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Hi George

Yes you do.  It's important to understand that you are not comparing the MTZ file ("the data") with the PDB file ("the model"): that's not possible, at least not directly.  So you can't simply change the PDB file, redo the comparison and hope to get sensible results.  EDSTATS is _not_ "fitting" the PDB file into the density.  Rather, what you are doing is comparing 2 density maps both calculated using the _same_ MTZ file (since it contains multiple columns), specifically the "observed" (2mFo-DFc) exp(i phic) density with the "calculated" DFc exp(i phic) density.

The function of the PDB file is first to calculate Fc & phic and the map coefficients: you have to do that yourself using Refmac, and then in EDSTATS to define the regions of density where the comparisons are to take place (using the atomic co-ordinates & calculated radii).  So the PDB file supplied to EDSTATS must be _exactly_ the same one that was used to calculate SFs in Refmac (i.e. the one output by Refmac).  The Fc and phic values needed to calculate both maps require the whole model, otherwise the results will be meaningless.  When you talk about the model of a structure, you mean the entire structure (as far as it is known), not selected bits of it.

HTH

Cheers

-- Ian


On 11 June 2014 01:24, George Devaniranjan <[log in to unmask]> wrote:
Thank you Ethan.

Supposing I want to compare with the experimental map, a small fragment of the model (let's say residues 15-30 in a protein of 100 residues).

Supposing I start with one model but now extract from that model residues 15-30 (let's call it model 1)  , modify it and now want to check if the modified model (model 2) is better than model1?
Of course residues 1-14 and 30-100 (in a 100 residue protein) are the same. 

How can I measure which fragment (model 1 or model 2) is better. 
Do I have to insert model2 where model 1 was and use EDStats for the whole protein?








On Tue, Jun 10, 2014 at 8:04 PM, Ethan A Merritt <[log in to unmask]> wrote:
On Tuesday, 10 June, 2014 19:13:57 George Devaniranjan wrote:
> Thank you Ian.
> To clarify,  I actually want to compare the new PDB file to the old MTZ
> file to see how well the residues fit. This is why I mentioned that I have
> the old MTZ file I generated from SF's which I got from the PDB.
>
> I am not trying to improve the deposited structure, I am trying to get a
> metric of how "bad" the residues become if I change certain residue phi and
> psi values when I fit into the original electron density.

That is not a valid test.  The old map resulted from refinement of the
old model, and it corresponds to phases that are only correct for that
same old model.   If you perturb the model you will of course get a
different map, but "different" != "bad".  The old model won't agree
with your new map and the new model won't agree with the old map.
That doesn't prove that either the old model or the new model is
better or worse.

What you want is a test for how well each model agrees with its own map.
It is fair to argue that the model that is more self-consistent
(agrees better with its own map) is the better model.  But you won't learn that
by comparing model A to map B.

Caveat:  This all assumes that the map phases are generated entirely
from the model.  If you have a map generated from experimental phases,
then it certainly makes sense to ask which of several models is in better
agreement with the experimental map.

        cheers,

                Ethan


>
>
>
> On Tue, Jun 10, 2014 at 5:55 PM, Ian Tickle <[log in to unmask]> wrote:
>
> > Hi, sorry small clarification.
> >
> > The "complete PDB file that you used to run the refinement job" (i.e. the
> > input PDB file) will obviously only be suitable in the case that you did 0
> > cycles of refinement.  If you did some refinement of the model then the
> > co-ordinates will have changed, and then you need the _output_ PDB file
> > from that refinement as input to EDSTATS (clearly if you did 0 cycles the
> > input and output PDB files from the refinement will be the same & it
> > doesn't matter which one you use).
> >
> > Cheers
> >
> > -- Ian
> >
> >
> > On 10 June 2014 21:46, Ian Tickle <[log in to unmask]> wrote:
> >
> >>
> >> Hi, I'm puzzled by what you are trying to do.  You say you have the
> >> original MTZ/MAP files.  What have the original files got to do with it?
> >> EDSTATS requires the MTZ/MAP file calculated for the supplied model.  The
> >> documentation states: "... the PDB file and the maps should all be from
> >> the same refinement job.".  The refinement job referred to could be 0
> >> cycles but the MTZ file must have been calculated from the PDB file
> >> supplied.  If you have changed the PDB file then the original MTZ/MAP files
> >> will no longer be suitable.  This means you have to supply exactly the same
> >> complete PDB file that you used to run the refinement job.
> >>
> >> Cheers
> >>
> >> -- Ian
> >>
> >>
> >> On 10 June 2014 19:52, George Devaniranjan <[log in to unmask]>
> >> wrote:
> >>
> >>> HI,
> >>>
> >>>
> >>> I want to calculate real-space R factor/RSCC and such parameters using
> >>> EDSTATS in CCP4 but only for a selected fragment that has been
> >>> extracted and then modified (changed the Phi and Psi) from the native.
> >>>
> >>>
> >>> I have the original MTZ and MAP.
> >>>
> >>>
> >>> Is it even possible to calculate these values without inserting the
> >>> extracted fragment back into the rest of the PDB (the unmodified part)?
> >>>
> >>>
> >>> I am reluctant to do that since I have many such fragments I have
> >>> extracted and modified and wish to compare with the native.
> >>>
> >>>
> >>> Thank you,
> >>>
> >>> George
> >>>
> >>
> >>
> >
--
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742