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. 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 >>> >> >> >
