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 <merr...@u.washington.edu> 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 <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 > >
