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 <ianj...@gmail.com> 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 <ianj...@gmail.com> 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 <devaniran...@gmail.com>
> >> 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
