AM, Pedro M. Matias
<mat...@itqb.unl.pt> wrote:
>> The funny thing is that I also have MTZ files from PHENIX that work
>> perfectly in COOT.
>
> I think it will be dependent on having F(obs) already on an
> approximately absolute scale. This can be accomplished by scaling
> them during conversion from intensities, based on the Wilson plot (I
> think). I should note that while the CCP4 conversion tools usually
> take care of this, if you supply Phenix with intensities it will
> simply take the square root (the French-Wilson correction doesn't
> affect the overall scale). It would probably be useful to do the same
> thing in our code; I think it's pretty straightforward but I'm not
> sure about the math.
>
> My guess would be that some of the MTZ files you used were either a)
> already on an absolute scale, or b) accidentally ended up being
> approximately correct. However, if you're willing to send me the
> inputs and outputs for Phenix and Refmac for the structures you've had
> a problem with, I can confirm my guesses.
>
>> And although I cannot be 100% sure, since the run was in
>> Dec-2012 I believe the PHENIX version is the same in both cases
(it would be
>> nice if PHENIX wrote the version number in the PDB header).
>
> It should already do this - but you need to look further down in the
> remarks, where you will see something like this:
>
> REMARK 3 PROGRAM : PHENIX (phenix.refine: 1.7.3_928)
>
> Probably not a bad idea to display it at the very top too, however.
>
>> Bernhard has suggested tweaking some parameter in COOT
>>
>> Extensions->Refinement->Set Density Fit Graph Weight
>>
>> But the question is: which value should be used ?
>
> I suspect that this will also be completely arbitrary - btw, the fact
> that this option even exists seems to be confirmation that the graphs
> are not displaying a CC. I think the way Coot is doing this is
> completely broken, for what it's worth - but I also think it would be
> helpful if the maps from Phenix were at least on approximately the
> correct scale, instead of being (potentially) orders of magnitude off.
>
> -Nat
Industry and Medicine Applied Crystallography
Macromolecular Crystallography Unit
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